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Sample GSM1368022 Query DataSets for GSM1368022
Status Public on Apr 11, 2014
Title 4suRNA_MOV10siRNA
Sample type SRA
Source name HEK293 cell culture
Organism Homo sapiens
Characteristics purification: oligo(dT) beads
cell line: HEK293
transfection: MOV10 siRNA
Treatment protocol For global mRNA for half-life measurements, mock- or MOV10 siRNA transfected HEK293 cells were labeled with 700 µM 4SU for 60 min.
Growth protocol HEK293 were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the miRNeasy kit (Qiagen). 4SU residues were biotinylated using EZ-Link biotin-HPDP (Thermo Fisher Scientific). Biotinylated 4SU-labled RNA was separated from non-labeled RNA using μMACS Streptavidin MicroBeads (Miltenyi) and 4SU-labeled RNA was eluted from μColumns by addition of 100 mM DTT. RNA was recovered from the flow-though and 4SU-labeled fractions using MinElute Spin columns (Qiagen). Input (total), flow-though (non-labeled RNA) and eluted (4SU-labled RNA) samples were used for poly(A)+ mRNA library preparation following the TruSeq RNA sample Prep v2 LS protocol (Illumina). The libraries were sequenced on an Illumina HiSeq2500 for 100 cycles (multiplexed 1× 101 + 7 index). mRNA half-lives were computed as previously described (Schwanhausser et al., 2011)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Read demultiplexing, read filtering and adapter trimming was done using flexbar (Dodt et al, 2012).
We used TopHat2 (version 2.06) (Trapnell et al., 2009 and Kim et al. 2013) for spliced alignment of reads to the human reference genome sequence (hg18).
mRNA half-lives were determined as described in Schwanhaeusser et al. Nature 2011 from the three fractions total/4suRNA/flowthrough
Genome_build: hg18
Submission date Apr 11, 2014
Last update date May 15, 2019
Contact name Markus Landthaler
Phone +49-30-9406-3026
Organization name Max-Delbrück-Center for Molecular Medicine
Department Berlin Institute for Medical Systems Biology
Street address Robert-Rössle-Straße 10
City Berlin
ZIP/Postal code 13125
Country Germany
Platform ID GPL16791
Series (2)
GSE56748 MOV10 Is a 5' to 3' RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3'UTRs (expression)
GSE56751 MOV10 Is a 5' to 3' RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3'UTRs
BioSample SAMN02726093
SRA SRX515682

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

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