|
Status |
Public on Apr 19, 2024 |
Title |
KTBpool9-White American, 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: White American
|
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.
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|
|
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 KTBpool11_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
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|
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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 |
SAMN37669358 |
SRA |
SRX21983637 |