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cellranger vdj output files  (10X Genomics)

 
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    10X Genomics cellranger vdj output files
    a , Left: barplot of proportion of contigs that are productive or non-productive in each locus. Right: barplot showing the causes of non-productive contigs in each locus. For both plots, sc-γδTCR, -αβTCR and -BCR data were taken from Suo et al. 2022 excluding thymus samples. b , Schematic illustration showing that mRNA without V genes would be captured by 5′RACE + Switch oligo technique but not by multiplex PCR strategy. c , Pointplot of proportion of contigs with multi-J mapping in the presence of V gene in control and cycloheximide-treated PBMC samples. Points are colored by locus of TCR/BCR. For both IGH and IGL/IGK, the proportions were 0% in control and treated. d , Schematic illustration showing the factors associated with multi-J mapping and the proposed mechanisms. e , Boxplots of sc-γδTCR contig counts annotated by 10X <t>cellranger</t> vdj v6.1.2 versus v7.0.0 using data from n = 33 independent samples from Suo et al. 2022 . Left: all high confidence contigs ( P -value 5.43e-6, r 0.91 in the two-sided Wilcoxon signed-rank test). Right: high confidence productive contigs ( P -value 1.69e-6, r 0.96 in the two-sided Wilcoxon signed-rank test). Boxes capture the first to third quartiles and whisks span a further 1.5X interquartile range on each side of the box.
    Cellranger Vdj Output Files, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/filtered_contig_annotations%2Ecsv+output+from+cellranger/cellranger+vdj/pmc10791579-40-9-7
    Average 86 stars, based on 1 article reviews
    cellranger vdj output files - by Bioz Stars, 2026-10
    86/100 stars

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    1) Product Images from "Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins"

    Article Title: Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

    Journal: Nature Biotechnology

    doi: 10.1038/s41587-023-01734-7

    a , Left: barplot of proportion of contigs that are productive or non-productive in each locus. Right: barplot showing the causes of non-productive contigs in each locus. For both plots, sc-γδTCR, -αβTCR and -BCR data were taken from Suo et al. 2022 excluding thymus samples. b , Schematic illustration showing that mRNA without V genes would be captured by 5′RACE + Switch oligo technique but not by multiplex PCR strategy. c , Pointplot of proportion of contigs with multi-J mapping in the presence of V gene in control and cycloheximide-treated PBMC samples. Points are colored by locus of TCR/BCR. For both IGH and IGL/IGK, the proportions were 0% in control and treated. d , Schematic illustration showing the factors associated with multi-J mapping and the proposed mechanisms. e , Boxplots of sc-γδTCR contig counts annotated by 10X cellranger vdj v6.1.2 versus v7.0.0 using data from n = 33 independent samples from Suo et al. 2022 . Left: all high confidence contigs ( P -value 5.43e-6, r 0.91 in the two-sided Wilcoxon signed-rank test). Right: high confidence productive contigs ( P -value 1.69e-6, r 0.96 in the two-sided Wilcoxon signed-rank test). Boxes capture the first to third quartiles and whisks span a further 1.5X interquartile range on each side of the box.
    Figure Legend Snippet: a , Left: barplot of proportion of contigs that are productive or non-productive in each locus. Right: barplot showing the causes of non-productive contigs in each locus. For both plots, sc-γδTCR, -αβTCR and -BCR data were taken from Suo et al. 2022 excluding thymus samples. b , Schematic illustration showing that mRNA without V genes would be captured by 5′RACE + Switch oligo technique but not by multiplex PCR strategy. c , Pointplot of proportion of contigs with multi-J mapping in the presence of V gene in control and cycloheximide-treated PBMC samples. Points are colored by locus of TCR/BCR. For both IGH and IGL/IGK, the proportions were 0% in control and treated. d , Schematic illustration showing the factors associated with multi-J mapping and the proposed mechanisms. e , Boxplots of sc-γδTCR contig counts annotated by 10X cellranger vdj v6.1.2 versus v7.0.0 using data from n = 33 independent samples from Suo et al. 2022 . Left: all high confidence contigs ( P -value 5.43e-6, r 0.91 in the two-sided Wilcoxon signed-rank test). Right: high confidence productive contigs ( P -value 1.69e-6, r 0.96 in the two-sided Wilcoxon signed-rank test). Boxes capture the first to third quartiles and whisks span a further 1.5X interquartile range on each side of the box.

