phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | transcriptomic 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— “Last, the mean fraction of UMI counts from the other species was 0.9% in both human and mouse GEMs, indicating a low level of cross-talk between cell barcodes (Online Supplementary Methods).” | |
| claim-type | method— “To overcome these challenges, we developed a droplet-based system that enables 3′ messenger RNA (mRNA) digital counting of thousands of single cells. Approximately 50% of cells loaded into the system can be captured, and up to eight samples can be processed in parallel per run. Reverse transcription takes place inside each droplet, and… | |
| method — evidence | — “Within each microfluidic channel, ∼100,000 GEMs are formed per ∼6-min run, encapsulating thousands of cells in GEMs. Cells are loaded at a limiting dilution to minimize co-occurrence of multiple cells in the same GEM.” | |
| object of study — evidence | — “To overcome these challenges, we developed a droplet-based system that enables 3′ messenger RNA (mRNA) digital counting of thousands of single cells. Approximately 50% of cells loaded into the system can be captured, and up to eight samples can be processed in parallel per run. Reverse transcription takes place inside each droplet, and… | |
| research question — evidence | — “However, previously described scRNA-seq methods face practical challenges when scaling to tens of thousands of cells or when it is necessary to capture as many cells as possible from a limited sample. Commercially available, microfluidic-based approaches have limited throughput. Plate-based methods often require time-consuming… | |
| contribution — evidence | — “Current clinical chimerism tests have a number of limitations, namely (1) the flow-sorted cell populations are limited by cell surface markers, (2) only populations with sufficient cell counts can be used for PCR assays and (3) they are not intended for the detection of minimal residual disease. Here we present a simple method that addresses… | |
| transfer | from genome sequencing: the GemCode gel-bead-in-emulsion barcoding platform, carried from genome haplotyping, structural variant analysis and de novo genome assembly into single-cell RNA counting— “The scRNA-seq microfluidics platform builds on the GemCode technology, which has been used for genome haplotyping, structural variant analysis and de novo assembly of a human genome.” | transfers[0] |
| transfer | from statistics: the two-genome mixture model with a Gibbs sampler and Stephens relabelling, carried from mixture-model statistics into deciding which transplanted cells are whose— “While previous studies have used existing SNVs from DNA sequencing or large-scale copy number changes in the transcriptome data to distinguish cells by genotype, these methods cannot be applied to transplant samples where donor and host genotype is not known a priori, and when donor and host are closely matched in genotype.” | transfers[1] |
| mechanism | limiting dilution as the price of purity cells 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— “Within each microfluidic channel, ∼100,000 GEMs are formed per ∼6-min run, encapsulating thousands of cells in GEMs. Cells are loaded at a limiting dilution to minimize co-occurrence of multiple cells in the same GEM.” | mechanisms[0] |
| mechanism | a droplet with no biology in it synthetic 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— “The ERCC experiments also allowed us to estimate the relative proportion of biological and technical variation. Since ERCCs are in solution, they do not introduce biological variation related to differences in cell size, RNA content or transcriptional activity. Thus, technical variation is the only source of variation.” | mechanisms[1] |
| mechanism | two species as a doublet detector a 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— “In the mouse and human mixing experiments, multiplet rate was defined as twice the rate of cell barcodes with significant UMI counts from both mouse and human, where top 1% of UMI counts was considered significant. The extent of barcode crosstalk was assessed by the fraction of mouse reads in human barcodes, or vice versa.” | mechanisms[2] |
| mechanism | identity read twice from one molecule the ~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— “In the 1:1 mixed sample, 45% 293T cells primarily (96%) harbored 293T-enriched SNVs, whereas 50% Jurkat cells primarily (94%) harbored Jurkat-enriched SNVs (Fig. 2f and Supplementary Data 2). Jurkat and 293T cells inferred from marker-based analysis are 99% consistent with SNV-based assignment.” | mechanisms[3] |
| mechanism | posterior correction of a barcode without a whitelist match an 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— “All of the known listed of barcodes that are 1-Hamming-distance away from an observed barcode are considered. Then, the posterior probability that the observed barcode was produced by a sequencing error is computed, given the base qualities of the observed barcode and the prior probability of observing the candidate barcode (taken from the… | mechanisms[4] |
| critiques | existing scRNA-seq methods - microfluidic approaches with limited throughput, plate methods needing FACS into many plates, and droplet methods requiring custom devices and reagents— “However, previously described scRNA-seq methods face practical challenges when scaling to tens of thousands of cells or when it is necessary to capture as many cells as possible from a limited sample. Commercially available, microfluidic-based approaches have limited throughput. Plate-based methods often require time-consuming… | claim_relations[0] |
| critiques | 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— “Current clinical chimerism tests have a number of limitations, namely (1) the flow-sorted cell populations are limited by cell surface markers, (2) only populations with sufficient cell counts can be used for PCR assays and (3) they are not intended for the detection of minimal residual disease. Here we present a simple method that addresses… | claim_relations[1] |
| extends | 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— “While previous studies have used existing SNVs from DNA sequencing or large-scale copy number changes in the transcriptome data to distinguish cells by genotype, these methods cannot be applied to transplant samples where donor and host genotype is not known a priori, and when donor and host are closely matched in genotype.” | claim_relations[2] |
