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Sample GSM1065670 Query DataSets for GSM1065670
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: 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
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
SRA SRX218207
BioSample SAMN01889076

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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