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| Status |
Public on Nov 28, 2023 |
| Title |
M1_donor3_rep2_Multiome H3K27ac |
| Sample type |
SRA |
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| Source name |
Multiome H3K27ac Paired-Tag
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| Organism |
Homo sapiens |
| Characteristics |
donor id: H19.30.004
age: 58 y.o.
Sex: M
antibody: ab4729
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
nuclei preparation protocol: Cells from frozen tissue were extracted by douncing in douncing buffer (0.25 M sucrose (Sigma, S7903), 25 mM KCl (Sigma, P9333), 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT (Sigma, D9779), 1× Protease Inhibitor, 0.5 U µl−1 RNase OUT, 0.5 U µl−1 SUPERase Inhibitor). The cell suspension was filtered through a 30-µm Cell-Tric (Sysmex) to remove debris and spun down for 10min at 300g, 4 °C. Cell pellets were washed once with douncing buffer, spun down again, and resuspended in cold nuclei permeabilization buffer for 10mins. Permeablized nuclei were pelleted by centrifuge for 10 min at 1,000g, 4 °C, and washed with sort buffer (1× PBS (Gibco, 10010023), 1×Protease Inhibitor (Roche, 05056489001), 0.5 U µl−1 RNase OUT (Invitrogen, 10777-019), 0.5 U µl−1 SUPERase Inhibitor (Invitrogen, AM2694), 1mM EDTA (Invitrogen, 15575020), 1% BSA (Sigma, A1595)). Nuclei were resuspended in sort buffer and stained with μM 7-AAD (Invitrogen, A1310) for 10mins on ice, and proceed to Fluorescence-activated cell sorting (FACS) with an SH800 cell sorter (Sony) to isolate of single nucleus. Nuclei were collected in collection buffer (1× PBS (Gibco, 10010023), 5×Protease Inhibitor (Roche, 05056489001), 2.5 U µl−1 RNase OUT (Invitrogen, 10777-019), 2.5 U µl−1 SUPERase Inhibitor (Invitrogen, AM2694), 1mM EDTA (Invitrogen, 15575020), 5% BSA (Sigma, A1595)) at 5 °C. After centrifugation for 10min at 750g at 4 °C. Nuclei were washed twice with sort buffer and counted on an RWD C100-pro fluorescence cell counter with DAPI staining. For each histone modification, around 0.5 million sorted nuclei were aliquoted and proceeded to Paired-Tag experiments.
DNA and RNA libraries were generated according to the Chromium Single Cell ATAC Library kit manual with increased number of amplification cycles (12-13 cycles) for DNA library.
All sequencing was performed with an Illumina Nextseq2000 sequencer.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Fastq files are demultiplexed using cellranger-arc v.2.0.0 (10x Genomics) with command `cellranger-arc mkfastq`. DNA and RNA data were preprocessed using cellranger-atac v.2.0.0 and cellranger v.6.1.2, respectively, and barcodes were manually paired with custom script using the matching relationship provided in cellranger-arc.
Assembly: hg38 GRCh38
Supplementary files format and content: "barcode.tsv.gz" contains cell barcode information. "features.tsv.gz" consists of rows containing features (genes and peaks) and columns containing cell-associated barcodes. "matrix.mtx.gz" contains sparse feature-barcode matrix.
Library strategy: mutiome-seq
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| Submission date |
Nov 01, 2023 |
| Last update date |
Sep 06, 2024 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@health.ucsd.edu
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| Organization name |
UCSD
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE246760 |
Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate motor cortex [H3K27ac] |
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| Relations |
| BioSample |
SAMN38061063 |
| SRA |
SRX22328665 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7876403_BI012_barcodes.tsv.gz |
74.5 Kb |
(ftp)(http) |
TSV |
| GSM7876403_BI012_fragments.tsv.gz |
607.5 Mb |
(ftp)(http) |
TSV |
| GSM7876403_BI012_matrix.mtx.gz |
55.1 Mb |
(ftp)(http) |
MTX |
| GSM7876403_BI012_peaks.bed.gz |
789.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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