|
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 |