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Sample GSM534493 Query DataSets for GSM534493
Status Public on Sep 30, 2010
Title hASC_t4_PpargAb1
Sample type SRA
Source name hASC, ChIP
Organism Homo sapiens
Characteristics cell type: Adipose stromal cell (ASC) adipocyte
time (relative to induction): day 9
chip epitope: PPARG (H-100)
chip antibody: SCBT, Cat# SC-7196X, Lot# A0380
Treatment protocol N/A
Growth protocol hASCs were grown in MesenPRO RS medium (Invitrogen) plus 4ng/ml FGF-2 on plates coated with 10ug/cm2 collagen I (Invitrogen). Two days after confluence, the cells were placed in induction medium (DMEM/F12 supplemented with 10% FBS plus 1uM dexamethasone, 1.7uM insulin, 0.5mM IBMX, 5uM rosiglitazone, 40ng/ml BMP4, 17uM pantothenic acid, and 33uM biotin). 72h later, the medium was replaced with maintenance medium (DMEM/F12 with 10% FBS plus 1uM dexamethasone, 1.7uM insulin, 17uM pantothenic acid, and 33uM biotin) and media was replaced every two days thereafter.
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 PPARG
Data processing Alignments: Reads were aligned to the mouse reference genome (hg18) 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 19, 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 GPL9052
Series (2)
GSE20752 Comparative Epigenomic Analysis of Murine and Human Adipogenesis
GSE21366 Epigenomic profiling of hASC adipogenesis
SRA SRX019520
BioSample SAMN00011881

Supplementary file Size Download File type/resource
GSM534493_hASCt4.PpargAb1.aligned.txt.gz 173.3 Mb (ftp)(http) TXT
GSM534493_hASCt4.PpargAb1.density.wig.gz 22.7 Mb (ftp)(http) WIG
GSM534493_hASCt4.PpargAb1.intervals.txt.gz 555.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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