| confirms | Klein et al.'s estimate that technical variance accounts for about half of the total variance in droplet scRNA-seq— “The squared CV (CV2) is ∼7% among all the ERCC experiments. In comparison, CV2 in samples of mouse and human cells is ∼11–19% (Supplementary Fig. 1d), suggesting that technical variance accounts for ∼50% of total variance, consistent with the observations from Klein et al.” | claim_relations[3] |
| qualifies | its own PBMC classification - the correlation-based assignment blurs T-cell subpopulation boundaries, and an independent package fails on a different pair— “We have also tried to cluster the 68k PBMC data with Seurat (Supplementary Methods). While it was able to distinguish inferred CD4+ naive from inferred CD8+ naive T cells, it was not able to cleanly separate out inferred activated cytotoxic T cells from inferred NK cells (Supplementary Fig. 5i). Such populations have overlapping functions… | claim_relations[4] |
| sense | multiplet 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— “In the mouse and human mixing experiments, multiplet rate was defined as twice the rate of cell barcodes with significant UMI counts from both mouse and human, where top 1% of UMI counts was considered significant. The extent of barcode crosstalk was assessed by the fraction of mouse reads in human barcodes, or vice versa.” | senses[0] |
| sense | multiplet 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— “Cells were labelled as Jurkat or 293T based on Jurkat- and 293T-specific SNV counts, where the fraction of counts from the other species is <0.2. Cells with a fraction of SNV from either species between 0.2 and 0.8 are considered multiplets. The inferred multiplet rate is 2* observed multiplet rate (to account for Jurkat:Jurkat and… | senses[1] |
| sense | the method's level of detection - AS STATED IN RESULTS: 3%, with minor genotypes identified at >95% sensitivity and PPV and nothing recovered below it— “Our method was able to identify minor genotypes as low as 3% at >95% sensitivity and PPV (Fig. 4a,b). A minor population could not be detected when the mixed ratio was below 3%” | senses[2] |
| sense | the 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 | senses[3] |
| sense | variation in UMI counts - IN A DROPLET HOLDING A CELL: biological and technical together, CV2 ~11-19% | senses[4] |
| sense | variation in UMI counts - IN A DROPLET HOLDING SYNTHETIC RNA: technical only, by construction, CV2 ~7% 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. | senses[5] |
| control | a 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 — held 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. — rules out 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 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. | controls[0] |
| control | a cell titration across six different cell loads, recovering 1,200 to 9,500 cells — held 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. — rules out 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 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. | controls[1] |
| control | high-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 — partial 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. — rules out the Poisson loading claim resting on the same data it explains - the imaging can disagree with the sequencing, and it does, by 16% 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. | controls[2] |
| control | ERCC synthetic spike-in RNAs at known concentration loaded into GEMs in place of cells, in two mixes and two dilutions — held 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. — rules out biological variation as a contributor to the measured variance, and the conversion efficiency being inferred from data with no known answer 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. | controls[3] |
| control | droplet digital PCR on eight genes in Jurkat cells, against the RNA copy number measured in bulk from the same cell type — held 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. — rules out 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 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. | controls[4] |
| control | 293T-only and Jurkat-only samples run through the identical PCA, alongside the mixed ones — held 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. — rules out 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 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. | controls[5] |
| control | cell identity assigned a second time from SNVs alone, independently of any marker gene, and compared cell by cell with the marker-based assignment — held 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. — rules out the choice of marker genes as the source of the cluster identities - genotype and expression are different measurements and could have disagreed 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. | controls[6] |
| control | in 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 — held 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. — rules out a detection limit asserted rather than measured - the floor is found by mixing downward until the method stops recovering the minor population 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. | controls[7] |
| control | the same two donors mixed in vitro at 50:50, 90:10 and 99:1 before sequencing, rather than mixed computationally afterwards — held 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. — rules out 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 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. | controls[8] |
| control | 11 pairwise genotype comparisons between samples from the same individual and 15 between different individuals, computed before any patient sample was interpreted — held 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. — rules out 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 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. | controls[9] |
| control | the routine clinical chimerism assay, PowerPlex 16 on a genetic analyser, run on the same post-transplant samples — held 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. — rules out the new method being its own witness - the chimerism call is checked against the assay currently trusted for that decision, in both patients 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. | controls[10] |
