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| Status |
Public on Feb 20, 2012 |
| Title |
hnRNPF 293T CLIPseq 1 |
| Sample type |
SRA |
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| Source name |
human 293T cells
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| Organism |
Homo sapiens |
| Characteristics |
antibody: hnRNPF
antibody manufacturer: Santa Cruz
antibody catalog #: sc-10045
antibody lot #: J1306
cell line: 293T
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| Growth protocol |
Human 293T cells were obtained from ATCC and cultured in DMEM supplemented with 10% FBS at 37 ̊C and 5% CO2.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Cross-linking IP against hnRNPF
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| 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
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| Organization name |
UCSD
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| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| 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 |
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| Relations |
| SRA |
SRX115505 |
| BioSample |
SAMN00771624 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM859983_hnRNPF_293T_CLIPseq_1.hg18.bowtie.gz |
116.2 Mb |
(ftp)(http) |
BOWTIE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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