|
| Status |
Public on Mar 18, 2015 |
| Title |
HuR iCLIP Biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ES cells
cell line: v6.5
gender: male
antibody: anti-HuR (Santa Crus sc-5483)
|
| Treatment protocol |
Cells were UV crosslinked at 254nm for 0.3J/cm^2 to in vivo fix RNA-RBP interactions
|
| Growth protocol |
mESCs were grown on gelatin plates with serum and LIF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysates were clarified from sonicated mESCs and HuR-RNA complexes were isolated with anti-HuR (Santa Crus sc-5483) antibody.
Libraries were prepared according to the FAST-iCLIP protocol (PMID: 25411354)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Protein enriched RNA
HuR_iCLIP_v65.bw
|
| Data processing |
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the mouse (mm9) genome using bowtie2
RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file containing high confidence RT stops from HuR iCLIP in mESCs generated from biological duplicates and mapped to the mm9 murine genome.
|
| |
|
| Submission date |
Dec 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Alexander Flynn |
| E-mail(s) |
raflynn@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
380 Roth Way, Room 265
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE64168 |
Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation [iCLIP] |
| GSE64169 |
Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation |
|
| Relations |
| BioSample |
SAMN03265578 |
| SRA |
SRX810308 |
