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Sample GSM340804 Query DataSets for GSM340804
Status Public on Dec 10, 2008
Title DH 11_RXR_Day4_3T3L1_ChIP-seq
Sample type SRA
Source name 3T3L1 cells
Organism Mus musculus
Characteristics DMI induced day4
Growth protocol 3T3-L1 fibroblasts were differentiated to adipocytes by standard DMI procedure (stimulation with 3-isobutyl-1-methylxanthine, dexamethasone, and insulin; Helledie et al., 2002, J. Biol. Chem. 277: 26821-26830).
Extracted molecule genomic DNA
Extraction protocol Chromatin was harvested at Day0, 1, 2, 3, 4 and 6 during adipocyte differentiation. Chromatin was fixed in 1% formaldehyde for 10 minutes, sonicated for 8x30sec at high power using a Bioruptor (Diagenode), immunoprecipitated PPARg (Sc-7196, Santa Cruz), RXR (Sc-774, Santa Cruz) and RNAPII ((AC-0555-100, Diagenode) antibodies, purified and sequenced using Illumina Genome Analyzer as recommended by the manufacturer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description Chromatin IP against RXR
Antibody RXR
Day of adipocyte differentiation
Data processing Reads (32 bp) were aligned to the Mouse (Mus muscules) reference genome. The July 2007 mouse (Mus musculus) genome data were obtained from the Build 37 assembly by NCBI and the Mouse Genome Sequencing Consortium. . RNAPII tracks for the different days were equalized for the total number of mapped tags by random removal of sequenced tags. The same was done for the transcription factor binding sites. For PPARg and RXR, enriched intervals were identified using Findpeaks. For RNAPII number of tags within ENSEMBLE genes (from +250 from TSS to end of gene) were counted and gene regulation was expressed as ratio of tags on a given day divided by tags in same gene region on day 0.
Submission date Nov 07, 2008
Last update date May 15, 2019
Contact name H.G. Stunnenberg
Phone +31-24-3610520
Organization name Radboud University
Department Department of Molecular Biology (274)
Street address Geert Grooteplein 28
City Nijmegen
ZIP/Postal code 6525 GA
Country USA
Platform ID GPL9185
Series (1)
GSE13511 Genome-wide profiling of PPARĪ³:RXR and RNA polymerase II
SRA SRX003139
BioSample SAMN02195672

Supplementary file Size Download File type/resource
GSM340804_RXR_Day4_FindPeaks.wig.gz 1.9 Mb (ftp)(http) WIG
GSM340804_RXR_day4_norm.wig.gz 7.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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