|
| Status |
Public on Jun 20, 2015 |
| Title |
Nuclear HNRNPA2B1 HITS-CLIP rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231_HNRNPA2B1_HITS-CLIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MDA-MB-231
|
| Treatment protocol |
After cells underwent selection no further treatment was performed
|
| Growth protocol |
Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were UV cross-linked and prepared as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22) and the nuclear fraction was isolated and used for the immunprecipitation of HNRNPA2B1 using an anti-HNRNPA2B1 antibody obtained from PIERCE (cat#PA5-34939).
Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
protocol: HITS-CLIP
HNRNPA2B1 co-immunoprecipitated RNA
|
| Data processing |
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build hg19).
ChIPseeqer (strand-specific) was then used to identify the HNRNPA2B1 CLIP reads (Giannopoulou et al, BMC Bioinformatics 2011, 12:277). Tags between the replicates were then overlapped between the two biological replicates.
HNRNPA2B1 binding sites were then used to generate shuffled sequences, based on a 1st order Markov model (built-in ChIPseeqer function), for further comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files containing the chromosomal location and intensities of the peaks obtained from the HITS-CLIP experiments.
|
| |
|
| Submission date |
Jun 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Claudio Alarcon |
| E-mail(s) |
calarcon@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Department |
Systems Cancer Biology
|
| Lab |
Sohail Tavazoie
|
| Street address |
1230 York Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE70061 |
Nuclear HNRNPA2B1 HITS-CLIP and RNA-seq |
|
| Relations |
| BioSample |
SAMN03783298 |
| SRA |
SRX1066866 |
