Journal: Genome Biology

Article Title: txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility

doi: 10.1186/s13059-023-03150-1

Figure Lengend Snippet: txci-ATAC-seq generates high-quality single-cell ATAC libraries at high throughput. a Schematic of molecular details of txci-ATAC-seq library generation. b Experimental workflow for txci-ATAC-seq barnyard library generation. After 96-plex tagmentation, nuclei are overloaded on a 10X Chromium microfluidics device. Following nucleus encapsulation in the formed droplets, 10% of the GEMs can be used for quality control and the remaining 90% for data analysis. c-e) txci-ATAC-seq QC metrics for human (GM12878) and mouse (CH12) cell lines supplemented with SBS primer during in-droplet PCR. c “Knee” plot showing the unique reads (log 10 scale) against the rank of each barcode (log 10 scale) ordered from most unique reads (left) to least (right). The dashed line indicates the threshold (1000 reads) used to identify cell barcodes (orange points). d Scatter plots showing the number of unique reads mapped to either the human or mouse genome for both true and pseudo-barnyard experiments. Values were log 10 -transformed after adding a pseudo-count of 1 to all values. The percentage shown in the true barnyard panel (6.6%) represents the estimated collision rate. e Scatter plots showing the FRiDHS against the estimated complexity for each cell barcode detected as either mouse (blue) or human (red) cell. The estimated complexity is shown on a log 10 scale

Article Snippet: After quenching enzyme activity, the nuclei were pooled into a 12-tube strip and then transferred to a 15-ml conical tube preloaded with 400 μl tagmentation washing buffer (TMG, which contains 10 mM Tris acetate pH 7.8 (Boston BioProducts, Cat. BB-2412), 5 mM magnesium acetate (Sigma, Cat. 63,052-100ML), and 10% (v/v) glycerol (VWR, Cat. RC3290-32) diluted in nuclease-free water.

Techniques: High Throughput Screening Assay, Encapsulation, Control, Transformation Assay

Journal: Genome Biology

Article Title: txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility

doi: 10.1186/s13059-023-03150-1

Figure Lengend Snippet: txci-ATAC-seq generates high-quality single-cell ATAC libraries at high throughput. a Schematic of molecular details of txci-ATAC-seq library generation. b Experimental workflow for txci-ATAC-seq barnyard library generation. After 96-plex tagmentation, nuclei are overloaded on a 10X Chromium microfluidics device. Following nucleus encapsulation in the formed droplets, 10% of the GEMs can be used for quality control and the remaining 90% for data analysis. c-e) txci-ATAC-seq QC metrics for human (GM12878) and mouse (CH12) cell lines supplemented with SBS primer during in-droplet PCR. c “Knee” plot showing the unique reads (log 10 scale) against the rank of each barcode (log 10 scale) ordered from most unique reads (left) to least (right). The dashed line indicates the threshold (1000 reads) used to identify cell barcodes (orange points). d Scatter plots showing the number of unique reads mapped to either the human or mouse genome for both true and pseudo-barnyard experiments. Values were log 10 -transformed after adding a pseudo-count of 1 to all values. The percentage shown in the true barnyard panel (6.6%) represents the estimated collision rate. e Scatter plots showing the FRiDHS against the estimated complexity for each cell barcode detected as either mouse (blue) or human (red) cell. The estimated complexity is shown on a log 10 scale

Article Snippet: Tagmented nuclei were then pooled into a single 15-ml conical tube; 5 ml of tagmentation wash buffer (TMG) was prepared consisting of a final concentration of 10 mM Tris acetate pH 7.5 (Sigma 93,352 and Sigma A6283, respectively), 5 mM magnesium acetate (Sigma M5661), and 10% (v/v) glycerol (Sigma G5516), diluted in PCR grade water; 1 ml of TMG was added on top of the chilled tagmented nuclei.

Techniques: High Throughput Screening Assay, Encapsulation, Transformation Assay

Journal: bioRxiv

Article Title: txci-ATAC-seq, a massive-scale single-cell technique to profile chromatin accessibility

