|
| Status |
Public on Jun 25, 2017 |
| Title |
sox11crush.B |
| Sample type |
SRA |
| |
|
| Source name |
RGCs
|
| Organism |
Mus musculus |
| Characteristics |
tissue: retina
cell type: retinal ganglion cell
genotype: AAV-So11
rna sample type: Sorted by FACS
condition: crushed
|
| Treatment protocol |
Eyes were injected with either AAV-Control or AAV-Sox11 for 2 weeks. Each replicate of each treatment group consisted of 3 retinas (from 3 different animals). Then, optic nerve crush was performed 3 days before sacrifice.
|
| Growth protocol |
Mice were approximately 3-4 weeks when starting. Mice were pseudo-randomly sorted from litters into treatment groups, and approximately balanced for age and sex between treatment groups.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After sacrifice, retinas were dissected in serum-free culture media and kept cool on ice. 3 retinas were pooled for each treatment condition for each replicate. Then, retinas were dissociated with papain, quenched with trypsin inhibitor, triturated, and stained with anti-Thy1-PE-Cy7 antibody and SYTOX live-dead cell stain. Cells were then sorted directly into Arcturus PicoPure extraction buffer, lysed immediately, and RNA was extracted according to manufacturer's instructions.
Nugen Ovation RNA Ultra Low Input (500 pg) +TruSeq Nano
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Removal of low expressed transcripts (minimum of 10 counts for at least one condition (all replicates)
Normalization (TMM) and removal of unwanted variation using residual (k=1) with R-package RUVSeq
Genome_build: mm10
Supplementary_files_format_and_content: Complete_geneList_EdgeR_Zhigang.csv
|
| |
|
| Submission date |
Sep 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Riki Kawaguchi |
| E-mail(s) |
rkawaguchi@mednet.ucla.edu
|
| Phone |
4244424783
|
| Organization name |
University of California Los Angeles
|
| Department |
Department of Neurology and Department of Psychiatry
|
| Lab |
Informatics Center for Neurogenetics and Neurogenomics (ICNN).
|
| Street address |
760 Westwood Plaza, Room 37-420
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-1759 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE87046 |
Sox11 expression in adult retina promotes regeneration of some ganglion cell types but kills others |
|
| Relations |
| BioSample |
SAMN05785623 |
| SRA |
SRX2173440 |
