|
| Status |
Public on May 15, 2011 |
| Title |
RNA_Ago2_PAR-CLIP_mildMNase_repA |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
clip variant: PAR-CLIP
enzymatic digestion: mild MNase digestion
protein: Ago2
|
| Treatment protocol |
For samples subjected to PAR-CLIP, 4-Thiouridine was added to cells grown in monolayer at 1mM final concentration 12-14 hours prior to crosslinking at 365 nm UV. For samples subjected to CLIP, the cells were directly crosslinked at 254 nm UV.
|
| Growth protocol |
HEK293 cells were routinely grown in DMEM supplemented with 10% FCS in the presence of antibiotics.
|
| Extracted molecule |
cytoplasmic RNA |
| Extraction protocol |
CLIP, PAR-CLIP
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
The raw reads were processed on the CLIPZ server (Khorshid et al., Nucleic Acids Research 2011, 39:D245)
|
| |
|
| Submission date |
Apr 26, 2011 |
| Last update date |
Jul 17, 2019 |
| Contact name |
Jean Hausser |
| Organization name |
Weizmann Institute of Science
|
| Street address |
Herzl St.
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE28859 |
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (CLIP) |
| GSE28865 |
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins |
|
| Relations |
| SRA |
SRX058621 |
| BioSample |
SAMN00260290 |
