|
| Status |
Public on Dec 31, 2020 |
| Title |
scRNA_Retina_WT_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
wild type_retina
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype: wild type
tissue/cell type: retina
molecule subtype: 3’ RNA
|
| Extracted molecule |
total RNA |
| 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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
1657569_WT_Rep_1_S15_L004
processed data file:
scRNA_WT_barcodes.tsv.gz
scRNA_WT_features.tsv.gz
scRNA_WT_matrix.mtx.gz
scRNA_WT_VSX2-SEKO_barcodes.tsv.gz
scRNA_WT_VSX2-SEKO_features.tsv.gz
scRNA_WT_VSX2-SEKO_matrix.mtx.gz
|
| 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] |
|
| Relations |
| BioSample |
SAMN17185299 |
| SRA |
SRX9756765 |
