Massively parallel digital transcriptional profiling of single cells

Grace Zheng, Jessica M. Terry, Phillip Belgrader, Paul Ryvkin, Zachary Bent, Ryan J. Wilson, Solongo B. Ziraldo, Tobias D. Wheeler, Geoff P. McDermott, Junjie Zhu, Mark Gregory, Joe Shuga, Luz Montesclaros, Jason G. Underwood, Donald A Masquelier, Stefanie Y. Nishimura, Michael Schnall-Levin, Paul W. Wyatt, Christopher M. Hindson, Rajiv Bharadwaj, Alexander Wong, Kevin D. Ness, Lan Beppu, H. Joachim Deeg, Christopher McFarland, Keith R. Loeb, William J. Valente, Nolan G. Ericson, Emily A. Stevens, Jerald P. Radich, Tarjei S. Mikkelsen, Benjamin J. Hindson, Jason H. Bielas · Nature Communications · 2017 · genomics · 10.1038/ncomms14049 · record zheng2017-massively-parallel-digital-transcr
tag layer · index · concepts · authors · עברית
Where this record's text came from. 2026-08-21 schema-0.3 pass: every quote verified as an exact substring of the staged text and anchored at merge time; concept terms verified present; every edge endpoint an existing node.
How to read this page. The article itself is not reproduced here — this paper is not cleared for redistribution, so what follows is the tag layer alone. The evidence sentences are withheld with the article. The table at the foot lists every tag the record carries; each row names the facet it belongs to, and the whose words column says whether the tag records the paper's own wording or the tagger's sentence about the paper. Every tag links to each other paper in the corpus carrying it. The machine-readable edition of the same thing is the TEI file beside this one, where the tags live in standOff, and the article is at its publisher via the link below. 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 WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below.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 An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason.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.
Other fields define these differently the same word, defined another way in another discipline
sensitivity 8 fields

Tags on this paper

Every tag the record carries, each linking to every other paper in the corpus that carries it. A tag appears here whether or not its words occur in the article — the spans below are only the ones a sentence in this paper licenses. Of the 14 concept tags on this paper, all 14 are grounded in a quoted sentence. All carry the tagger's gloss of what the term means in this paper, which is not something the article can license.
GEM UMI multiplet rate multiplets cell capture rate cross-talk technical variation biological variation ERCC SNVs chimerism genotype overlap Seurat Poisson distribution limiting dilution as the price of purity a droplet with no biology in it two species as a doublet detector identity read twice from one molecule posterior correction of a barcode without a whitelist match sensitivity PPV omics-profiling
Method, as described: cells loaded at limiting dilution into gel-bead emulsions, reverse transcribed in droplet with a 14 bp barcode and a 10 bp UMI, amplified in bulk, sequenced short-read, and processed by Cell Ranger into a gene-barcode matrix

Legend

relation to other workclaim_relationshow this paper stands to another: agrees, contradicts, extends, qualifies
claim typeclaim_typethe shape of the claim: existence, mechanism, method, critique, prediction, null
concept edgeconcept_edgesan asserted relation between two concepts, with the sentence asserting it
conceptconceptsan idea the paper works with, quoted where the paper uses it
content tagcontent_tagsa finding, definition, quantity, statistic or variable named in the paper
contributioncontributionwhat the paper claims to add
controlcontrolsan experiment run to eliminate a rival explanation
limitationlimitationswhat the paper says its evidence cannot support
mechanismmechanismshow the reported effect is said to come about
methodmethodhow the paper produced its evidence
object of studyobject_of_studywhat the paper is about — the thing it investigates
phenomenonphenomenonthe effect or regularity under study
research questionresearch_questionthe question the paper sets itself
sensesensesa distinct use of a term, quoted where the paper fixes it
transfertransfersa method or concept carried in from another field

The paper

The full text is not reproduced here. This article is not cleared for redistribution, so the page carries the tag layer only. Its evidence sentences are withheld; the grounding status remains with each tag, and the article itself is at https://doi.org/10.1038/ncomms14049. The reading view exists for the papers whose licence permits it.

