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Series GSE45888 Query DataSets for GSE45888
Status Public on Apr 24, 2014
Title Definition of the fibroblast SRF-mediated immediate-early transcriptional response
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary To control transcription, SRF recruits signal-regulated co-activators, the Ternary Complex Factors (TCFs) and the Myocardin-related Transcription Factors (MRTFs), which compete for a common site on its DNA-binding domain. The TCFs - SAP-1, Elk-1 and Net - are Ets proteins that link SRF activity to Ras-ERK signalling. In contrast, the two MRTFs, MRTF-A and MRTF-B, link SRF activity to Rho-actin signalling. In this novel signalling pathway, the actin-binding MRTF RPEL domain acts as a G-actin sensor, controlling MRTF nuclear accumulation in response to signal-induced depletion of the G-actin pool. Previous studies have suggested that the Ras-ERK signalling and Rho-actin pathways control specific subsets of SRF target genes. We used ChIP-seq and RNA-seq to analyse the immediate-early transcriptional response in NIH3T3 fibroblasts, using pathway-specific inhibitors to identify the contributions of Ras-ERK and Rho-actin signalling
Overall design Chromatin immunoprecipitation and sequencing (ChIP-seq) in NIH3T3 fibroblast after serum stimulation in presence or absence of LatrunculinB or U0126 drugs and using antibodies against SRF, MRTF-A, MRTF-B, SAP1, ELK1, NET, Pol II, PolII S5P, PolII S2P and total H3. Validation by ChIP-PCR. Strand specific total-RNA-seq following DSN normalisation and validation by qRT-PCR from NIH3T3 stimulated by serum or Cytochalasin D in presence or absence of LatrunculinB and/or U0126 drugs.
Contributor(s) Esnault C, Stewart A, East P, Horswell S, Matthews N, Gualdrini F, Treisman R
Citation(s) 24732378
Submission date Apr 09, 2013
Last update date May 15, 2019
Contact name Francesco Gualdrini
Organization name Francis Crick Institute
Lab Treisman
Street address 44 Lincoln's Inn Fields
City London
ZIP/Postal code WC2A 3LY
Country United Kingdom
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (69)
GSM1118301 SRF_03_replicate-1
GSM1118302 SRF_03_replicate-2
GSM1118303 SRF_15_replicate-1
SRA SRP020638
BioProject PRJNA196820

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE45888_RAW.tar 87.5 Gb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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