| control | the 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 — held 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. — rules out freeze-thaw as an explanation of any composition difference in the frozen repository specimens the method is meant to be used on 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. | controls[11] |
| control | ten bead-enriched, separately profiled subpopulations of PBMCs from the same donor, each clustered on its own and checked against FACS — held 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. — rules out 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 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. | controls[12] |
| control | Seurat, an independently written clustering package, run on the same 68k gene-barcode matrix — partial 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. — rules out 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 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. | controls[13] |
| weight | existing scRNA-seq methods - microfluidic approaches with limited throughput, plate methods needing FACS into many plates, and droplet methods requiring custom devices and reagents — 0.95 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[0] |
| weight | 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 — 0.95 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] |
| weight | 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 — 0.95 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[2] |
| weight | Klein et al.'s estimate that technical variance accounts for about half of the total variance in droplet scRNA-seq — 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[3] |
| weight | its own PBMC classification - the correlation-based assignment blurs T-cell subpopulation boundaries, and an independent package fails on a different pair — 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[4] |
| differs in (stated by the tagger, no quotation) | technical variation —distinct-from→ biological variation — whether the source of the variance is the cell or the instrument | concept_edges[0] |
| relation | technical variation —distinct-from→ biological variation — an ERCC droplet contains no cell, so nothing biological can vary in it 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. 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. | concept_edges[0] |
| weight | technical variation —distinct-from→ biological variation — 0.95 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. | concept_edges[0] |
| audit | multiplet rate —operationalised-as→ UMI — 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. 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. | concept_edges[1] |
| relation | multiplet rate —operationalised-as→ UMI — defined as twice the rate of barcodes carrying significant UMI counts from both genomes 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. 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. | concept_edges[1] |
| weight | multiplet rate —operationalised-as→ UMI — 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. | concept_edges[1] |
| audit | multiplets —contrasted-with→ Poisson distribution — 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. 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. | concept_edges[2] |
| differs in (stated by the tagger, no quotation) | multiplets —contrasted-with→ Poisson distribution — whether cells enter droplets independently, or arrive already stuck together | concept_edges[2] |
| relation | multiplets —contrasted-with→ Poisson distribution — the imaged rate of multiple encapsulations exceeded the Poisson expectation by 16% 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. 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. | concept_edges[2] |
| weight | multiplets —contrasted-with→ Poisson distribution — 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. | concept_edges[2] |
| outcome | control — held 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. 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. | controls[0] |
| outcome | control — held 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. | controls[1] |
| outcome | control — partial 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. | controls[2] |
| outcome | control — held 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. 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. | controls[3] |
| outcome | control — held 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. | controls[4] |
| outcome | control — held 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. | controls[5] |
| outcome | control — held 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. | controls[6] |
| outcome | control — held 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. | controls[7] |
| outcome | control — held 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. | controls[8] |
| outcome | control — held 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. | controls[9] |
| outcome | control — held 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. | controls[10] |
| outcome | control — held 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. 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. | controls[11] |
| outcome | control — held 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. | controls[12] |
| outcome | control — partial 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. | controls[13] |
| limitation | the 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 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. | limitations[0] |
| limitation | the same discrepancy, from the Methods side - K=1 is selected when the mixture fraction is below 4% of 6,000 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. | limitations[1] |
| limitation | multiplets 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 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. | limitations[2] |
| limitation | a 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 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. | limitations[3] |
| limitation | imaged 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 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. | limitations[4] |
| limitation | classification blurred the boundaries between T-cell subpopulations, with part of the inferred CD4+ naive population classified as CD8+ T 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. | limitations[5] |
| limitation | the transplant work is a proof of principle on BMMCs from two patients 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. | limitations[6] |
