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| Status |
Public on Sep 30, 2010 |
| Title |
hASC_WCE |
| Sample type |
SRA |
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| Source name |
hASC, Whole Cell Extract (input control)
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Adipose stromal cell (ASC) pre-adipocytes and adipocytes
time (relative to induction): n/a
chip epitope: None
chip antibody: None
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| Treatment protocol |
N/A
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| 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.
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| 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)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Whole cell extract (input control)
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| 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.
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| Submission date |
Apr 19, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Tarjei S Mikkelsen |
| Organization name |
Broad Institute
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| Street address |
7 Cambridge Center
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (2) |
| GSE20752 |
Comparative Epigenomic Analysis of Murine and Human Adipogenesis |
| GSE21366 |
Epigenomic profiling of hASC adipogenesis |
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| Relations |
| SRA |
SRX019491 |
| BioSample |
SAMN00011852 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM534464_hASC.WCE.aligned.txt.gz |
572.7 Mb |
(ftp)(http) |
TXT |
| GSM534464_hASC.WCE.density.wig.gz |
53.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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