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Series GSE40468 Query DataSets for GSE40468
Status Public on May 01, 2013
Title Cold induced RNA-binding proteins influence alternative polyadenylation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We employed PAR-CLIP, a recently developed method based on RNA-protein crosslinking, to identify Cirbp and Rbm3 binding sites at transcriptome-level. Genome-wide RNA-seq analysis indicated that cold temperature leads to extensive 3’UTR lengthening whereas the loss of Cirbp or Rbm3 resulted in 3’UTR shortening. Combining with PAR-CLIP results, we found that these two RBPs repress the polyadenylation adjacent to their binding sites.
Overall design Examination of the binding sites of Cirbp and Rbm3 by PAR-CLIP and their influence on the transcriptome by RNA-seq. PARCLIP was performed as in Hafner et al. 2010 Cell 141, 129–141, with MEFs cell lines stably expressing FLAG-tagged Cirbp and Rbm3. We used 4-thiouridine (4SU) to enhance the crosslink. For RNA-seq, polyadenylated RNA from the mock-transfected cells at 37°C or 32°C with two replicates, siCirbp-1, siCirbp-2, siRbm3-1 and siRbm3-2 MEFs at 37°C were sequenced on Solexa GAII using 76bp single-end kits according to the manufacturer’s instructions.
Contributor(s) Liu Y, Yan J
Citation(s) 23792593
Submission date Aug 29, 2012
Last update date Feb 07, 2020
Contact name Yuting Liu
Phone 02154920548
Organization name PICB
Department Functional Genomics
Lab Functional Genomics
Street address YueyangRoad320
City Shanghai
State/province -
ZIP/Postal code 200031
Country China
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (10)
GSM994702 Cirbp_PAR-CLIP
GSM994703 Rbm3_PAR-CLIP
GSM994704 Mock_37-1_RNA-seq
BioProject PRJNA174190
SRA SRP015331

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Supplementary file Size Download File type/resource
GSE40468_RAW.tar 8.0 Mb (http)(custom) TAR (of BED, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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