The Human Cell Atlas — TEI-tagged view

Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Göttgens, Nir Hacohen, Muzlifah Haniffa, Martin Hemberg, Seung Kim, Paul Klenerman, Arnold Kriegstein, Ed Lein, Sten Linnarsson, Emma Lundberg, Joakim Lundeberg, Partha Majumder, John C Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe'er, Anthony Phillipakis, Chris P Ponting, Stephen Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua Sanes, Rahul Satija, Ton N Schumacher, Alex Shalek, Ehud Shapiro, Padmanee Sharma, Jay W Shin, Oliver Stegle, Michael Stratton, Michael J T Stubbington, Fabian J Theis, Matthias Uhlen, Alexander van Oudenaarden, Allon Wagner, Fiona Watt, Jonathan Weissman, Barbara Wold, Ramnik Xavier, Nir Yosef, Human Cell Atlas Meeting Participants · 2017 · biology · doi:10.7554/elife.27041 · TEI xml · tagged edition · index · concepts · authors
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Other fields define these differently the same word, defined another way in another discipline
scRNA-seq 6 fields · quality control 3 fields · map 3 fields · open data 3 fields · proteins 3 fields · atlas 2 fields · and 1 more →
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cell type10 cell state Cell-type taxonomies markers4 Cell Theory scRNA-seq10 Human Cell Atlas comprehensive reference catalog stable properties transient features locations abundances map4 relationships2 fundamental processes system of coordinates human cell defined set of molecular markers expression level 20,000 human protein-coding genes point in ~20,000-dimensional space non-coding genes alternatively spliced forms chromatin state promoter and enhancer post-translationally modified form reduced representations histological and anatomical information temporal information disease status2 molecular profiles Single-cell multi-omics transcriptomic genomic epigenomic proteomic causal chains genetic variation regulatory mechanisms phenotypic outcome Multiplex in situ analysis spatial techniques nucleic acids proteins4 hybridization antibody staining sequencing2 tagging strategies dissociated cells spatial relationships cell-cell communication2 MERFISH Seq-FISH microscopy-based quantification Imaging Mass Cytometry tissue clearing expansion4 Histology2 tissue architecture expression signatures multi-gene signatures cell's molecular profile information about its neighborhood absolute coordinates relative terms machine vision development5 partly asynchronous branching pathways of development molecular changes gene-expression patterns trajectories in high-dimensional space Waddington's landscape2 sharp transitions sampling density sorting strategies rare, transient populations relative proportions of cells duration of each phase progenitor cells rate of cell proliferation death2 true lineage trees common progenitor cell type synthetic circuits molecular barcode lineage barcodes VDJ recombination somatic hypermutation lineage tracing somatic point mutations repeat expansions at microsatellite loci sound statistical sampling biological enrichment purification adaptive, iterative approach initial sparse sampling decisions about further sampling Sky Dive banking fixed or frozen tissues mixed strategy2 low coverage of the transcriptome deep profiles large-scale uniform sampling stratified sampling specialized sampling atlas5 cellular branch spatial branch massively parallel transcriptome analysis chromatin3 genome folding somatic mutations2 preserved tissue specimens 10 billion cells all tissues, organs, and systems world's diversity rarity of cell types/states spatial resolution coverage of disease and diversity functional assessment model organism atlases engineering animals validation and functional follow-up studies by proxy technically reproducible biological variation3 measurement noise rigorous protocols, standards, and benchmarks clinical annotations consistent meta-data dissociating samples into single cells fixation2 freezing5 validated standard operating procedures computational pipelines benchmarking samples and data sets open data4 standard models identifiable data platforms efficient aggregation and storage quality control10 analytical software user-friendly portals intellectually and technologically flexible criteria for 'completion' review319
Method, as described: single-cell genomic profiling at scale, with unsupervised clustering as an initial framework for discovering types

Our tag layer for this paper

Cross-disciplinary analysis
content-tags & facets: phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text
phenomenoncells as points in a high-dimensional molecular space, where similar cells are close but never identical— “Thus, a cell 'type' might be defined as a region or a probability distribution ( Kim and Eberwine, 2010; Sul et al., 2012) either in the full-dimensional space or in a projection onto a lower-dimensional space that reflects salient features. While this notion is intuitively compelling, it is challenging to give a precise definition…
claim-typemethod— “An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease.”
method — evidence— “However, only in the past few years has it begun to seem feasible to undertake the kind of systematic, high-resolution characterization of human cells necessary to create a systematic cell atlas. The key has been the recent ability to apply genomic profiling approaches to single cells.”
object of study — evidence— “The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology).”
research question — evidence— “The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body.”
contribution — evidence— “For all the reasons above, we have not attempted to propose a precise definition of 'cell type'. Rather, the definition should evolve based on empirical observation.”