Every tag on this page

claim_relations 5 · claim_type 1 · concept_edges 3 · concepts 14 · content_tags 20 · contribution 1 · controls 14 · limitations 8 · mechanisms 5 · method 1 · object_of_study 1 · phenomenon 1 · research_question 1 · senses 6 · transfers 2

Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; 3 of 3 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.

facettagfieldconf.whose words
object_of_study3' mRNA counting of tens of thousands of individual cells in parallel - and, separately, telling whose cells they are from the same reads
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
object_of_studythe paper's words
research_questionwhether tens of thousands of single cells can be captured and barcoded without custom microfluidics or plate sorting, and at what multiplet, capture and conversion rates
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
research_questionthe paper's words
contributiona gel-bead-in-emulsion platform capturing ~50% of loaded cells across 8 parallel channels, with its multiplet rate, cross-talk and conversion efficiency each measured against a control of known composition; plus a de novo SNV method that resolves transplant chimerism without either genotype
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
contributionthe paper's words
claim_typemethod
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
claim_typethe paper's words
phenomenontranscriptomic heterogeneity that population-averaged measurement hides, and the droplet-level artefacts - multiplets, barcode cross-talk, technical variance - that appear once you measure cells one at a time
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
phenomenonthe paper's words
methodomics-profiling
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
methodthe paper's words
mechanismscells are loaded far below one per droplet so that two rarely share a barcode; the same dilution that suppresses multiplets is what throws away the cells that are never captured, so the multiplet rate and the capture rate are two readings of one loading decision
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[0]0.95the tagger's words
mechanismssynthetic RNAs at a known concentration are loaded in place of cells, so every difference between the expected and observed counts must come from the instrument - the variance that remains is technical by construction rather than by argument
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[1]0.95the tagger's words
mechanismsa barcode carrying substantial human and mouse counts can only have held two cells, so mixing species converts an invisible failure into a countable one - and the count must then be doubled, because same-species doublets are equally likely and leave no trace
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[2]0.95the tagger's words
mechanismsthe ~250 nt of cDNA that gives an expression count also carries sequence variants, so each cell has an expression identity and a genotype identity from the same reads; agreement between them is evidence neither could give alone
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[3]0.95the tagger's words
mechanismsan observed barcode one Hamming step from known sequences is reassigned by posterior probability from base qualities and the overall barcode count distribution, above 0.975, with lexical order as the stated tie-break rather than a silent one
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[4]0.95the tagger's words
limitationsthe level of detection of the genotype method is given as 3% in Results and as 4% of 6,000 cells in Methods, for the same in silico mixing experiment, and the two are never reconciled
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[0]0.95the tagger's words
limitationsthe same discrepancy, from the Methods side - K=1 is selected when the mixture fraction is below 4% of 6,000 cells
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[1]0.95the tagger's words
limitationsmultiplets of identical or highly similar cell types cannot be detected by any of the measures used here, and the authors say more sophisticated methods will be required
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[2]0.95the tagger's words
limitationsa 15-20% error in the cell counts feeds directly into the capture efficiency, and the authors name it as a source of the variability in that figure
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[3]0.95the tagger's words
limitationsimaged multiple-encapsulation was 16% higher than the Poisson expectation, ascribed to subsampling error or to cell-cell clumping seen during the manual count
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[4]0.95the tagger's words
limitationsclassification blurred the boundaries between T-cell subpopulations, with part of the inferred CD4+ naive population classified as CD8+ T cells
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[5]0.95the tagger's words
limitationsthe transplant work is a proof of principle on BMMCs from two patients
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[6]0.95the tagger's words
limitationsthe unexpected absence of monocytes after transplant is reported without explanation and left for further study
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[7]0.95the tagger's words
