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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 23, 2014 |
| Title |
TNF24H_WCE |
| Sample type |
SRA |
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| Source name |
3T3L1
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| Organism |
Mus musculus |
| Characteristics |
cell line: 3T3L1
chip antiboy: WCE
treatment: TNF
time: 24H
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| Treatment protocol |
Murine 3T3-L1 adipocytes were treated separately with dexamethasone (Dex; 20nM) or tumor necrosis factor-alpha. To comprehensively assess epigenomic changes caused by Dex and TNF in a time-dependent manner, we profiled cells at early (2 hours), intermediate (24 hours), and late (6 days) points in the development of insulin resistance.
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| Growth protocol |
Cells from the stromal-vascular fraction (SVF) were plated in culture and differentiated as described .
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The chromatin was then fragmented to a size range of ~200 to 600 bp using a Branson 250 digital sonifier (sonication conditions were separately optimized for each sample). Solubilized chromatin was then diluted and incubated with 1-2 ug antibody overnight at 4°C. Immune complexes were captured with ~ 0.02 ml protein A-sepharose, washed and eluted. Enriched chromatin was then subjected to crosslink reversal and proteinase K digestion at 65°C, phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. Isolated ChIP DNA was resuspended in RNAase treated water and quantified using the Qubit assay (Invitrogen).
ChIP assays were performed using the following antibodies: H3K4me1 (Abcam ab8895, lot 38311/659352, H3K4me3 (Milipore 07-473, lot DAM1623866), H3K27ac (Active Motif 39133, lot 31610003), H3K36me3 (Abcam ab9050, lot 499302, H3K27me3 (Millipore 07-449, lot DAM1514011), H3K79me2 (Cell Signaling 9757, lot 1).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
ChIP-seq reads were aligned to mouse genome (mm9) using MAQ
Duplicated reads were removed using Samtools.
Reads were sorted by Samtools
peaks were called using in-home made algorihtm..
peaks of same epitopes from different treatments were merged.
Genome_build: mm9
Supplementary_files_format_and_content: text file containing information of peaks called.
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| Submission date |
Jun 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Evan Rosen |
| E-mail(s) |
erosen@bidmc.harvard.edu
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| Organization name |
Beth Israel Deconess Medical Center
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| Department |
Endocrinology
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| Lab |
Rosen Lab
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| Street address |
3 Blackfan Cir
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE58491 |
Characterizing the profiles of histone markers in mouse adipocytes during insulin resistance |
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| Relations |
| BioSample |
SAMN02854597 |
| SRA |
SRX597209 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not applicable for this record |
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