mechanisma cell TYPE is proposed as a REGION or a PROBABILITY DISTRIBUTION in the full-dimensional molecular space or a projection of it - the category becomes a geometry rather than a list of properties— “Thus, a cell 'type' might be defined as a region or a probability distribution ( Kim and Eberwine, 2010; Sul et al., 2012) either in the full-dimensional space or in a projection onto a lower-dimensional space that reflects salient features. While this notion is intuitively compelling, it is challenging to give a precise definition…mechanisms[0]
mechanismtypes discovered as regions in feature space are then to be DISTILLED into simple molecular and morphological signatures, so that independent laboratories can index and compare cells at all— “Whereas cell types are initially defined based on regions in feature space, it will be important eventually to distill them into simpler molecular and morphological signatures that can be used to index cells in the atlas, aggregate and compare results from independent labs and different individuals, and create tools and reagents for…mechanisms[1]
critiques the existing molecular classification of cells, on the ground that it is ad hoc - built on markers discovered by accident or chosen for convenience— “In addition, molecular classification of cells has largely been ad hoc – based on markers discovered by accident or chosen for convenience – rather than systematic and comprehensive.”claim_relations[0]
extends Cell Theory as settled between 1838 and 1855, which named the cell as the unit and left the catalogue of kinds open for 150 years— “Between 1838 and 1855, Schleiden, Schwann, Remak, Virchow and others crystalized an elegant Cell Theory ( Harris, 2000), stating that all organisms are composed of one or more cells; that cells are the basic unit of structure and function in life; and that all cells are derived from pre-existing cells”claim_relations[1]
sensecell type - DELIBERATELY UNDEFINED HERE. Proposed as a region or probability distribution in molecular space, described as intuitively compelling and hard to state precisely, and left to evolve from the data— “For all the reasons above, we have not attempted to propose a precise definition of 'cell type'. Rather, the definition should evolve based on empirical observation.”senses[0]
sensecell type against cell state - type implies PERSISTENCE (a hepatic stellate cell), state implies TRANSIENCE (the G1 phase), and the paper says the boundary between the two concepts can be blurred— “At a conceptual level, one challenge is that we lack a rigorous definition of what we mean by the intuitive terms 'cell type' and 'cell state'. Cell type often implies a notion of persistence ( e.g., being a hepatic stellate cell or a cerebellar Purkinje cell), while cell state often refers to more transient properties (…senses[1]
senseCell-type taxonomies - a hierarchy over morphological, physiological and molecular differences, which the paper says may not be strict and whose three axes may not agree with one another— “Cell-type taxonomies are often represented as hierarchies based on morphological, physiological, and molecular differences ( Sanes and Masland, 2015). Whereas higher distinctions are easily agreed upon, finer ones may be less obvious and may not obey a strict hierarchy, either because distinct types share features, or because some…senses[2]
sense`scRNA-seq` - A NAME FOR A CLASS, NOT A PROTOCOL, AND THE PAPER SAYS SO IN ITS DEFINING SENTENCE. `(scRNA-seq) refers to a class of methods for profiling the transcriptome of individual cells.` Two papers both reporting `scRNA-seq` may share no step of their procedure - the review goes straight on to distinguish methods taking a census of mRNA at the 3' or 5' end from those assessing full transcripts. The term is a citation-level abstraction that is never a method-level one.— “(scRNA-seq) refers to a class of methods for profiling the transcriptome of individual cells.”senses[3]
sense`Cell Theory` - A THEORY DEFINED AS THREE CONJOINED CLAIMS, TWO STRUCTURAL AND ONE HISTORICAL. `all organisms are composed of one or more cells; that cells are the basic unit of structure and function in life; and that all cells are derived from pre-existing cells.` The first two say what a thing IS MADE OF and what the parts DO; the third is a claim about ORIGIN and is the only one that could have been false without the others failing with it. A citation to `Cell Theory` selects one of the three and the name records which no better than a coin.— “all organisms are composed of one or more cells; that cells are the basic unit of structure and function in life; and that all cells are derived from pre-existing cells”senses[4]
senseHuman Cell Atlas - a relational map and reference catalog of cell properties, features, locations, and abundances— “At its most basic level, the Human Cell Atlas must include a comprehensive reference catalog of all human cells based on their stable properties and transient features, as well as their locations and abundances. Yet, an atlas is more than just a catalog: it is a map that aims to show the relationships among its elements. By doing so, it can…senses[5]
senseAtlas coordinate system - molecular dimensions plus anatomical, temporal, and disease annotations that can be collapsed into application-specific views— “Moreover, an atlas must provide a system of coordinates on which one can represent and harmonize concepts at many levels (geopolitical borders, topography, roads, climate, restaurants, and even dynamic traffic patterns). Features can be viewed at any level of magnification, and high-dimensional information collapsed into simpler views. So, a…senses[6]
senseSingle-cell multi-omics - two or more molecular data types measured in the same cell to connect variation, regulation, and phenotype— “Single-cell multi-omics_** techniques aim to collect two or more types of data (transcriptomic, genomic, epigenomic, and proteomic) from the same single cell. Recent studies have simultaneously profiled the transcriptome together with either the genome ( Angermueller et al., 2016; Dey et al., 2015; Macaulay et al., 2015), the epigenome (…senses[7]
