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Sample GSM1480372 Query DataSets for GSM1480372
Status Public on Feb 04, 2015
Title RNA Vehicle Rep3
Sample type SRA
 
Source name adipocyte_RNA Vehicle
Organism Homo sapiens
Characteristics cell type: SGBS adipocyte D10
treated with: vehicle for 90min
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 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).
Library preparation was performed using TruSeq2 RNA Sample Preparation protocol according to the manufacturers (Illumina) instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description processed data file: RNA_Exon_counts.txt
processed data file: RNA_Intron_counts.txt
Data processing alignment: RNA-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters.
quantification: Total RNA-seq coverage within exons and introns were quantified using the iRNA-seq pipeline (Madsen et al, Submitted), to asses mature and primary transcript levels, repectively
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
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense M
ZIP/Postal code 5230
Country Denmark
 
Platform ID GPL18460
Series (1)
GSE60462 iRNA-seq: Computational method for genome wide assessment of acute transcriptional regulation from total RNA-seq data
Relations
BioSample SAMN02996452
SRA SRX682089

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

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