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a , Schematic overview of Droplet Paired-Tag; TSO, template switch oligo. b , Distribution of the unique number of fragments per cell across different single-cell epigenomic assays with the indicated samples and histone targets; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3), 5,111 (scCUT&Tag, H3K27ac), 9,039 (scCUT&Tag-pro, H3K27ac) and 12,585 (scCUT&Tag-pro, H3K27me3); PBMCs, peripheral blood <t>mononuclear</t> cells. c , d , Distribution of unique transcript ( c ) or gene ( d ) numbers per cell across different single-cell multiomic assays. For all box plots, hinges were drawn from the 25th to 75th percentiles, with the middle line denoting the median and whiskers denoting a maximum 2× the interquartile range; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3) and 2,711 (10x Multiome, ATAC). e , Genome-wide SCCs between mESC histone modification datasets from Droplet Paired-Tag (indicated with ‘sc’), bulk CUT&Tag and ChIP–seq (indicated with ‘bulk’); rep, replicate. f , Genome browser view showing examples of pseudo-bulk and single-cell histone modification signals of Droplet Paired-Tag in mESCs, along with bulk ChIP–seq and CUT&Tag. The pluripotent gene ( Sox2 ), along with its superenhancer (SCR), and the repressed gene ( Gata4 ) are highlighted in pink; chr, chromosome. g , Number and overlap of peaks called using H3K27ac Droplet Paired-Tag compared to those from ChIP–seq datasets. h , Scatter plot showing the relationships between the total number of H3K27ac peaks called and the number of nuclei after downsampling. The dashed line indicates the cutoff of the number of nuclei that could recover 85% of peaks.
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a , Schematic overview of Droplet Paired-Tag; TSO, template switch oligo. b , Distribution of the unique number of fragments per cell across different single-cell epigenomic assays with the indicated samples and histone targets; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3), 5,111 (scCUT&Tag, H3K27ac), 9,039 (scCUT&Tag-pro, H3K27ac) and 12,585 (scCUT&Tag-pro, H3K27me3); PBMCs, peripheral blood <t>mononuclear</t> cells. c , d , Distribution of unique transcript ( c ) or gene ( d ) numbers per cell across different single-cell multiomic assays. For all box plots, hinges were drawn from the 25th to 75th percentiles, with the middle line denoting the median and whiskers denoting a maximum 2× the interquartile range; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3) and 2,711 (10x Multiome, ATAC). e , Genome-wide SCCs between mESC histone modification datasets from Droplet Paired-Tag (indicated with ‘sc’), bulk CUT&Tag and ChIP–seq (indicated with ‘bulk’); rep, replicate. f , Genome browser view showing examples of pseudo-bulk and single-cell histone modification signals of Droplet Paired-Tag in mESCs, along with bulk ChIP–seq and CUT&Tag. The pluripotent gene ( Sox2 ), along with its superenhancer (SCR), and the repressed gene ( Gata4 ) are highlighted in pink; chr, chromosome. g , Number and overlap of peaks called using H3K27ac Droplet Paired-Tag compared to those from ChIP–seq datasets. h , Scatter plot showing the relationships between the total number of H3K27ac peaks called and the number of nuclei after downsampling. The dashed line indicates the cutoff of the number of nuclei that could recover 85% of peaks.
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a , Schematic overview of Droplet Paired-Tag; TSO, template switch oligo. b , Distribution of the unique number of fragments per cell across different single-cell epigenomic assays with the indicated samples and histone targets; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3), 5,111 (scCUT&Tag, H3K27ac), 9,039 (scCUT&Tag-pro, H3K27ac) and 12,585 (scCUT&Tag-pro, H3K27me3); PBMCs, peripheral blood <t>mononuclear</t> cells. c , d , Distribution of unique transcript ( c ) or gene ( d ) numbers per cell across different single-cell multiomic assays. For all box plots, hinges were drawn from the 25th to 75th percentiles, with the middle line denoting the median and whiskers denoting a maximum 2× the interquartile range; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3) and 2,711 (10x Multiome, ATAC). e , Genome-wide SCCs between mESC histone modification datasets from Droplet Paired-Tag (indicated with ‘sc’), bulk CUT&Tag and ChIP–seq (indicated with ‘bulk’); rep, replicate. f , Genome browser view showing examples of pseudo-bulk and single-cell histone modification signals of Droplet Paired-Tag in mESCs, along with bulk ChIP–seq and CUT&Tag. The pluripotent gene ( Sox2 ), along with its superenhancer (SCR), and the repressed gene ( Gata4 ) are highlighted in pink; chr, chromosome. g , Number and overlap of peaks called using H3K27ac Droplet Paired-Tag compared to those from ChIP–seq datasets. h , Scatter plot showing the relationships between the total number of H3K27ac peaks called and the number of nuclei after downsampling. The dashed line indicates the cutoff of the number of nuclei that could recover 85% of peaks.
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a , Schematic overview of Droplet Paired-Tag; TSO, template switch oligo. b , Distribution of the unique number of fragments per cell across different single-cell epigenomic assays with the indicated samples and histone targets; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3), 5,111 (scCUT&Tag, H3K27ac), 9,039 (scCUT&Tag-pro, H3K27ac) and 12,585 (scCUT&Tag-pro, H3K27me3); PBMCs, peripheral blood <t>mononuclear</t> cells. c , d , Distribution of unique transcript ( c ) or gene ( d ) numbers per cell across different single-cell multiomic assays. For all box plots, hinges were drawn from the 25th to 75th percentiles, with the middle line denoting the median and whiskers denoting a maximum 2× the interquartile range; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3) and 2,711 (10x Multiome, ATAC). e , Genome-wide SCCs between mESC histone modification datasets from Droplet Paired-Tag (indicated with ‘sc’), bulk CUT&Tag and ChIP–seq (indicated with ‘bulk’); rep, replicate. f , Genome browser view showing examples of pseudo-bulk and single-cell histone modification signals of Droplet Paired-Tag in mESCs, along with bulk ChIP–seq and CUT&Tag. The pluripotent gene ( Sox2 ), along with its superenhancer (SCR), and the repressed gene ( Gata4 ) are highlighted in pink; chr, chromosome. g , Number and overlap of peaks called using H3K27ac Droplet Paired-Tag compared to those from ChIP–seq datasets. h , Scatter plot showing the relationships between the total number of H3K27ac peaks called and the number of nuclei after downsampling. The dashed line indicates the cutoff of the number of nuclei that could recover 85% of peaks.
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Image Search Results