doi: 10.1101/2023.05.11.540245

Figure Lengend Snippet: a) Schematic of molecular details of txci-ATAC-seq library generation. b) Experimental workflow for txci-ATAC-seq barnyard library generation. After 96-plex tagmentation, nuclei are overloaded on a 10X Chromium microfluidics device. Following nucleus encapsulation in the formed droplets, 10% of the GEMs can be used for quality control and the remaining 90% for data analysis. c-e) txci-ATAC-seq QC metrics for human (GM12878) and mouse (CH12) cell lines supplemented with SBS primer during in-droplet PCR. c) “Knee” plot showing the unique reads (log 10 scale) against the rank of each barcode (log 10 scale) ordered from most unique reads (left) to least (right). The dashed line indicates the threshold (1000 reads) used to identify cell barcodes (orange points). d) Scatter plots showing the number of unique reads mapped to either the human or mouse genome for both true and pseudo-barnyard experiments. Values were log 10 -transformed after adding a pseudo-count of 1 to all values. The percentage shown in the true barnyard panel (6.6%) represents the estimated collision rate. e) Scatter plots showing the FRiDHS against the estimated complexity for each cell barcode detected as either mouse (blue) or human (red) cell. The estimated complexity is shown on a log 10 scale.

Article Snippet: After quenching enzyme activity, the nuclei were pooled into a 12-tube strip and then transferred to a 15 ml conical tube preloaded with 400 μl tagmentation washing buffer (TMG, which contains 10mM Tris Acetate pH 7.8 (Boston BioProducts, Cat. BB-2412), 5mM Magnesium acetate (Sigma, Cat. 63052-100ML) and 10% (v/v) glycerol (VWR, Cat. RC3290-32) diluted in nuclease-free water).

Techniques: Encapsulation, Control, Transformation Assay

Journal: bioRxiv

Article Title: txci-ATAC-seq, a massive-scale single-cell technique to profile chromatin accessibility

doi: 10.1101/2023.05.11.540245

Figure Lengend Snippet: a) Well assignment for each cell source and barnyard design. The wells with a mixture of species are shown as half-circles of two different colors corresponding to each species. The wells where tagmentation was done with the 10X ATAC buffer are highlighted by orange outer circles. b) The scatter plots showing the number of reads mapped to either the human or mouse genome for each barnyard design. The plots on the left-hand side include all cell barcodes, and the plots on the right-hand side only visualize the 10X bead barcodes associated with a single Tn5 barcode. The percentage represents the estimated collision rate for each plot. The x- and y-axes are capped at 3×10 4 reads, and the cells with more than 3×10 4 reads are denoted by triangles. c) the theoretical model of the process of Tn5 barcode swapping. d), the proposed strategies to block barcode swapping.

Article Snippet: After quenching enzyme activity, the nuclei were pooled into a 12-tube strip and then transferred to a 15 ml conical tube preloaded with 400 μl tagmentation washing buffer (TMG, which contains 10mM Tris Acetate pH 7.8 (Boston BioProducts, Cat. BB-2412), 5mM Magnesium acetate (Sigma, Cat. 63052-100ML) and 10% (v/v) glycerol (VWR, Cat. RC3290-32) diluted in nuclease-free water).

Techniques: Blocking Assay

Journal: bioRxiv

Article Title: txci-ATAC-seq, a massive-scale single-cell technique to profile chromatin accessibility

doi: 10.1101/2023.05.11.540245

Figure Lengend Snippet: a) Two-dimensional density map of cells passing initial read filters for percent unique reads (library saturation) and unique read counts. b) Mixed-species tagmentation wells were subject to alignment in both human and mouse reference genomes. c) Number of cells per droplet quantified on a histogram, showing a majority of droplets still contain only a single cell. d) Quantification of cells in 25,000 and 75,000 library pools. Conditions include doublets uncovered either through cross-species alignment (“mixed doublet”) or through a reduced dimension detection strategy (see Methods). Other cells passing these filters are colored by identified species and tagmentation conditions. e,f) Hierarchically clustered heatmap of cell identification in the human cortex (e) and mouse whole brain (f) samples using gene activity scores for label transfer. The Brain Map M1 Cortex RNA dataset was used to annotate human cells and the Brain Map mouse cortex and hippocampus RNA dataset and mouse cerebellum (GSE165371) were used to annotate mouse cells. Values reflect the percentage of cells per cluster with each label as its maximum predicted value. g) Density plots of fragment length for fragments ranging from 1-1000 bp per technology. h) Grouped boxplots of projected unique read count per sequencing effort for each cell by technology.

Article Snippet: After quenching enzyme activity, the nuclei were pooled into a 12-tube strip and then transferred to a 15 ml conical tube preloaded with 400 μl tagmentation washing buffer (TMG, which contains 10mM Tris Acetate pH 7.8 (Boston BioProducts, Cat. BB-2412), 5mM Magnesium acetate (Sigma, Cat. 63052-100ML) and 10% (v/v) glycerol (VWR, Cat. RC3290-32) diluted in nuclease-free water).

Techniques: Activity Assay, Sequencing