senseMultiplex in-situ analysis - selected RNA or protein targets measured inside tissue so dissociated-cell profiles can be mapped back into spatial context— “Multiplex in situ analysis and other spatial techniques_** aim to detect a limited number of nucleic acids and/or proteins in situ in tissue samples – by hybridization (for RNA), antibody staining (for proteins), sequencing (for nucleic acids), or other tagging strategies. These in situ results can then be used to map massive amounts of…senses[8]
senseDevelopmental trajectory - branching paths in high-dimensional molecular space reconstructed from cross-sectional single-cell observations— “Cells arrive at their final differentiated cell types through partly asynchronous branching pathways of development ( Ferrell, 2012), which are driven by and reflected in molecular changes, especially gene-expression patterns (see, for example, Chao et al., 2008; Jojic et al., 2013). It should therefore be possible to reconstruct development…senses[9]
senseLineage tracing - ancestry inferred from engineered or naturally accumulated molecular barcodes— “In animal models, it should be possible to create true lineage trees by marking a common progenitor cell type. For example, one might use synthetic circuits that introduce a molecular barcode only in cells expressing an RNA pattern characteristic of the cell type in order to recognize its descendants ( Gagliani et al., 2015; McKenna et al.…senses[10]
senseSky Dive - adaptive sampling that moves from uniform to stratified to specialized sampling while increasing resolution— “While an adult human has ~2 x 1013 nucleated cells, it is neither possible nor necessary to study them all to recover the fine distinctions among human cells. The key will be to combine sound statistical sampling, biological enrichment purification, and insights from studies of model organisms. It is likely beneficial to apply an adaptive…senses[11]
senseTwo-branch atlas - individual-cell molecular profiling paired with in-situ spatial mapping of tissue organization— “The atlas must combine two branches – a cellular branch, focused on the properties of individual cells, and a spatial branch, describing the histological organization of cells in the tissue. For the cellular branch, massively parallel transcriptome analysis of individual single cells or nuclei will likely be the workhorse for efforts in the…senses[12]
senseFull-atlas scope - at least ten billion cells across tissues, organs, systems, health states, and population diversity, with explicit resolution and functional limits— “The full atlas, will ultimately describe at least 10 billion cells, covering all tissues, organs, and systems. Specimens will come from both healthy research participants and small cohorts of patients with relevant diseases. The cells and tissues will be studied using a broad range of techniques, to obtain cellular and spatial information…senses[13]
senseAtlas quality - reproducibility through shared protocols, metadata, tissue handling, pipelines, and benchmarking materials— “In creating a reference map to be used by thousands of investigators, it is critical to ensure that the results are of high quality and technically reproducible. This is especially important in view of the inherent biological variation and expected measurement noise. Substantial investment will be needed in the development, comparison, and…senses[14]
senseOpen-data infrastructure - aggregation, storage, quality control, analysis software, and portals under participant and legal constraints— “The Human Genome Project made clear the power of open data that can be used by all and freely combined with other datasets. A Human Cell Atlas should similarly be an open endeavor, to the full extent permitted by participants' wishes and legal regulation. While the underlying sequence data contains many polymorphisms that make it…senses[15]
controlthe definition of 'cell type' is deferred to empirical observation rather than fixed in advance, and the deferral is stated as a decision with its reasons — held— “Cell-type taxonomies are often represented as hierarchies based on morphological, physiological, and molecular differences ( Sanes and Masland, 2015). Whereas higher distinctions are easily agreed upon, finer ones may be less obvious and may not obey a strict hierarchy, either because distinct types share features, or because some… — rules out a catalogue whose categories were settled before the data that was supposed to produce them - and the paper's own reasons are that the hierarchy may not hold, the distinctions may be graded, and the axes may not agree— “For all the reasons above, we have not attempted to propose a precise definition of 'cell type'. Rather, the definition should evolve based on empirical observation.”controls[0]
controltypes found as regions in feature space must be distilled into signatures that independent laboratories can apply — held— “Whereas cell types are initially defined based on regions in feature space, it will be important eventually to distill them into simpler molecular and morphological signatures that can be used to index cells in the atlas, aggregate and compare results from independent labs and different individuals, and create tools and reagents for… — rules out a taxonomy that exists only inside the clustering run that produced it and cannot be used to index, aggregate or compare across labs and individuals— “Whereas cell types are initially defined based on regions in feature space, it will be important eventually to distill them into simpler molecular and morphological signatures that can be…controls[1]
weightthe existing molecular classification of cells, on the ground that it is ad hoc - built on markers discovered by accident or chosen for convenience — 0.95
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claim_relations[0]
weightCell Theory as settled between 1838 and 1855, which named the cell as the unit and left the catalogue of kinds open for 150 years — 0.9
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
claim_relations[1]
auditcell state —distinct-from→ cell type — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says the boundaries between cell type and cell state CAN BE BLURRED; distinct-from is hedged.