| limitation | the unexpected absence of monocytes after transplant is reported without explanation and left for further study 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. | limitations[7] |
finding · quantity · variable · definition · key-term — grounded in the full text| finding | 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.findings[1] |
| finding | 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.findings[2] |
| finding | 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.findings[3] |
| finding | 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.findings[4] |
| finding | 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.findings[5] |
| finding | 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.findings[6] |
| quantity | the inferred multiplet rate at 1,012 cell-containing GEMs in the species-mixing run 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.quantities[0] |
| quantity | the mean fraction of UMI counts from the other species - the barcode cross-talk level 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.quantities[1] |
| quantity | the error in the cell counts that feeds into every capture-efficiency figure 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.quantities[2] |
| quantity | genotype overlap between samples from the same individual - the positive control that makes 97% readable as host 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.quantities[3] |
| value source note | quantity — 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] |
| quantity | genotype overlap between different individuals - the negative control that makes 78% readable as donor 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.quantities[4] |
| value source note | quantity — 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] |
| variable | multiplet rate 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[0] |
| variable | genotype overlap 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] |
| variable | technical variation 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] |
| definition | multiplet rate 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] |
| definition | cell capture rate 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] |
| definition | GEM 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] |
| concept | GEM — not defined in this paper's own words; Gel bead in EMulsion - the reaction vessel; one gel bead, ideally one cell, and the barcode that makes everything inside it one cell's 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[0] |
| concept | UMI — not defined in this paper's own words; a 10 bp randomer that indexes the molecule rather than the cell, so PCR duplicates can be collapsed and counts become digital 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] |
| concept | multiplet rate — not defined in this paper's own words; the share of droplets holding more than one cell; measured here at 1.6%, and blind by construction to doublets of similar 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[2] |
| concept | multiplets — not defined in this paper's own words; two or more cells sharing one barcode - detectable when the cells differ in species, genotype or marker, and invisible when they do not 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] |
| concept | cell capture rate — not defined in this paper's own words; cells detected by sequencing over cells loaded - ~50%, and the figure that decides whether a scarce sample can be used at all 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] |
| concept | cross-talk — not defined in this paper's own words; UMI counts from one cell appearing under another cell's barcode; 0.9% here, and the thing a species mixture measures that a single-species run cannot 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] |
| concept | technical variation — not defined in this paper's own words; variance from droplet size, reagent concentration and RT/PCR efficiency rather than from the cell - isolable only by putting something with no biology in the droplet 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] |
| concept | biological variation — not defined in this paper's own words; variance from cell size, RNA content and transcriptional activity - the signal, and absent by construction from an ERCC droplet 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] |
| concept | ERCC — not defined in this paper's own words; synthetic spike-in RNAs at known concentration, loaded in place of cells so that the machine's answer can be compared with an answer already known 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] |
| concept | SNVs — not defined in this paper's own words; single nucleotide variants read off the same ~250 nt cDNA the expression comes from - a second, independent identity for each 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[9] |
| concept | chimerism — not defined in this paper's own words; the mixture of host and donor cells after a transplant; the clinical question this method answers per cell rather than per flow-sorted population 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] |
| concept | genotype overlap — not defined in this paper's own words; the share of matching genotype calls between two samples - a number that means nothing until the same-individual and different-individual baselines exist 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] |
| concept | Seurat — not defined in this paper's own words; an independent clustering package run on the same matrix, which separated one pair the authors' pipeline blurred and blurred one it separated 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[12] |
| concept | Poisson distribution — not defined in this paper's own words; the loading model the multiplet rate is predicted from - approximately obeyed, and exceeded by 16% in the imaging count because cells clump 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] |
| sensitivity | 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] |
| PPV | 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[1] |
| Poisson 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[2] |
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.
Tag layer © the Meta-Tagging Project, CC BY 4.0. The paper text is © its authors/publisher
and is linked, not reproduced. Excerpts shown are short quotations for identification and verification.
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