|
| Status |
Public on Jan 08, 2020 |
| Title |
IMJCWT3: Wild-type replicate 3 mRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Mus musculus |
| Characteristics |
tissue: retina
age: post natal day 21
genotype/variation: wild-type
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Libraries were prepared from this RNA starting with 1 g per sample and using the mRNA‐seq Sample Prep Kit (Illumina) as per recommended instructions. After Ribozero purification and removing only ribosomal RNA, barcoded libraries were prepared according to Illumina's instructions (2013) accompanying the TruSeq RNA Sample prep kit v2 (Part# RS‐122‐2001). Libraries were quantitated using the Agilent Bio‐analyzer (model 2100) and pooled in equimolar amounts. The pooled libraries were sequenced with stranded 50-bp single-end reads on the HiSeq2500 in Rapid Run Mode
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNAseq
|
| Data processing |
Reads were mapped to mouse genome with TopHat2 (v 2.1.1). Reads mapped to the mitochondrial genome, and with phred score < 30 were excluded. Counts were retrieved with HTseq (v.0.6.0)60 in union mode. Lastly, counts were analyzed for differential expression with R (3.4) package DEseq
Genome_build: mm9
|
| |
|
| Submission date |
Aug 28, 2019 |
| Last update date |
Jan 08, 2020 |
| Contact name |
Ivan Moskowitz |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Chicago
|
| Department |
Pediatrics, Pathology, and Human Genetics
|
| Street address |
900 E 57th St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE136564 |
Transcriptional profiling of the adult mouse retina in wild-type and Nrl deficient mice |
| GSE136565 |
Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types |
|
| Relations |
| BioSample |
SAMN12647667 |
| SRA |
SRX6780721 |