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concept_edges[0]
differs in (stated by the tagger, no quotation)cell state —distinct-from→ cell type — persistence against transience - and the paper says the boundary is blurredconcept_edges[0]
relationcell state —distinct-from→ cell type — type implies PERSISTENCE and state implies TRANSIENCE - and the paper says in the same passage that the boundary between the two CAN BE BLURRED, so the distinction is asserted and qualified together
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concept_edges[0]
weightcell state —distinct-from→ cell type — 0.95
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concept_edges[0]
notecomprehensive reference catalog —part-of→ Human Cell Atlas — The atlas must include the comprehensive reference catalog.
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concept_edges[1]
audithuman cell —operationalised-as→ point in ~20,000-dimensional space — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says ONE MIGHT describe each cell as such a point; a proposal, hedged.
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concept_edges[2]
notehuman cell —operationalised-as→ point in ~20,000-dimensional space — The paper proposes representing each cell as a point whose dimensions are gene-expression levels.
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concept_edges[2]
weighthuman cell —operationalised-as→ point in ~20,000-dimensional space — 0.7
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concept_edges[2]
auditinitial sparse sampling —causes→ decisions about further sampling — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says an adaptive approach is LIKELY beneficial, with sparse sampling driving later sampling; hedged.
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concept_edges[3]
effect directioninitial sparse sampling —causes→ decisions about further sampling — increases
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concept_edges[3]
noteinitial sparse sampling —causes→ decisions about further sampling — The paper says initial sparse sampling drives later sampling decisions.
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concept_edges[3]
notecellular branch —part-of→ atlas — The atlas must combine a cellular and a spatial branch.
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concept_edges[4]
notespatial branch —part-of→ atlas — The atlas must combine a cellular and a spatial branch.
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concept_edges[5]
outcomecontrol — held
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controls[0]
outcomecontrol — held
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controls[1]
no type for thisHuman Cell Atlas → relationships — The atlas shows relationships among catalogued elements. Shows is absent from the eight governed types.
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unhoused_relations[0]
no type for thisduration of each phase → relative proportions of cells — Relative cell proportions convey information about the duration of each phase. Conveys-information-about is absent from the eight governed types.
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unhoused_relations[1]
no type for thisdevelopment → trajectories in high-dimensional space — The paper proposes reconstructing development as trajectories in molecular space. Reconstructs-as is absent from the eight governed types.
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unhoused_relations[2]
no type for thisSingle-cell multi-omics → causal chains — Multi-omic measurements could help fill in causal chains. Enables is absent from the eight governed types.
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unhoused_relations[3]
no type for thisdissociated cells → tissue samples — In-situ results map genomic information from dissociated cells back onto tissue samples. Maps-onto is absent from the eight governed types.
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unhoused_relations[4]
no type for thisexpression data → absolute coordinates — Cell expression data can help map cell position in absolute coordinates. Maps-position is absent from the eight governed types.
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unhoused_relations[5]
no type for thislow coverage of the transcriptome → cell types — Low-coverage transcriptomes can identify many cell types reliably. Identifies is absent from the eight governed types.
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unhoused_relations[6]
no type for thisadaptive, iterative approach → Sky Dive — The adaptive approach is explicitly termed a Sky Dive. Naming is absent from the eight governed types.
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unhoused_relations[7]
no type for thisdeep profiles → low-coverage data — A smaller set of deep profiles helps interpret the broad low-coverage data. Helps-interpret is absent from the eight governed types.
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unhoused_relations[8]
no type for thispreserved tissue specimens → analyzed later — Preserved specimens allow collection now and analysis after methods mature. Enables-deferred-analysis is absent from the eight governed types.
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unhoused_relations[9]
no type for thisvalidation and functional follow-up studies → conclusions drawn in the human atlas — Model-organism studies help validate human-atlas conclusions by proxy. Validates-by-proxy is absent from the eight governed types.
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unhoused_relations[10]
no type for thisdata platforms → efficient aggregation and storage — Atlas data platforms must provide aggregation and storage. Provides is absent from the eight governed types.