transfersthe GemCode gel-bead-in-emulsion barcoding platform, carried from genome haplotyping, structural variant analysis and de novo genome assembly into single-cell RNA counting
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
transfers[0]0.95the tagger's words
transfersthe two-genome mixture model with a Gibbs sampler and Stephens relabelling, carried from mixture-model statistics into deciding which transplanted cells are whose
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
transfers[1]0.95the tagger's words
controlsa mixture of ~1,200 human 293T and ~1,200 mouse 3T3 cells loaded together, so that a droplet holding two cells leaves a two-genome barcode behind it
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: multiplets and barcode cross-talk being invisible - in a single-species run a doublet and a large cell produce the same data, and neither rate can be read · outcome: held
controls[0]0.95the tagger's words
controlsa cell titration across six different cell loads, recovering 1,200 to 9,500 cells
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the 1.6% figure being a fixed property of the instrument - if the rate did not track the load, the mechanism would not be Poisson co-encapsulation at all · outcome: held
controls[1]0.95the tagger's words
controlshigh-speed imaging of every GEM as it formed, with ~28k frames counted by hand, as a measurement of cell occupancy that does not pass through sequencing
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the Poisson loading claim resting on the same data it explains - the imaging can disagree with the sequencing, and it does, by 16% · outcome: partial
controls[2]0.95the tagger's words
controlsERCC synthetic spike-in RNAs at known concentration loaded into GEMs in place of cells, in two mixes and two dilutions
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: biological variation as a contributor to the measured variance, and the conversion efficiency being inferred from data with no known answer · outcome: held
controls[3]0.95the tagger's words
controlsdroplet digital PCR on eight genes in Jurkat cells, against the RNA copy number measured in bulk from the same cell type
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: naked spike-in RNA standing in for a real transcript inside a real cell - ERCC molecules are not lysed out of anything, and could convert at a different rate · outcome: held
controls[4]0.95the tagger's words
controls293T-only and Jurkat-only samples run through the identical PCA, alongside the mixed ones
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the clustering method itself as the source of the two clusters - a procedure that splits a pure sample would have produced the same picture from nothing · outcome: held
controls[5]0.95the tagger's words
controlscell identity assigned a second time from SNVs alone, independently of any marker gene, and compared cell by cell with the marker-based assignment
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the choice of marker genes as the source of the cluster identities - genotype and expression are different measurements and could have disagreed · outcome: held
controls[6]0.95the tagger's words
controlsin silico mixing of two donors' reads at 12 ratios from 0 to 50%, where the true label of every cell is known, with sensitivity and PPV computed against it
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: a detection limit asserted rather than measured - the floor is found by mixing downward until the method stops recovering the minor population · outcome: held
controls[7]0.95the tagger's words
controlsthe same two donors mixed in vitro at 50:50, 90:10 and 99:1 before sequencing, rather than mixed computationally afterwards
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: in silico mixing as the reason the floor holds - reads combined by arithmetic never pass through a shared droplet, a shared PCR or a shared flow cell · outcome: held
controls[8]0.95the tagger's words
controls11 pairwise genotype comparisons between samples from the same individual and 15 between different individuals, computed before any patient sample was interpreted
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: reading a genotype-overlap percentage with no scale - 97% and 78% are host and donor only because the same-individual and different-individual ranges exist · outcome: held
controls[9]0.95the tagger's words
controlsthe routine clinical chimerism assay, PowerPlex 16 on a genetic analyser, run on the same post-transplant samples
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the new method being its own witness - the chimerism call is checked against the assay currently trusted for that decision, in both patients · outcome: held
controls[10]0.95the tagger's words
controlsthe remaining fresh PBMCs from the same donor frozen and re-run three weeks later, compared with the fresh library gene by gene and cluster by cluster
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: freeze-thaw as an explanation of any composition difference in the frozen repository specimens the method is meant to be used on · outcome: held
controls[11]0.95the tagger's words
controlsten bead-enriched, separately profiled subpopulations of PBMCs from the same donor, each clustered on its own and checked against FACS
