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| Status |
Public on Dec 31, 2020 |
| Title |
scATAC_Retina_WT |
| Sample type |
SRA |
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| Source name |
wild type_retina
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype: wild type
tissue/cell type: retina
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| 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
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
1603317_ATAC_WT_S2_L001
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| 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
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| Submission date |
Dec 30, 2020 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Michael A Dyer |
| Organization name |
St. Jude Children's Research Hospital
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| Department |
DNB
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| Street address |
262 Danny Thomas
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| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| 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] |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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