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Sample GSM1709932 Query DataSets for GSM1709932
Status Public on Jun 17, 2015
Title RNA-seq DMSO TNF 1
Sample type SRA
 
Source name Adipocyte
Organism Homo sapiens
Characteristics cell type: SGBS adipocyte D10
Treatment protocol Mature SGBS adipocyte D10 were treated with 10ng/ml TNF or vehicle for 90/60 min before harvest of total RNA or chromatin for ChIP-seq respectively. p65 knockdown was achieved by transduction of SGBS adipocytes at day 6 of differentiation with shRNA-expressing lentivira. For JQ1 experiments, vehicle and TNF treated adipocytes were cotreated with 500nM JQ1 or DMSO for 90 min.
Growth protocol SGBS cells were grown to confluence in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham’s supplemented with 10% fetal bovine serum, 33 µM biotin, 17 µM pantothenate, 100 µg/ml streptomycin, 62.5 µg/ml penicillin, 1ng/µl fibroblast growth factors (FGF) 1, and 90 µg/µl heparin. At two days postconfluency, SGBS cells were stimulated to differentiate with serum-free growth medium supplemented with 10 nM insulin, 200 pM triiodothyronine, 1 µM cortisol, 2 µM BRL 49653, 0.115 mg/ml MIX, 0.25 mmol/L DEX, and 0.01 mg/ml human transferrin. After 3 days, the medium was replaced with the differentiation medium without FGF1 and heparin, and after 6 days Rosiglitazone/BRL49653, MIX, and DEX was removed from the medium.
Extracted molecule total RNA
Extraction protocol Following Isol extraction and column purification of total RNA, ribosomal RNAs were removed using the Ribo-Zero Human/Mouse/Rat kit (Epicentre).
Libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description RNA.JQ1.counts.txt (DT1)
Data processing RNA-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters.
Total RNA-seq coverage within exons were quantified using the iRNA-seq pipeline (Madsen et al, Nucl. Acids Res. 43 (6): e40). Log2 (Reads pr. kilobase pr. mio reads) are provided in RNA.JQ1.counts.txt
Genome_build: hg19
 
Submission date Jun 12, 2015
Last update date May 15, 2019
Contact name Susanne Mandrup
E-mail(s) s.mandrup@bmb.sdu.dk
Phone +45 6550 2340
Organization name University of Southern Denmark
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense M
ZIP/Postal code 5230
Country Denmark
 
Platform ID GPL18460
Series (1)
GSE64233 Acute TNF-induced repression of cell identity genes is mediated by NFkB-directed redistribution of cofactors from super-enhancers
Relations
BioSample SAMN03775341
SRA SRX1058798

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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