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| Status |
Public on Sep 30, 2010 |
| Title |
3T3L1_t2_H3K4me2 |
| Sample type |
SRA |
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| Source name |
3T3-L1
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| Organism |
Mus musculus |
| Characteristics |
cell type: 3T3-L1 pre-adipocytes
time (relative to induction): day 0
chip epitope: H3K4me2
chip antibody: Abcam, Cat# ab7766, Lot# 56293
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| Treatment protocol |
N/A
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| 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.
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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 |
Chromatin IP against H3K4me2
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| 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.
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| Submission date |
Apr 21, 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 |
GPL9185 |
| Series (2) |
| GSE20752 |
Comparative Epigenomic Analysis of Murine and Human Adipogenesis |
| GSE21365 |
Epigenomic profiling of 3T3-L1 adipogenesis |
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| Relations |
| SRA |
SRX019371 |
| BioSample |
SAMN00011742 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM535749_3T3L1t2.H3K4me2.aligned.txt.gz |
107.5 Mb |
(ftp)(http) |
TXT |
| GSM535749_3T3L1t2.H3K4me2.density.wig.gz |
14.4 Mb |
(ftp)(http) |
WIG |
| GSM535749_3T3L1t2.H3K4me2.intervals.txt.gz |
826.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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