a , Schematic overview of Droplet Paired-Tag; TSO, template switch oligo. b , Distribution of the unique number of fragments per cell across different single-cell epigenomic assays with the indicated samples and histone targets; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3), 5,111 (scCUT&Tag, H3K27ac), 9,039 (scCUT&Tag-pro, H3K27ac) and 12,585 (scCUT&Tag-pro, H3K27me3); PBMCs, peripheral blood mononuclear cells. c , d , Distribution of unique transcript ( c ) or gene ( d ) numbers per cell across different single-cell multiomic assays. For all box plots, hinges were drawn from the 25th to 75th percentiles, with the middle line denoting the median and whiskers denoting a maximum 2× the interquartile range; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3) and 2,711 (10x Multiome, ATAC). e , Genome-wide SCCs between mESC histone modification datasets from Droplet Paired-Tag (indicated with ‘sc’), bulk CUT&Tag and ChIP–seq (indicated with ‘bulk’); rep, replicate. f , Genome browser view showing examples of pseudo-bulk and single-cell histone modification signals of Droplet Paired-Tag in mESCs, along with bulk ChIP–seq and CUT&Tag. The pluripotent gene ( Sox2 ), along with its superenhancer (SCR), and the repressed gene ( Gata4 ) are highlighted in pink; chr, chromosome. g , Number and overlap of peaks called using H3K27ac Droplet Paired-Tag compared to those from ChIP–seq datasets. h , Scatter plot showing the relationships between the total number of H3K27ac peaks called and the number of nuclei after downsampling. The dashed line indicates the cutoff of the number of nuclei that could recover 85% of peaks.

Journal: Nature Structural & Molecular Biology

Article Title: Droplet-based single-cell joint profiling of histone modifications and transcriptomes

doi: 10.1038/s41594-023-01060-1

Figure Lengend Snippet: a , Schematic overview of Droplet Paired-Tag; TSO, template switch oligo. b , Distribution of the unique number of fragments per cell across different single-cell epigenomic assays with the indicated samples and histone targets; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3), 5,111 (scCUT&Tag, H3K27ac), 9,039 (scCUT&Tag-pro, H3K27ac) and 12,585 (scCUT&Tag-pro, H3K27me3); PBMCs, peripheral blood mononuclear cells. c , d , Distribution of unique transcript ( c ) or gene ( d ) numbers per cell across different single-cell multiomic assays. For all box plots, hinges were drawn from the 25th to 75th percentiles, with the middle line denoting the median and whiskers denoting a maximum 2× the interquartile range; n = 13,664 (Droplet Paired-Tag, H3K27ac), 4,501 (Droplet Paired-Tag, H3K27me3), 2,066 (Paired-Tag, H3K27ac), 418 (Paired-Tag, H3K27me3), 3,031 (CoTECH, H3K27me3) and 2,711 (10x Multiome, ATAC). e , Genome-wide SCCs between mESC histone modification datasets from Droplet Paired-Tag (indicated with ‘sc’), bulk CUT&Tag and ChIP–seq (indicated with ‘bulk’); rep, replicate. f , Genome browser view showing examples of pseudo-bulk and single-cell histone modification signals of Droplet Paired-Tag in mESCs, along with bulk ChIP–seq and CUT&Tag. The pluripotent gene ( Sox2 ), along with its superenhancer (SCR), and the repressed gene ( Gata4 ) are highlighted in pink; chr, chromosome. g , Number and overlap of peaks called using H3K27ac Droplet Paired-Tag compared to those from ChIP–seq datasets. h , Scatter plot showing the relationships between the total number of H3K27ac peaks called and the number of nuclei after downsampling. The dashed line indicates the cutoff of the number of nuclei that could recover 85% of peaks.

Article Snippet: Other external datasets were downloaded from NCBI GEO with the following accession numbers: mESC H3K27me3 ChIP–seq data ( GSE156589 ), Paired-Tag data ( GSE152020 ), CoTECH data ( GSE158435 ), scCUT&Tag data from peripheral blood mononuclear cells ( GSE157910 ), scCUT&Tag data from brain ( GSE163532 ), scCUT&Tag-pro data ( GSE195725 ), snm3C-seq data from brain ( GSE156683 ) and ChIP–seq data from mouse cortex excitatory neurons ( GSE141587 ).

Techniques: Genome Wide, Modification, ChIP-sequencing