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Sample GSM1480367

Query DataSets for GSM1480367

Status

Public on Feb 04, 2015

Title

RNAPII ChIP-seq Vehicle Rep2

Sample type

SRA

Source name

adipocyte_RNAPII ChIP-seq Vehicle

Organism

Homo sapiens

Characteristics

cell type: SGBS adipocyte D10
treated with: vehicle for 90min
chip antibody: RNAPII
chip antibody vendor: Diagenode
chip antibody cat. #: C15200004

Treatment protocol

Mature SGBS adipocyte D10 were treated with 10ng/ml TNFα or vehicle for 90 min before harvest of total RNA or chromatin.

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

genomic DNA

Extraction protocol

ChIP experiments were performed according to standard protocol as described in (Siersbæk et al. 2012, MCB, 32: 3452-3463)
ChIP-seq 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

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 1500

Description

processed data file: RNAPII_Gene_counts.txt

Data processing

alignment: ChIP-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) specifying --alignIntronMax 1 to avoid potentially aligning across exon-exon junctions.
quantification: RNAPII ChIP-seq coverage within gene bodies were quantified using the iRNA-seq pipeline (Madsen et al, Submitted). The first 500 bp of the gene were omitted to avoid quantifying stalled RNAPII
Genome_build: hg19

Submission date

Aug 17, 2014

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