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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 16, 2023 |
| Title |
DM_1_scATACseq |
| Sample type |
SRA |
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| Source name |
Hepatic organoids
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| Organism |
Homo sapiens |
| Characteristics |
treatment: Differentiation medium
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sample extraction was prepared using Chromium Single Cell ATAC Reagent Kits v1 (10X Genomics) according to the manufacturer’s protocols.
Sequencing library was prepared using Chromium Single Cell ATAC Reagent Kits v1 (10X Genomics) according to the manufacturer’s protocols.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
scRNA-seq
The preprocessing was followed by a pipeline provided by 10X genomics (https://support.10xgenomics.com/single-cell-gene-expression).
The process of converting raw sequencing data (bcl files) into fastqs and aligning to the human reference genome [http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-hg19-3.0.0.tar.gz, v.3.0.0, hg19] were performed using a Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
The Cell Ranger count module was used to generate the raw gene expression matrix.
Genome_build: hg19
Supplementary_files_format_and_content: 10x cell ranger count output (raw gene expression matrix, cell barcode and gene information table)
scATAC seq
The preprocessing was followed by a pipeline provided by 10X genomics (https://support.10xgenomics.com/single-cell-atac).
The process of converting raw sequencing data (bcl files) into fastqs and aligning to the human reference genome [https://cf.10xgenomics.com/releases/cell-atac/cellranger-atac-1.1.0.tar.gz, v.1.1.0, hg19] were performed using a Cell Ranger atac software (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
The Cell Ranger ATAC count module was used to generate the raw peak count matrix and transcription factors.
Genome_build: hg19
Supplementary_files_format_and_content: 10x cell ranger atac count output (raw peak count matrix, raw transcription factor count matrix, cell barcode, peak and transcription factor information table)
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| Submission date |
Oct 19, 2020 |
| Last update date |
Oct 16, 2023 |
| Contact name |
Jong Hwan Kim |
| E-mail(s) |
kkjjhhk@kribb.re.kr
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| Phone |
0821093299557
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| Organization name |
Korea Research Institute of Bioscience and Biotechnology
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| Department |
Genome structure research center
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| Street address |
125 Gwahak-ro, Yuseong-gu
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| City |
Daejeon |
| ZIP/Postal code |
ASI|KR|KS015|DAEJEON |
| Country |
South Korea |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE159557 |
Integrative analysis of transcriptomic and epigenomic dynamics of liver organoids using single cell RNA-seq and ATAC-seq. |
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| Relations |
| BioSample |
SAMN16475007 |
| SRA |
SRX9299040 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4832485_DM-1_hg19_TF_barcodes.tsv.gz |
31.3 Kb |
(ftp)(http) |
TSV |
| GSM4832485_DM-1_hg19_TF_matrix.mtx.gz |
18.6 Mb |
(ftp)(http) |
MTX |
| GSM4832485_DM-1_hg19_TF_motifs.tsv.gz |
4.7 Kb |
(ftp)(http) |
TSV |
| GSM4832485_DM-1_hg19_barcodes.tsv.gz |
31.2 Kb |
(ftp)(http) |
TSV |
| GSM4832485_DM-1_hg19_matrix.mtx.gz |
196.0 Mb |
(ftp)(http) |
MTX |
| GSM4832485_DM-1_hg19_peaks.bed.gz |
1.7 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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