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Status |
Public on Jun 17, 2015 |
Title |
RNA-seq shp65 Vehicle 1 |
Sample type |
SRA |
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Source name |
Adipocyte
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Organism |
Homo sapiens |
Characteristics |
cell type: SGBS adipocyte D10
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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.
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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.
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
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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 introns were quantified using the iRNA-seq pipeline (Madsen et al, Nucl. Acids Res. 43 (6): e40), to asses primary transcript levels. Log2 (Reads pr. kilobase pr. mio reads) are provided in RNA.KD.counts.txt hg19
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Submission date |
Dec 16, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Susanne Mandrup |
E-mail(s) |
s.mandrup@bmb.sdu.dk
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Phone |
+45 6550 2340
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Organization name |
University of Southern Denmark
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Department |
Biochemistry and Molecular Biology
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Street address |
Campusvej 55
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City |
Odense M |
ZIP/Postal code |
5230 |
Country |
Denmark |
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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 |
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Relations |
BioSample |
SAMN03266608 |
SRA |
SRX813786 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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