|
| Status |
Public on Feb 28, 2013 |
| Title |
AGO2_4su_3_ML_LG |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: AGO2 11A9 (Ruedel et al., 2008 RNA)
cell line: HEK293
|
| Treatment protocol |
HEK293 cells were grown in medium supplemented with 4-thiouridine at a final concentration of 100 microM for 16 hour. Cells were UV-crosslinked at 365 nm.
|
| Growth protocol |
HEK293 cells were grown in DMEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129–141)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
library strategy: PAR-CLIP
|
| Data processing |
Adapters were removed with FAR 1.86 (the felxible adapter remover: http://sourceforge.net/projects/theflexibleadap/) and aligned to hg19 reference sequence with BWA 0.5.8c.
Unique alignments were grouped into read clusters and scored for characteristic conversions and read variability with a custom script.
The mappings of all libraries were analyzed with two published (Hafner et al. 2010 Cell 141, 129–141) AGO1, AGO3 libraries (see also our Suppl. Methods).
After stringent false-positive filtering, using clusters that aligned antisense to a catalog of transcripts as decoys (see Lebedeva et al. 2011 Mol Cell 43, 340–352 for details), remaining clusters were output as bed files.
Genome_build: hg19
Supplementary_files_format_and_content: bed file; binding sites
|
| |
|
| Submission date |
Jan 17, 2013 |
| 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 |
GPL10999 |
| Series (2) |
| GSE43573 |
Circular RNAs are a large class of animal RNAs with regulatory potency (PAR-CLIP) |
| GSE43574 |
Circular RNAs are a large class of animal RNAs with regulatory potency |
|
| Relations |
| SRA |
SRX218207 |
| BioSample |
SAMN01889076 |
