|
| Status |
Public on Jun 30, 2011 |
| Title |
HeLa 4SU SILAC PAR-CLIP |
| Sample type |
SRA |
| |
|
| Source name |
HeLa 4U 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 |
SRX083306 |
| BioSample |
SAMN00668443 |