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unhoused_relations[11]
no type for thisstandard models → identifiable — Mapping sequence data onto standard gene models is proposed to mitigate identifiability. Mitigates is absent from the eight governed types.
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unhoused_relations[12]
limitationTHE PROJECT DECLINES TO DEFINE ITS CENTRAL TERM AND SAYS SO: `we have not attempted to propose a precise definition of 'cell type'. Rather, the definition should evolve based on empirical observation` - in a paper whose stated aim is to define all human cell types
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limitations[0]
limitationthe field lacks a rigorous definition of BOTH `cell type` and `cell state`, and the boundary between them is blurred because cells change over time in ways not fully understood
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limitations[1]
limitationTHE TAXONOMY MAY NOT BE A TAXONOMY: finer distinctions may not obey a strict hierarchy, some distinctions are graded rather than discrete, and IT REMAINS UNCLEAR WHETHER THE MORPHOLOGICAL, MOLECULAR AND PHYSIOLOGICAL AXES AGREE WITH EACH OTHER
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limitations[2]
limitationthe existing molecular classification is AD HOC - built on markers discovered by accident or chosen for convenience rather than systematically
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limitations[3]
limitationclustering supplies only a starting framework: the `right` features, the `right` similarity metric and the `right` level of granularity are all open, and the paper puts each of the three in scare quotes
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limitations[4]
limitationthe full lineage tree from zygote to adult is known for exactly one organism - C. elegans, transparent, with about 1,000 cells
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limitations[5]
Content tags
content-observations: finding · quantity · variable · definition · key-term — grounded in the full text
finding
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content_tags.findings[0]
finding
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content_tags.findings[1]
finding
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content_tags.findings[2]
finding
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content_tags.findings[3]
finding
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content_tags.findings[4]
quantityyears - the age of the effort to identify all human cell types, which this project proposes to complete
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content_tags.quantities[0]
quantitycells in C. elegans - the only organism whose full lineage tree from zygote to adult is known
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content_tags.quantities[1]
quantitythe years in which Schleiden, Schwann, Remak and Virchow crystallised Cell Theory
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content_tags.quantities[2]
variablegranularity
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content_tags.variables[0]
variablesimilarity metric
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
content_tags.variables[1]
variablemolecular profiles
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
content_tags.variables[2]
definitioncell type
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
content_tags.definitions[0]
definitionCell Theory
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
content_tags.definitions[1]
definitionthe Human Cell Atlas
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
content_tags.definitions[2]
Concepts
terms this paper carries, each with the sentence it was cut from — the layer that joins one paper to another. Terms with no quote yet are on CONCEPTS.html.
conceptcell type — not defined in this paper's own words; the atlas's unit of cataloguing, left undefined on purpose and proposed as a region in a high-dimensional molecular space
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concepts[0]
conceptcell state — not defined in this paper's own words; the transient counterpart of a type - the G1 phase, nutrient deprivation - with a boundary the paper calls blurred
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[1]
conceptCell-type taxonomies — not defined in this paper's own words; hierarchies over morphological, physiological and molecular differences, which may not be strict and whose axes may not agree
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[2]
conceptmarkers — not defined in this paper's own words; the molecules classification has used - discovered by accident or chosen for convenience, which is what makes the existing classification ad hoc
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[3]
conceptCell Theory — not defined in this paper's own words; the 1838-1855 settlement the atlas inherits: all organisms are made of cells, cells are the basic unit of structure and function, and all cells come from cells
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[4]
conceptscRNA-seq — not defined in this paper's own words; single-cell RNA-Seq - defined here as A CLASS OF METHODS rather than one protocol, which is why papers reporting 'scRNA-seq' are not reporting the same procedure as each other
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[5]
conceptHuman Cell Atlas — not defined in this paper's own words; international reference map whose fundamental unit is a human cell
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[6]
conceptcomprehensive reference catalog — not defined in this paper's own words; catalog component of the atlas
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[7]
conceptstable properties — not defined in this paper's own words; persistent cell features represented by the catalog
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[8]
concepttransient features — not defined in this paper's own words; temporary cell features represented by the catalog
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[9]
conceptlocations — not defined in this paper's own words; spatial coordinates represented by the catalog
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[10]
conceptabundances — not defined in this paper's own words; cell quantities represented by the catalog
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[11]
conceptmap — not defined in this paper's own words; relational representation that goes beyond a catalog
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concepts[12]
conceptrelationships — not defined in this paper's own words; relations among elements that the atlas is intended to expose
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[13]
conceptfundamental processes — not defined in this paper's own words; processes that can be revealed by a relational map
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concepts[14]
conceptsystem of coordinates — not defined in this paper's own words; common representational frame for harmonizing atlas concepts
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[15]
concepthuman cell — not defined in this paper's own words; fundamental observation represented in the atlas
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[16]
conceptdefined set of molecular markers — not defined in this paper's own words; proposed coordinates for representing each cell
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concepts[17]
conceptexpression level — not defined in this paper's own words; per-gene coordinate in the concrete transcriptomic representation
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concepts[18]