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: substructure being an artefact of clustering a mixed population - a purified sample that splits would indict the pipeline, and most of them did not split · outcome: held
controls[12]0.95the tagger's words
controlsSeurat, an independently written clustering package, run on the same 68k gene-barcode matrix
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the cell-type structure being specific to the authors' own PCA and k-means choices - a second package agreeing on some boundaries and not others locates which ones the data supports · outcome: partial
controls[13]0.95the tagger's words
conceptsGEM
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: GEM
concepts[0]0.95the paper's words
conceptsUMI
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: UMI
concepts[1]0.95the paper's words
conceptsmultiplet rate
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
concepts[2]0.95the paper's words
conceptsmultiplets
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: multiplets
concepts[3]0.95the paper's words
conceptscell capture rate
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
concepts[4]0.95the paper's words
conceptscross-talk
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: cross-talk
concepts[5]0.95the paper's words
conceptstechnical variation
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
concepts[6]0.95the paper's words
conceptsbiological variation
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
concepts[7]0.95the paper's words
conceptsERCC
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: ERCC
concepts[8]0.95the paper's words
conceptsSNVs
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: SNVs
concepts[9]0.95the paper's words
conceptschimerism
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: chimerism
concepts[10]0.95the paper's words
conceptsgenotype overlap
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
concepts[11]0.95the paper's words
conceptsSeurat
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: Seurat
concepts[12]0.95the paper's words
conceptsPoisson distribution
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
concepts[13]0.95the paper's words
sensesmultiplet rate - AS MEASURED BY SPECIES MIXING: twice the share of barcodes carrying significant UMI counts from both genomes, which can only see cross-species doublets
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[0]0.95the tagger's words
sensesmultiplet rate - AS MEASURED BY SNV: twice the share of cells whose SNV counts fall between the two cell lines, which still cannot see a doublet of two like cells
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[1]0.95the tagger's words
sensesthe method's level of detection - AS STATED IN RESULTS: 3%, with minor genotypes identified at >95% sensitivity and PPV and nothing recovered below it
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[2]0.95the tagger's words
sensesthe method's level of detection - AS STATED IN METHODS: 4% of 6,000 cells, from the same in silico mixing experiment; the paper never reconciles the two
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[3]0.95the tagger's words
sensesvariation in UMI counts - IN A DROPLET HOLDING A CELL: biological and technical together, CV2 ~11-19%
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[4]0.95the tagger's words
sensesvariation in UMI counts - IN A DROPLET HOLDING SYNTHETIC RNA: technical only, by construction, CV2 ~7%
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[5]0.95the tagger's words
claim_relationscritiques → existing scRNA-seq methods - microfluidic approaches with limited throughput, plate methods needing FACS into many plates, and droplet methods requiring custom devices and reagents
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
claim_relations[0]0.95the tagger's words
claim_relationscritiques → clinical chimerism testing by PCR on flow-sorted populations, which is bounded by cell-surface markers, needs sufficient cell counts per population, and is not intended to detect minimal residual disease
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
claim_relations[1]0.95the tagger's words
claim_relationsextends → genotype-based cell assignment, by inferring both genomes de novo from the transcriptome rather than requiring DNA sequencing or large copy-number changes known in advance
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
claim_relations[2]0.95the tagger's words
claim_relationsconfirms → Klein et al.'s estimate that technical variance accounts for about half of the total variance in droplet scRNA-seq
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
claim_relations[3]0.95the tagger's words
claim_relationsqualifies → its own PBMC classification - the correlation-based assignment blurs T-cell subpopulation boundaries, and an independent package fails on a different pair
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
claim_relations[4]0.95the tagger's words
concept_edgestechnical variation —distinct-from→ biological variation
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
differs in: whether the source of the variance is the cell or the instrument · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): whether the source of the variance is the cell or the instrument · the relation stated: an ERCC droplet contains no cell, so nothing biological can vary in it
concept_edges[0]0.95the tagger's words
