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Status |
Public on May 08, 2013 |
Title |
FBL (MNase) |
Sample type |
SRA |
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Source name |
HEK293
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Organism |
Homo sapiens |
Characteristics |
cell line: HEK293 antibody: Fibrillarin; mouse monoclonal; AFB01 antibody vendor: Cytoskeleton, Inc. lot number: 011 3' adaptor: 5' TGGAATTCTCGGGTGCCAAGG 3'
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Growth protocol |
HEK293 and HeLa cells were routinely generated by replating every 3 d on T75 flasks (Falcon, 353133) in DMEM supplemented with 10% FCS.
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Extracted molecule |
total RNA |
Extraction protocol |
PAR-CLIP samples were extracted following the PAR-CLIP method (Hafner et al. 2010; PMID: 20371350). For HEK293 small RNA-seq samples total RNA was extracted with TRI Reagent, radiolabeled and size-selected on a PAA gel. For HeLa Ago2-IP samples lysates were clarified and Ago2-RNA complexes isolated with an antibody, Ago2-associated RNA TRI Reagent-extracted, radiolabeled and size-selected on a PAA gel. PAR-CLIP library preparation as described in (Hafner et al. 2010; PMID: 20371350). Small RNA libraries for HEK293 cells were constructed as described in (Hafner et al. 2008; PMID: 18158127). For HeLa Ago2 IP-seq samples Ago2-associated RNAs were extracted and used to prepare cDNA libraries as described in (Hafner et al. 2008; PMID: 18158127).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
The raw reads were processed on the CLIPZ server (www.clipz.unibas.ch; Khorshid et al., Nucleic Acids Research 2011, 39:D245 (PMID 21087992)). For subsequent analyses only uniquely mapped reads were considered. Genome_build: hg19 Feb 2009 Supplementary_files_format_and_content: bed files with genomic coordinates of reads mapped; scores represent the number of reads
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Submission date |
Jan 22, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Andreas R Gruber |
E-mail(s) |
agruber@tbi.univie.ac.at
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Organization name |
University of Basel
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Department |
Biozentrum
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Lab |
Zavolan
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Street address |
Klingelbergstrasse 50-70
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City |
Basel |
ZIP/Postal code |
4056 |
Country |
Switzerland |
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Platform ID |
GPL11154 |
Series (1) |
GSE43666 |
Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing |
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Relations |
SRA |
SRX218960 |
BioSample |
SAMN01893948 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1067865_ETHZ_BSSE_110126_708K9AAXX_4.bed.gz |
10.6 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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