|
| Status |
Public on Apr 19, 2024 |
| Title |
KTBpool17_Asian, scATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Breast tissues from healthy women
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast
disease state: healthy donor
donors: five donors
ethnicity: Asian
|
| Growth protocol |
Cryopreserved tissues from healthy women were used.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei is isolated from these tissues using the protocol suggested for use with the chromium Next GEM Single Cell Multiome ATAC+Gene Expression protocol (CG000338).
was performed immediately as per Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338). In few instances (few samples from African American and European ancestry), the same protcol was used to generate nuclei but only snRNA-seq was performed.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
All samples are from healthy donors with no diseases
KTBpool17_Asian_per_barcode_metrics.csv
|
| Data processing |
cellranger-atac v2.0 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated.
Signac (v1.7) and Seurat (v4 were used to analyze the filtered barcode-peak matrices and fragment file generated from running cellragner-arc.
The gene expression and chromatin accessiblity data were process separately, WNN (weighted nearest neighbor) was used for cell clustering and visulization.
Assembly: GRCh38 (from 10X: refdata-cellranger-arc-GRCh38-2020-A-2.0.0)
Supplementary files format and content: 10x Genomics cellranger-arc output files (the files needed for further analysis): filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi, per_barcode_metrics.csv
|
| |
|
| Submission date |
Oct 03, 2023 |
| Last update date |
Apr 19, 2024 |
| Contact name |
Harikrishna Nakshatri |
| Organization name |
Indiana University School of Medicine
|
| Department |
General Surgery
|
| Street address |
980 W. Walnut St. R3C218C
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE244585 |
Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [10X single-cell multiome] |
| GSE244594 |
Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry |
|
| Relations |
| BioSample |
SAMN37669352 |
| SRA |
SRX21983643 |
