|
| Status |
Public on Dec 21, 2018 |
| Title |
La/SSB RIP 2 |
| Sample type |
SRA |
| |
|
| Source name |
La/SSB RIP, Sciatic nerve
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: SD
tissue: Sciatic nerve
rip antibody: La/SSB antibody
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA-RBP complex was immunoprecipitated from axoplasm using specific antibodies
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Immunoprecipitated RNAs
|
| Data processing |
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to Rn6 using STAR2.4.0
Count read using HT-seq0.6.1 using Rn6 RefSeq as reference
Normalization (TMM) and differential expression analysis using EdgeR. Genes with 10 counts or more for at least one condition (all 3 reps) were used
Genome_build: Rn6
Supplementary_files_format_and_content: excel file with FPKM, raw and normalized counts for each sample and logFC, pVal and FDR for each comparison
|
| |
|
| Submission date |
Sep 05, 2017 |
| 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 |
GPL22396 |
| Series (1) |
| GSE103444 |
Identification of mRNA subsets interacting to RNA binding proteins in regenerating axons |
|
| Relations |
| BioSample |
SAMN07604269 |
| SRA |
SRX3159154 |
