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| Status |
Public on Jul 01, 2024 |
| Title |
ATAC MA13 |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Heart
disease state: Donor
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Nuclei were isolated according to 10x Genomics protocol (CG00375; Nuclei Isolation Complex Sample for ATAC GEX Sequencing RevB) and flow cytometry for 7-AAD positive nuclei was used for sorting.
Protocol CG000338 from 10x Genomics was used for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. Briefly, following nuclei isolation, permeabilization was performed, followed by transposition, GEM generation and barcoding using ChipJ (10x Genomics; PN1000234), post-GEM clean up, pre-amplification PCR, cDNA amplification, library construction, and sequencing. Gene expression and ATAC libraires were sequenced to a read depth of 50,000 and 25,000 respectively.
snRNA-Seq; snATAC-Seq
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| Library strategy |
ATAC-seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
paired single nucleus RNA + assay for transposable accessible chromatin, ATAC
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| Data processing |
Raw fastq files were aligned to the human GRCh38 reference genome (v) using CellRanger ARC (10x Genomics, v6.1).
ArchR (https://www.archrproject.com) was used to process the ATAC fragments and Seurat was used to process RNA.
Assembly: GRCh38
Supplementary files format and content: metadata.csv contains metainformation of all samples with cells in rows and labels in columns. For each sample, the CellRanger ARC output filtered matrix files including barcodes.tsv, features.tsv and matrix.mtx were included as processed data files as well.
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| Submission date |
Jun 25, 2024 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Xin Luo |
| E-mail(s) |
xluo01@amgen.com
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| Organization name |
Amgen Inc
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| Department |
Research and Development
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| Street address |
750 Gateway Blvd
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| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE218392 |
Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis |
| GSE270788 |
Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis III |
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| Relations |
| BioSample |
SAMN42043808 |
| SRA |
SRX25058184 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8352078_MA13_atac_fragments.tsv.gz |
1.7 Gb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
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