|
Status |
Public on Jun 30, 2011 |
Title |
HeLa 6SG SILAC PAR-CLIP |
Sample type |
SRA |
|
|
Source name |
HeLa 6SG SILAC PAR-CLIP
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa antibody: 3A2 antibody manufacturer: Santa Cruz antibody catalog #: sc-5261 culture medium: SILAC
|
Extracted molecule |
total RNA |
Extraction protocol |
PARCLIP + small RNA Sequencing
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina Genome Analyzer II |
|
|
Description |
pull down RNA
|
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 for details.
|
|
|
Submission date |
Jun 13, 2011 |
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 |
GPL9115 |
Series (1) |
GSE29943 |
Unstressed HeLa cells and ELAVL1/HuR knock down conditions: polyA RNA-Seq, small RNA-Seq, and PAR-CLIP |
|
Relations |
SRA |
SRX083307 |
BioSample |
SAMN00668444 |