concept20,000 human protein-coding genes — not defined in this paper's own words; dimensions in the concrete gene-expression representation
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[19]
conceptpoint in ~20,000-dimensional space — not defined in this paper's own words; high-dimensional representation of one cell
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[20]
conceptnon-coding genes — not defined in this paper's own words; possible additional marker layer
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concepts[21]
conceptalternatively spliced forms — not defined in this paper's own words; possible transcript-level marker layer
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concepts[22]
conceptchromatin state — not defined in this paper's own words; possible regulatory marker layer
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concepts[23]
conceptpromoter and enhancer — not defined in this paper's own words; regulatory elements whose chromatin states could be represented
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[24]
conceptpost-translationally modified form — not defined in this paper's own words; possible protein-state marker layer
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concepts[25]
conceptreduced representations — not defined in this paper's own words; lower-dimensional views selected for particular applications
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[26]
concepthistological and anatomical information — not defined in this paper's own words; location, morphology, and tissue-context annotations
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[27]
concepttemporal information — not defined in this paper's own words; age and elapsed-exposure annotations
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[28]
conceptdisease status — not defined in this paper's own words; health-related atlas annotation
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[29]
conceptmolecular profiles — not defined in this paper's own words; cell descriptions harmonized with histology and function
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[30]
conceptSingle-cell multi-omics — not defined in this paper's own words; collection of at least two molecular data types from the same cell
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[31]
concepttranscriptomic — not defined in this paper's own words; RNA-expression data type in multi-omic profiling
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[32]
conceptgenomic — not defined in this paper's own words; genome data type in multi-omic profiling
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[33]
conceptepigenomic — not defined in this paper's own words; regulatory-state data type in multi-omic profiling
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[34]
conceptproteomic — not defined in this paper's own words; protein data type in multi-omic profiling
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[35]
conceptcausal chains — not defined in this paper's own words; linked path from variation through regulation to phenotype
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[36]
conceptgenetic variation — not defined in this paper's own words; upstream element in the proposed causal chain
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[37]
conceptregulatory mechanisms — not defined in this paper's own words; intermediate element in the proposed causal chain
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[38]
conceptphenotypic outcome — not defined in this paper's own words; downstream element in the proposed causal chain
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[39]
conceptMultiplex in situ analysis — not defined in this paper's own words; spatial detection of selected nucleic acids or proteins in tissue
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[40]
conceptspatial techniques — not defined in this paper's own words; methods retaining tissue location while measuring molecular targets
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[41]
conceptnucleic acids — not defined in this paper's own words; in-situ target class
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[42]
conceptproteins — not defined in this paper's own words; in-situ target class
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[43]
concepthybridization — not defined in this paper's own words; RNA-detection route for multiplex in-situ analysis
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[44]
conceptantibody staining — not defined in this paper's own words; protein-detection route for multiplex in-situ analysis
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[45]
conceptsequencing — not defined in this paper's own words; nucleic-acid detection route for multiplex in-situ analysis
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[46]
concepttagging strategies — not defined in this paper's own words; additional route for multiplex in-situ detection
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[47]
conceptdissociated cells — not defined in this paper's own words; cells whose genomic profiles are mapped back to tissue
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[48]
conceptspatial relationships — not defined in this paper's own words; tissue relationships recovered by mapping molecular data
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[49]
conceptcell-cell communication — not defined in this paper's own words; interaction process informed by spatial mapping
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[50]
conceptMERFISH — not defined in this paper's own words; multiplex RNA hybridization and imaging technique
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[51]
conceptSeq-FISH — not defined in this paper's own words; multiplex RNA hybridization and imaging technique
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[52]
conceptmicroscopy-based quantification — not defined in this paper's own words; imaging readout paired with multiplex hybridization
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[53]
conceptImaging Mass Cytometry — not defined in this paper's own words; heavy-metal antibody imaging method
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[54]
concepttissue clearing — not defined in this paper's own words; sample treatment improving spatial detection
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[55]
conceptexpansion — not defined in this paper's own words; sample treatment improving spatial resolution
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[56]
conceptHistology — not defined in this paper's own words; study of spatial positions of cells and molecules in tissue
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[57]
concepttissue architecture — not defined in this paper's own words; organization to be woven into the atlas
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[58]
conceptexpression signatures — not defined in this paper's own words; multi-marker patterns used to spatially map cell types
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[59]
conceptmulti-gene signatures — not defined in this paper's own words; spatially extended alternative to single-gene gradients
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[60]
conceptcell's molecular profile — not defined in this paper's own words; molecular description combined with neighborhood information
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[61]
conceptinformation about its neighborhood — not defined in this paper's own words; local spatial context for refining cell characterization
