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Sample GSM535760 Query DataSets for GSM535760
Status Public on Sep 30, 2010
Title 3T3L1_t3_H3K36me3
Sample type SRA
Source name 3T3-L1
Organism Mus musculus
Characteristics cell type: 3T3-L1 adipocytes
time (relative to induction): day 2
chip epitope: H3K36me3
chip antibody: Abcam, Cat# ab9050, Lot# 136353
Treatment protocol N/A
Growth protocol 3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days after confluence, the cells were induced with DMEM supplemented with 10% FBS, 1uM dexamethasone, 1.7uM insulin, and 0.5mM 3-isobutyl-1-methylxanthine (IBMX). 48h later, the medium was replaced with DMEM supplemented with 10% FBS and the cells were fed every two days.
Extracted molecule genomic DNA
Extraction protocol ChIP-Seq libraries were prepared as described by Mikkelsen et al. (Nature 2007; 448(7153):553-60; PMID: 17603471)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description Chromatin IP against H3K36me3
Data processing Alignments: Reads were aligned to the mouse reference genome (mm9) using MAQ v0.6.8 with default parameters, except '-C 10' (discard reads that match to more than 10 locations). Redundant reads (alinign to the same starting position and orientation) were discarded.
Densities: Aligned reads were extended to an assumed fragment length of 200 bp. The number of fragments overlapping nucleotide x in the reference sequnece were counted at 25bp resolution. The counts were then normalized to 'fragments per 10 million aligned reads'.
Peak calling (histones): The numbers of aligned ChIP and input reads were counted in sliding windows of 500 bp for H3K4me3/me2/me1/K27ac and 5000bp H3K27me3/K36me3 and a step size of 25bp. The likelihood of the null hypothesis (no ChIP enrichment) was calculated as the probability of observing at least the number of ChIP reads, given a Poisson distribution with a mean equal to the expected number of ChIP reads (given the window size, the genome size and the total number of aligned reads) multiplied by the ratio of observed over expected input reads in the same window. Windows with p < 0.0001 after Benjamini correction for multiple-hypothesis testing were kept and merged into non-overlapping intervals of arbitrary size.
Peak calling (CTCF and PPARG): Binding sites and ChIP enrichment intervals were inferred using QuEST v2.3 (Valouev et al. Nat Methods 2008; 5(9):829-834; PMID: 19160518) in the 'transcription factor' mode.
Submission date Apr 21, 2010
Last update date May 15, 2019
Contact name Tarjei S Mikkelsen
Organization name Broad Institute
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platform ID GPL9185
Series (2)
GSE20752 Comparative Epigenomic Analysis of Murine and Human Adipogenesis
GSE21365 Epigenomic profiling of 3T3-L1 adipogenesis
SRA SRX019382
BioSample SAMN00011753

Supplementary file Size Download File type/resource
GSM535760_3T3L1t3.H3K36me3.aligned.txt.gz 87.6 Mb (ftp)(http) TXT
GSM535760_3T3L1t3.H3K36me3.density.wig.txt.gz 11.4 Mb (ftp)(http) TXT
GSM535760_3T3L1t3.H3K36me3.intervals.txt.gz 209.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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