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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 10, 2008 |
| Title |
DH 1_PPARg_Day0_3T3L1_ChIP-seq |
| Sample type |
SRA |
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| Source name |
3T3L1 cells
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| Organism |
Mus musculus |
| Characteristics |
DMI induced day0
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| 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).
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| 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.
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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 PPARg
Antibody PPARg
Day of adipocyte differentiation
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| 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.
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| Submission date |
Nov 07, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
H.G. Stunnenberg |
| E-mail(s) |
h.stunnenberg@ncmls.ru.nl
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| Phone |
+31-24-3610520
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| Organization name |
Radboud University
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| Department |
Department of Molecular Biology (274)
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| Street address |
Geert Grooteplein 28
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| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
USA |
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| Platform ID |
GPL9185 |
| Series (1) |
| GSE13511 |
Genome-wide profiling of PPARĪ³:RXR and RNA polymerase II |
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| Relations |
| SRA |
SRX003137 |
| BioSample |
SAMN02195664 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM340794_PPAR_Day0_FindPeaks.wig.gz |
199.7 Kb |
(ftp)(http) |
WIG |
| GSM340794_PPAR_day0_norm.wig.gz |
7.8 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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