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[62]
conceptabsolute coordinates — not defined in this paper's own words; direct positional representation inferred from expression
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[63]
conceptrelative terms — not defined in this paper's own words; relative positional representation inferred from expression
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concepts[64]
conceptmachine vision — not defined in this paper's own words; computational source proposed for integrating profiles and architecture
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[65]
conceptdevelopment — not defined in this paper's own words; process reconstructed from cross-sectional single-cell observations
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[66]
conceptpartly asynchronous branching pathways of development — not defined in this paper's own words; developmental routes to differentiated types
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[67]
conceptmolecular changes — not defined in this paper's own words; changes driving and reflecting developmental pathways
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concepts[68]
conceptgene-expression patterns — not defined in this paper's own words; molecular patterns reflecting developmental change
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[69]
concepttrajectories in high-dimensional space — not defined in this paper's own words; representation used to reconstruct development
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[70]
conceptWaddington's landscape — not defined in this paper's own words; landscape analogy for developmental trajectories
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[71]
conceptsharp transitions — not defined in this paper's own words; rapid developmental changes inferred with dense sampling
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[72]
conceptsampling density — not defined in this paper's own words; number of observations needed for path reconstruction
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[73]
conceptsorting strategies — not defined in this paper's own words; iterative enrichment method for rare transient populations
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[74]
conceptrare, transient populations — not defined in this paper's own words; short-lived cell populations targeted by enrichment
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[75]
conceptrelative proportions of cells — not defined in this paper's own words; observations carrying timing and fate-allocation information
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[76]
conceptduration of each phase — not defined in this paper's own words; developmental timing inferred from cell proportions
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[77]
conceptprogenitor cells — not defined in this paper's own words; cells allocated among developmental fates
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[78]
conceptrate of cell proliferation — not defined in this paper's own words; rate needed to interpret observed proportions
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[79]
conceptdeath — not defined in this paper's own words; cell-loss rate needed to interpret observed proportions
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[80]
concepttrue lineage trees — not defined in this paper's own words; developmental ancestry reconstructed in animal models
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[81]
conceptcommon progenitor cell type — not defined in this paper's own words; ancestor marked to create a lineage tree
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[82]
conceptsynthetic circuits — not defined in this paper's own words; constructs introducing lineage barcodes
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[83]
conceptmolecular barcode — not defined in this paper's own words; heritable mark used to recognize descendants
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[84]
conceptlineage barcodes — not defined in this paper's own words; naturally occurring immune-cell lineage marks
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[85]
conceptVDJ recombination — not defined in this paper's own words; source of natural T- and B-cell lineage barcodes
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[86]
conceptsomatic hypermutation — not defined in this paper's own words; source of natural B-cell lineage barcodes
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[87]
conceptlineage tracing — not defined in this paper's own words; reconstruction of human cell ancestry from accumulated differences
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[88]
conceptsomatic point mutations — not defined in this paper's own words; accumulated DNA differences used for human lineage tracing
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[89]
conceptrepeat expansions at microsatellite loci — not defined in this paper's own words; accumulated DNA differences used as lineage evidence
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[90]
conceptsound statistical sampling — not defined in this paper's own words; sampling component for recovering cell distinctions
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[91]
conceptbiological enrichment purification — not defined in this paper's own words; enrichment component of the sampling strategy
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[92]
conceptadaptive, iterative approach — not defined in this paper's own words; sampling strategy that changes with resolution
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[93]
conceptinitial sparse sampling — not defined in this paper's own words; first-pass sampling that guides later sampling
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[94]
conceptdecisions about further sampling — not defined in this paper's own words; later sampling choices driven by the sparse first pass
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[95]
conceptSky Dive — not defined in this paper's own words; name for the adaptive sampling strategy
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[96]
conceptbanking — not defined in this paper's own words; storage of partially processed samples for later deeper analysis
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[97]
conceptfixed or frozen tissues — not defined in this paper's own words; preserved samples facilitating deferred analysis
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[98]
conceptmixed strategy — not defined in this paper's own words; combination of many shallow and fewer deep profiles
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[99]
conceptlow coverage of the transcriptome — not defined in this paper's own words; shallow profiling used for broad cell-type identification
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[100]
conceptdeep profiles — not defined in this paper's own words; smaller set used to interpret low-coverage observations
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[101]
conceptlarge-scale uniform sampling — not defined in this paper's own words; first operational stage of the Sky Dive
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[102]
conceptstratified sampling — not defined in this paper's own words; second operational stage of the Sky Dive
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[103]
conceptspecialized sampling — not defined in this paper's own words; lower-throughput final stage of the Sky Dive
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[104]
conceptatlas — not defined in this paper's own words; two-branch cellular and spatial representation
