|
| Status |
Public on Sep 30, 2017 |
| Title |
Satb1-/- Hb9 Rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Mus musculus retina, P6
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: retina
genotype/variation: Satb1-/- Hb9
development age: postnatal day 6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dissociated retinal cells were FACS sorted directly into lysis buffer from PicoPure RNA isolation kit (Invitrogen). RNA was extracted and purified with PicoPure RNA isolation kit (Invitrogen) and RNA Clean & Concentrator™- 5 Kit (Zymo). cDNA was synthesized and amplified with the Ovation RNA-Seq kit (Nugen)
RNA libraries were prepared for sequencing using ultralow system V2 kit (Nugen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
single end RNA-seq data
|
| Data processing |
Reads were aligned to a reference genome (mm10 Ensembl) using Tophat v2.0.10
Expression levels were quantified using cufflinks (inferred counts and tpm values)
FPKM was transformed into log10(TPM)
mm10
Genome_build: tab-delimited text files include lgTPM values for each Sample
|
| |
|
| Submission date |
Nov 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yi-Rong Peng |
| E-mail(s) |
yirongpeng@gmail.com
|
| Organization name |
University of California, Los Angeles
|
| Department |
Department of Ophthalmology
|
| Lab |
Yi-Rong Peng
|
| Street address |
100 Stein Plaza Driveway, B-133
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE90652 |
The transcriptome comparison between wildtype Hb9-GFP and Satb1-/-Hb9-GFP retinal ganglion cells (RGCs). |
| GSE90673 |
Expression profiles of retinal neuronal cells |
|
| Relations |
| BioSample |
SAMN06067971 |
| SRA |
SRX2381214 |
