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Sample GSM7821206 Query DataSets for GSM7821206
Status Public on Apr 19, 2024
Title C23_KTBpool-23_Hispanic, 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: Hispanic
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
KTBpool-23_Hispanic_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 SAMN37669351
SRA SRX21983644

Supplementary file Size Download File type/resource
GSM7821206_KTBpool-23_Hispanic_atac_fragments.tsv.gz 2.8 Gb (ftp)(http) TSV
GSM7821206_KTBpool-23_Hispanic_atac_fragments.tsv.gz.tbi.gz 1.3 Mb (ftp)(http) TBI
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Raw data are available in SRA

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