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Sample GSM1537678 Query DataSets for GSM1537678
Status Public on Dec 12, 2014
Title MED1 hMADS brite rep1, day 19
Sample type SRA
 
Source name human adipose-derived stem cells
Organism Homo sapiens
Characteristics cell line: hMADS-3
cell type: human adipose-derived stem cells
chip antibody: MED1 (M-255; sc-8998; Santa Cruz)
Treatment protocol Two days post confluence (day 0) hMADS cells were induced to differentiate in DMEM/Ham`s F12 (Lonza) supplemented with 10 μg/ml transferrin, 1 μM dexamethasone, 500 μM 3-isobutyl-1-methylxanthine (MIX), 0.85 μM insulin, and 0.2 nM T3. At day 3 of differentiation, MIX and dexamethasone were omitted from the media and 0.5 μM rosiglitazone was added until day 9 of differentiation and again from day 13-16 for induction of brite adipocytes. Control white adipocytes were treated with DMSO from day 13-16. From day 16 and forth the differentiation medium of both white and brite adipocytes was depleted of rosiglitazone. White and brite hMADS adipocytes were harvested on day 19, unless stated otherwise.
Growth protocol Human multipotent adipose-derived stem (hMADS-3) cells were cultured in DMEM (Lonza, low glucose) supplemented with 10% fetal bovine serum (Lonza), 10 mM Hepes, 2 mM L-glutamine (Lonza), penicillin (62.5 μg/ml), streptomycin (100 μg/ml), and 2.5 ng/ml hFGF2 (Peprotech).
Extracted molecule genomic DNA
Extraction protocol ChIP experiments were performed in mature hMADS adipocytes essentially as previously described (Siersbæk et al. 2012, MCB, 32: 3452-3463). For cross-linking of chromatin, 0.2 mM disuccinimidyl glutarate (DSG) was applied (Proteochem, Denver, CO) for 45 min followed by cross-linking using 1% formaldehyde for 10 min.
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing Alignment:
Sequence reads were trimmed and collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589) for visualization of binding profiles.
Genome_build: hg19
 
Submission date Nov 05, 2014
Last update date Feb 21, 2024
Contact name Anne Loft
E-mail(s) anlo@bmb.sdu.dk
Organization name University of Southern Denmark
Department Biochemistry & Molecular Biology
Street address Campusvej 55
City Odense M
ZIP/Postal code 5230
Country Denmark
 
Platform ID GPL18460
Series (1)
GSE59703 Browning of human adipocytes requires KLF11 and reprogramming of PPARγ super-enhancers
Relations
BioSample SAMN03164103
SRA SRX751298

Supplementary file Size Download File type/resource
GSM1537678_SM932_MED1_Brite_rep1.bedGraph.gz 30.3 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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