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Sample GSM936509 Query DataSets for GSM936509
Status Public on Jun 01, 2012
Title PARCLIP_CAPRIN1
Sample type SRA
 
Source name HEK293 cell culture
Organism Homo sapiens
Characteristics cell line: HEK293
cell line stably expressing: HIS/FLAG/HA-tagged CAPRIN1
par-clip antibody: FLAG
culture medium: DMEM
Treatment protocol HEK293 cells stably expressing His/FLAG/HA-tagged proteins of interest were grown in medium supplemented with 4-thiouridine at a final concentration of 200 microM for 16 hour. Cells were UV-crosslinked at 365 nm.
Growth protocol HEK293 cells were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin
Extracted molecule total RNA
Extraction protocol PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129–141)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description binding sites
barcode for 1_qseq.txt: TCTCCCATCGTATGCCGTCTTCTGCTTG
barcode for 2_qseq.txt: TCTCCCATCGTATGCCGTCTTCTGCTTG
Data processing Adapters were removed with FAR 1.81 (the felxible adapter remover: http://sourceforge.net/projects/theflexibleadap/) aligned to hg18 and a set of RefSeq pre-mRNA sequences with BWA 0.5.8c.
Unique alignments were converted to a pileup and read clusters scored for characteristic conversions and read variability with a custom script.
After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 Mol Cell 43, 340–352 for details
Genome_build: hg18
Supplementary_files_format_and_content: bed file reporting binding sites
 
Submission date May 24, 2012
Last update date May 15, 2019
Contact name Markus Landthaler
E-mail(s) markus.landthaler@mdc-berlin.de
Phone +49-30-9406-3026
Organization name Max-Delbrück-Center for Molecular Medicine
Department Berlin Institute for Medical Systems Biology
Street address Robert-Rössle-Straße 10
City Berlin
ZIP/Postal code 13125
Country Germany
 
Platform ID GPL11154
Series (2)
GSE38157 The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts
GSE38201 The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [PAR-CLIP]
Relations
SRA SRX149420
BioSample SAMN00998311

Supplementary file Size Download File type/resource
GSM936509_PARCLIP_CAPRIN1_sites.bed.gz 197.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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