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| Status |
Public on Feb 28, 2012 |
| Title |
HNRPA2B1_HITSCLIP_2 |
| Sample type |
SRA |
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| Source name |
MDA-MB-231
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| Organism |
Homo sapiens |
| Characteristics |
antibody: HNRPA2B1
antibody vendor: Origene
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| Treatment protocol |
Seventy-two hours post-transfection, cells were UV-crosslinked and lysed. Samples were collected and treated based on HITS-CLIP protocol (Chi et al., 2009, Nature, 460: 479-86).
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| Growth protocol |
MDA-MB-231 cells at 50% confluency were transfected with tagged HNRPA2B1 (Origene) using Lipofectamin LTX reagent (Invitrogen) according to manufacturer’s recommendations.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were constructed according to HITS-CLIP protocol (Chi et al., 2009, Nature, 460: 479-86).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
small RNA
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| Data processing |
Library strategy: CLIP-Seq
The raw data was aligned to hg18 human genome build using bowtie. ChIPseeqer (Giannopoulou and Elemeneto, 2011) was used to process the reads, find peak coordinates and create randomly generated peaks.
Genome Build:
HNRNPA2_rep2_real_random_peak_coordinates.txt: hg18
HNRNPA2_rep2_real_random_peaks.fa: hg18
HNRNPA2_rep2_real_random_peak_coordinates.txt: The discovered peaks along with their randomly generated counterparts (real peaks are set to '1' and random ones to '0'). The associated sequences are provided in the HNRNPA2_rep2_real_random_peaks.fa file.
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| Submission date |
Feb 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Hani Goodarzi |
| Organization name |
UCSF
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| Department |
Biochemistry and Biophysics
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| Street address |
600 16th St, GH S312D
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (2) |
| GSE35799 |
HNRPA2B1 HITS-CLIP |
| GSE35800 |
Systematic Discovery of Structural Elements Governing Mammalian mRNA Stability |
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| Relations |
| SRA |
SRX119733 |
| BioSample |
SAMN00788864 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM875074_HNRNPA2_rep2_real_random_peak_coordinates.txt.gz |
38.5 Kb |
(ftp)(http) |
TXT |
| GSM875074_HNRNPA2_rep2_real_random_peaks.fa.gz |
326.0 Kb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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