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Sample GSM4995565 Query DataSets for GSM4995565
Status Public on Dec 31, 2020
Title scATAC_Retina_WT
Sample type SRA
Source name wild type_retina
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype: wild type
tissue/cell type: retina
Extracted molecule genomic DNA
Extraction protocol Retinas were removed, dissociated with papain, and run through a 4% BSA cushion. Cells were processed using the 10x genomics protocols.
Library construction was completed using the 10x RNA(v3) and ATAC-seq(v1) single cell kits
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
Description 1603317_ATAC_WT_S2_L001
Data processing scRNA-sequencing data was processed individually then aggregated using cellranger v3.0.2
scATAC-sequencing data was processed using cellranger-atac v1.0.1
Genome_build: mm10
Supplementary_files_format_and_content: For scRNA-seq tab delimited features(genes) and barcodes file and matrix file.
Supplementary_files_format_and_content: For scATAC-seq tab delimited fragments and barcodes file, matrix file, peaks bed file, and tab delimited peak_annotation
Submission date Dec 30, 2020
Last update date Jan 01, 2021
Contact name Michael A Dyer
Organization name St. Jude Children's Research Hospital
Department DNB
Street address 262 Danny Thomas
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
Platform ID GPL24247
Series (2)
GSE87064 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis
GSE164044 Nucleome Dynamics during Retinal Development [scRNA-seq/scATAC-seq_Mm]
BioSample SAMN17185295
SRA SRX9756769

Supplementary file Size Download File type/resource
GSM4995565_scATAC_WT_barcodes.tsv.gz 74.2 Kb (ftp)(http) TSV
GSM4995565_scATAC_WT_fragments.tsv.gz 800.9 Mb (ftp)(http) TSV
GSM4995565_scATAC_WT_matrix.mtx.gz 106.6 Mb (ftp)(http) MTX
GSM4995565_scATAC_WT_peaks.bed.gz 502.6 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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