|
Status |
Public on Feb 20, 2012 |
Title |
hnRNPA1 293T CLIPseq 3 |
Sample type |
SRA |
|
|
Source name |
human 293T cells
|
Organism |
Homo sapiens |
Characteristics |
antibody: hnRNPA1 antibody manufacturer: Novus Biologicals cell line: 293T antibody catalog #: NB100-672 antibody lot #: clone: 4B10
|
Growth protocol |
Human 293T cells were obtained from ATCC and cultured in DMEM supplemented with 10% FBS at 37 ̊C and 5% CO2.
|
Extracted molecule |
total RNA |
Extraction protocol |
Three 10cm plates of confluent, untreated human 293T cells were subjected to UV cross-linking on ice. CLIP- seq libraries for hnRNP A1, A2/B1, F, M, and U were constructed as previously described (Yeo et al., 2009), using anti-hnRNP A1 (Novus Biologicals), anti-hnRNP A2/B1 (Santa Cruz Biotechnologies), anti-hnRNP F (Santa Cruz Biotechnologies), anti-hnRNP M (Aviva Systems Biology), and anti-hnRNP U (Bethyl Laboratories). Libraries were subjected to standard Illumina sequencing protocols.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer II |
|
|
Description |
Cross-linking IP against hnRNPA1
|
Data processing |
CLIP-seq reads were processed as previously described (Polymenidou et al., 2011). Briefly, reads were trimmed to remove sequencing adaptors and homopolymeric runs >10nt, and mapped to the human genome (hg18) using Bowtie (version 0.12.2 with parameters –q –l 20 –m 5 –k 5 ––best).
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|
|
Submission date |
Jan 10, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Gene Yeo |
E-mail(s) |
geneyeo@ucsd.edu
|
Organization name |
UCSD
|
Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
|
|
Platform ID |
GPL9115 |
Series (2) |
GSE34993 |
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq) |
GSE34996 |
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins |
|
Relations |
SRA |
SRX115502 |
BioSample |
SAMN00771621 |