    Techniques Used: Multiplex Assay, Control

    a , Left—barplot of proportion of contigs that are productive or nonproductive in each locus. Right—barplot showing the causes of nonproductive contigs in each locus. b , Schematic illustration of the V(D)J rearrangement process and the potential cause of multi-J mapping. c , Boxplot of the proportion of contigs with multi-J mapping, in the presence (blue) or absence (orange) of V genes. Only samples with at least ten contigs are shown. Boxes capture the first to third quartiles and whisks span a further 1.5× interquartile range on each side of the box (two-sided Wilcoxon rank-sum test). The sample sizes of all boxplots from left to right are 51, 46, 52, 55, 26, 29, 20, 29, 33, 27, 33, 29, 34 and 25. d , Top—logistic regression formula to explore factors associated with multi-J mapping. Bottom—volcano plot summarizing logistic regression results (ref. ); y axis: −log 10 (BH adjusted P value); x axis: log(odds ratio). Variables that were also significant in our control/cycloheximide-treated PBMC dataset are highlighted in red (associated with increased multi-J mapping) or blue (associated with decreased multi-J mapping). e , Sequence logos covering the last 11 and first 10 nucleotides at 3′ ends (position 1–11) and the neighboring intron (position 12–21), respectively, for genes associated with increased (top) or decreased (bottom) multi-J mapping. J genes associated with increased multi-J mapping were less likely to have T in position 17 (logistic regression; two-tailed P value). ‘GTAAGT’ is a known consensus motif for splicing in position 12–17 that is +1 to +6 in the intron. They were also more likely to have T in position 6 (logistic regression; two-tailed P value). f , Swarmplots of fraction difference of sc-γδTCR contigs ( n = 33) annotated by Dandelion versus 10X cellranger vdj (v6.1.2). The red dashed line marks the threshold of 0, above which Dandelion recovers more γδTCR contigs than 10X. Left—all high confidence contigs. Right—high confidence productive contigs. Data for a , c , d (bottom) and f were taken from ref. and each dot represents a sample.
    Figure Legend Snippet: a , Left—barplot of proportion of contigs that are productive or nonproductive in each locus. Right—barplot showing the causes of nonproductive contigs in each locus. b , Schematic illustration of the V(D)J rearrangement process and the potential cause of multi-J mapping. c , Boxplot of the proportion of contigs with multi-J mapping, in the presence (blue) or absence (orange) of V genes. Only samples with at least ten contigs are shown. Boxes capture the first to third quartiles and whisks span a further 1.5× interquartile range on each side of the box (two-sided Wilcoxon rank-sum test). The sample sizes of all boxplots from left to right are 51, 46, 52, 55, 26, 29, 20, 29, 33, 27, 33, 29, 34 and 25. d , Top—logistic regression formula to explore factors associated with multi-J mapping. Bottom—volcano plot summarizing logistic regression results (ref. ); y axis: −log 10 (BH adjusted P value); x axis: log(odds ratio). Variables that were also significant in our control/cycloheximide-treated PBMC dataset are highlighted in red (associated with increased multi-J mapping) or blue (associated with decreased multi-J mapping). e , Sequence logos covering the last 11 and first 10 nucleotides at 3′ ends (position 1–11) and the neighboring intron (position 12–21), respectively, for genes associated with increased (top) or decreased (bottom) multi-J mapping. J genes associated with increased multi-J mapping were less likely to have T in position 17 (logistic regression; two-tailed P value). ‘GTAAGT’ is a known consensus motif for splicing in position 12–17 that is +1 to +6 in the intron. They were also more likely to have T in position 6 (logistic regression; two-tailed P value). f , Swarmplots of fraction difference of sc-γδTCR contigs ( n = 33) annotated by Dandelion versus 10X cellranger vdj (v6.1.2). The red dashed line marks the threshold of 0, above which Dandelion recovers more γδTCR contigs than 10X. Left—all high confidence contigs. Right—high confidence productive contigs. Data for a , c , d (bottom) and f were taken from ref. and each dot represents a sample.

    Techniques Used: Control, Sequencing, Two Tailed Test



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