|
| Status |
Public on Jul 01, 2023 |
| Title |
jcov42 [MultiomeATAC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMC
age (in years): 37
Sex: Male
clinical status: Severe:2-4mo
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated using 10X Genomics-provided protocol "CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevB".
Library was generated following 10X Genomics-provided protocols; "CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevE" for Multiome.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Multiome FASTQ files were processed using cellranger-arc.
Multiome ATAC count matrices were processed using Signac.
Signac and Amulet were used to filter out low quality cells and doublets for Multiome ATAC samples.
Multiome ATAC samples were merged using Signac. Further cells were removed post reduction and clustering for the merged object.
Cells removed during Multiome RNA processing were also removed from the Multiome ATAC object to maintain uniformity.
The Multiome ATAC object was annotated using the Multiome RNA annotated object and differential analysis was carried out using Signac.
Genome_build: hg38
Supplementary_files_format_and_content: Peak/Cell Raw count matrix for merged samples post QC for Multiome ATAC object. Metadata tables for Multiome ATAC object.
|
| |
|
| Submission date |
Feb 18, 2022 |
| Last update date |
Jul 01, 2023 |
| Contact name |
Jin-Gyu Cheong |
| E-mail(s) |
jic2016@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
1300 York Avenue
|
| City |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE196987 |
Durable Alterations of Hematopoiesis and Chromatin post-COVID-19 [MultiomeATAC-seq] |
| GSE196990 |
Durable Alterations of Hematopoiesis and Chromatin post-COVID-19 |
|
| Relations |
| BioSample |
SAMN26067759 |
| SRA |
SRX14222322 |