concept_edgesmultiplet rate —operationalised-as→ UMI
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
the relation itself is separately evidenced · strength of the relation: 0.9 · the relation stated: defined as twice the rate of barcodes carrying significant UMI counts from both genomes Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span defines the multiplet rate FROM UMI counts; operationalised-as is loose.
also in: multiplet rate · UMI
concept_edges[1]0.95the tagger's words
concept_edgesmultiplets —contrasted-with→ Poisson distribution
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
differs in: whether cells enter droplets independently, or arrive already stuck together · the relation itself is separately evidenced · strength of the relation: 0.9 · differs in (stated by the tagger, no quotation): whether cells enter droplets independently, or arrive already stuck together · the relation stated: the imaged rate of multiple encapsulations exceeded the Poisson expectation by 16% Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the multiplet rate exceeded the expected value; contrasted-with 'Poisson distribution' is loose.
concept_edges[2]0.95the tagger's words
content_tagsGenotype overlap averages about 98% between samples of the same individual and about 73% between different individuals.
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[1]0.95the tagger's words
content_tagstechnical variance accounts for about half of total variance, measured by loading synthetic RNA into droplets in place of cells
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[2]0.95the tagger's words
content_tagsDetecting multiplets of identical or highly similar cell types will require more sophisticated methods.
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[3]0.95the tagger's words
content_tagsimaged multiple-cell encapsulation ran 16% above the Poisson expectation, with cell clumps seen during the manual count
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[4]0.95the tagger's words
content_tagsmarker-based and SNV-based cell assignment agree at 99% on the 293T/Jurkat mixture
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[5]0.95the tagger's words
content_tagsThe SNV result was consistent with a clinical chimerism assay showing only 12% donor in the post-transplant sample.
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[6]0.95the tagger's words
content_tagstwice the rate of cell barcodes with significant UMI counts from both mouse and human, where the top 1% of UMI counts counts as significant
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.definitions[0]0.95the tagger's words
content_tagsthe ratio of the number of cells detected by sequencing to the number of cells loaded
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.definitions[1]0.95the tagger's words
content_tagsGel bead in EMulsion - one gel bead carrying barcoded oligonucleotides, encapsulated with cells and reagents in an 8-channel microfluidic chip
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: GEM
content_tags.definitions[2]0.95the tagger's words
content_tagsthe inferred multiplet rate at 1,012 cell-containing GEMs in the species-mixing run
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[0]0.95the tagger's words
content_tagsthe mean fraction of UMI counts from the other species - the barcode cross-talk level
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[1]0.95the tagger's words
content_tagsthe error in the cell counts that feeds into every capture-efficiency figure
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[2]0.95the tagger's words
content_tagsgenotype overlap between samples from the same individual - the positive control that makes 97% readable as host
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
value source note: THE DESCRIPTION DRAWS ON THE PAPER BEYOND THIS QUOTE: the 97% is the transplant result the control is used to read ('the post-transplant sample was 97% similar…').
content_tags.quantities[3]0.95the tagger's words
content_tagsgenotype overlap between different individuals - the negative control that makes 78% readable as donor
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
value source note: THE DESCRIPTION DRAWS ON THE PAPER BEYOND THIS QUOTE: the 78% is the transplant result the control is used to read ('The sample only shared 78% similarity with AML035 host cells').
content_tags.quantities[4]0.95the tagger's words
content_tagssensitivity
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: sensitivity
content_tags.statistics[0]0.95the tagger's words
content_tagsPPV
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: PPV
content_tags.statistics[1]0.95the tagger's words
content_tagsPoisson distribution
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.statistics[2]0.95the tagger's words
content_tagsmultiplet rate
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.variables[0]0.95the tagger's words
content_tagsgenotype overlap
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.variables[1]0.95the tagger's words
content_tagstechnical variation
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.variables[2]0.95the tagger's words

Interpretive choices

Tags that could not be placed in the text:

What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.

© 2026 Shir Sivroni · ORCID 0009-0000-2597-2824