|
| Status |
Public on Nov 08, 2023 |
| Title |
RNA-seq_p10_khet_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Retina
strain: C57BL/6
genotype: CrxK88N/+
developmental stage: Post-natal day 10
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each genotype, three biological replicates, two retinas per replicate from one male and one female mouse were harvested and flash frozen in Trizol reagent. All retinas were processed for RNA simultaneously using TRIzol™ Reagent following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
k_het_p10_1
|
| Data processing |
Sequencing reads were first run through Trim Galore (v0.6.1) to remove adapter sequences.
Trimmed reads were then mapped to the mm10 genome and quantified with kallisto (v0.46.2).
Kallisto output transcript-level abundance matrices were then imported and summarized into gene-level matrices with R package tximport (v1.18.0).
Assembly: mm10
Supplementary files format and content: Tsv file with raw counts by gene
|
| |
|
| Submission date |
Jan 22, 2023 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Yiqiao Zheng |
| E-mail(s) |
yiqiao.zheng@wustl.edu
|
| Phone |
314-747-4351
|
| Organization name |
Washington University in St Louis
|
| Department |
Department of Ophthalmology & Visual Sciences
|
| Lab |
Shiming Chen, Ph.D.
|
| Street address |
517 South Euclid Avenue
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE223439 |
Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms [RNA-seq] |
| GSE223659 |
Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms |
|
| Relations |
| BioSample |
SAMN32867392 |
| SRA |
SRX19135925 |
