|
| Status |
Public on Dec 15, 2021 |
| Title |
Center_4 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse central retinas
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
age: P30
tissue: central retinas
rna marker: CAR+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The tissue was dissociated fresh, and cells were, fixed, and labeled with CAR antibody. Specific cellular or nuclear populations were FACS isolated and the RNA was extracted from the cells or nuclei using the RecoverAll Kit.
cDNA was generated using the SMART-Seq v.4 kit. The indices were added using the Nextera XT Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality control of RNA-seq reads were performed using fastqc version 0.10.1
RNA-seq reads were clipped and mapped onto onto the either the mouse genome (Ensembl GRCm38.90) using STAR version 2.5.2b. Parameters used were as follows: --runThreadN 6 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --clip3pAdapterSeq --quantMode TranscriptomeSAM GeneCounts
Read counts were generated by HT-seq version 0.9.1. Sample parameters used were as follows: -i gene_name -s no
Genome_build: Ensembl GRCm38.90
Supplementary_files_format_and_content: Text files with the read counts for every gene for each sample.
|
| |
|
| Submission date |
Oct 26, 2021 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Ryoji Amamoto |
| E-mail(s) |
ryoji_amamoto@hms.harvard.edu
|
| Phone |
6177498955
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Lab |
Cepko
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE186612 |
Retinoic acid signaling mediates peripheral cone photoreceptor survival in a mouse model of retina degeneration |
|
| Relations |
| BioSample |
SAMN22574204 |
| SRA |
SRX12779872 |