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[105]
conceptcellular branch — not defined in this paper's own words; atlas branch focused on individual-cell properties
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[106]
conceptspatial branch — not defined in this paper's own words; atlas branch describing tissue organization
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[107]
conceptmassively parallel transcriptome analysis — not defined in this paper's own words; initial workhorse for the cellular branch
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[108]
conceptchromatin — not defined in this paper's own words; emerging single-cell profile beyond transcriptomes
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[109]
conceptgenome folding — not defined in this paper's own words; emerging single-cell profile beyond transcriptomes
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[110]
conceptsomatic mutations — not defined in this paper's own words; emerging single-cell profile beyond transcriptomes
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[111]
conceptpreserved tissue specimens — not defined in this paper's own words; banked material enabling future reanalysis
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[112]
concept10 billion cells — not defined in this paper's own words; minimum intended scale of the full atlas
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[113]
conceptall tissues, organs, and systems — not defined in this paper's own words; anatomical scope of the full atlas
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[114]
conceptworld's diversity — not defined in this paper's own words; population diversity the sample design should represent
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[115]
conceptrarity of cell types/states — not defined in this paper's own words; one stated resolution boundary
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[116]
conceptspatial resolution — not defined in this paper's own words; second stated resolution boundary
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[117]
conceptcoverage of disease and diversity — not defined in this paper's own words; stated representativeness boundary
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[118]
conceptfunctional assessment — not defined in this paper's own words; validation scope that facilitates but does not replace functional work
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[119]
conceptmodel organism atlases — not defined in this paper's own words; coordinated sister atlases supporting the human atlas
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[120]
conceptengineering animals — not defined in this paper's own words; animal-only route to facilitate lineage tracing
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[121]
conceptvalidation and functional follow-up studies — not defined in this paper's own words; model-organism work used to test human-atlas conclusions
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[122]
conceptby proxy — not defined in this paper's own words; status of model-organism validation for human conclusions
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[123]
concepttechnically reproducible — not defined in this paper's own words; quality requirement for the atlas reference map
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[124]
conceptbiological variation — not defined in this paper's own words; inherent variation motivating rigorous quality controls
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[125]
conceptmeasurement noise — not defined in this paper's own words; technical variation motivating rigorous quality controls
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[126]
conceptrigorous protocols, standards, and benchmarks — not defined in this paper's own words; quality infrastructure for reproducibility
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[127]
conceptclinical annotations — not defined in this paper's own words; sample metadata required across the atlas
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[128]
conceptconsistent meta-data — not defined in this paper's own words; standardized form of atlas clinical annotations
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[129]
conceptdissociating samples into single cells — not defined in this paper's own words; processing step that must preserve all cell types
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[130]
conceptfixation — not defined in this paper's own words; processing method for in-situ assays
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[131]
conceptfreezing — not defined in this paper's own words; processing method for transport
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[132]
conceptvalidated standard operating procedures — not defined in this paper's own words; documented experimental workflows supporting comparability
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[133]
conceptcomputational pipelines — not defined in this paper's own words; standardized analysis workflows supporting comparability
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[134]
conceptbenchmarking samples and data sets — not defined in this paper's own words; reference materials supporting comparability
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[135]
conceptopen data — not defined in this paper's own words; data access principle inherited from the Human Genome Project
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[136]
conceptstandard models — not defined in this paper's own words; gene-level mappings proposed to reduce identifiability
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[137]
conceptidentifiable — not defined in this paper's own words; privacy property arising from polymorphisms in sequence data
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[138]
conceptdata platforms — not defined in this paper's own words; infrastructure required to make the atlas useful
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[139]
conceptefficient aggregation and storage — not defined in this paper's own words; data-platform capability
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[140]
conceptquality control — not defined in this paper's own words; data-platform capability
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[141]
conceptanalytical software — not defined in this paper's own words; data-platform capability
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[142]
conceptuser-friendly portals — not defined in this paper's own words; data-platform access capability
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[143]
conceptintellectually and technologically flexible — not defined in this paper's own words; required adaptive property of the project
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[144]
conceptcriteria for 'completion' — not defined in this paper's own words; project boundary expected to evolve
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
concepts[145]
Statistics — cross-field join keys
field-invariant statistical terms, used in their statistical sense (gated on a number / symbol / test). A p-value or a standard deviation means the SAME thing in physics, biology, psychology and sociology — so these are the strongest cross-field join keys. Grounded verbatim.
probability distribution
Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher.
content_tags.statistics[0]

When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.

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