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Sample GSM1548749 Query DataSets for GSM1548749
Status Public on Nov 20, 2014
Title PAR-CLIP of PACT (PRKRA), replicate 2
Sample type SRA
 
Source name cell culture
Organism Homo sapiens
Characteristics strain: FLAG:PRKRA Flp-In HEK293 T-Rex
cell line: HEK293
Extracted molecule total RNA
Extraction protocol PAR-CLIP (Hafner et al. 2010)
Illumina small RNA
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description library strategy: PAR-CLIP
Data processing removal of default 3'adapter sequence with FLEXBAR (see supplementary methods) and random dinucleotides on 5' and 3' ends with custom script
collapsing distinct read-sequences with custom script
alignment with BWA 0.7.5a-r405 to hg19 and decoy
scanning around DICER1 binding sites or control binding sites for aligned reads
Genome_build: hg19
Supplementary_files_format_and_content: fixed width WIG files with depth-of-coverage
 
Submission date Nov 18, 2014
Last update date May 15, 2019
Contact name Marvin Jens
E-mail(s) marvin.jens@mdc-berlin.de
Phone +493094062989
Organization name Max Delbrueck Center for Molecular Medicine
Department Systems Biology of Gene Regulatory Elements
Lab Rajewsky lab
Street address Robert Rössle Str. 10 (H. 87)
City Berlin
ZIP/Postal code 13092
Country Germany
 
Platform ID GPL11154
Series (2)
GSE55333 Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates
GSE63437 A variety of Dicer substrates in human and C. elegans (HEK PAR-CLIP)
Relations
BioSample SAMN03201290
SRA SRX763659

Supplementary file Size Download File type/resource
GSM1548749_PACT1_4su_2.wig.gz 112.4 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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