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| Status |
Public on Nov 08, 2023 |
| Title |
PBMC, 10xTn5 |
| Sample type |
SRA |
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| Source name |
Peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripheral blood mononuclear cells
tissue: Peripheral blood
disease state: Healthy
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
PBMCs were isolated as previously described and stored viably frozen in serum containing DMSO (JP Mallm et al. 2019, Mol Sys Bio; doi:10.15252/msb.20188339). Prior to the experiments they were thawed in a water bath and immediately processed.
Libraries were prepared according to the Chromium single-cell ATAC v2 protocol (10x Genomics) using the provided Tn5 (10xTn5) or an in-house loaded Tn5 at high concentration (Tn5hc).
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
Raw data deposited at EGA; accession number:
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| Data processing |
Demultiplexing, barcode processing, genome mapping and aggregation were conducted using the Cell Ranger ATAC software v2.1.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: h5 single cell peak count matrix, tab-separated fragment file, comma-separated single cell info file
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| Submission date |
Jun 21, 2023 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Isabelle Seufert |
| Organization name |
DKFZ
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE235502 |
Enhancing sensitivity and versatility of Tn5-based single cell omics IV |
| GSE235506 |
Enhancing sensitivity and versatility of Tn5-based single cell omics |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM7504072_PBMC_10xTn5_CellRangerATAC_fragments.tsv.gz |
4.0 Gb |
(ftp)(http) |
TSV |
| GSM7504072_PBMC_10xTn5_CellRangerATAC_raw_peak_bc_matrix.h5 |
247.0 Mb |
(ftp)(http) |
H5 |
| GSM7504072_PBMC_10xTn5_CellRangerATAC_singlecell.csv.gz |
7.3 Mb |
(ftp)(http) |
CSV |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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