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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 04, 2015 |
| Title |
RNA Vehicle Rep2 |
| Sample type |
SRA |
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| Source name |
adipocyte_RNA Vehicle
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| Organism |
Homo sapiens |
| Characteristics |
cell type: SGBS adipocyte D10
treated with: vehicle for 90min
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| Treatment protocol |
Mature SGBS adipocyte D10 were treated with 10ng/ml TNFα or vehicle for 90 min before harvest of total RNA or chromatin.
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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).
Library preparation was performed using TruSeq2 RNA Sample Preparation protocol according to the manufacturers (Illumina) instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
processed data file: RNA_Exon_counts.txt
processed data file: RNA_Intron_counts.txt
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| 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
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| Submission date |
Aug 17, 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) |
| GSE60462 |
iRNA-seq: Computational method for genome wide assessment of acute transcriptional regulation from total RNA-seq data |
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| Relations |
| BioSample |
SAMN02996451 |
| SRA |
SRX682088 |
| 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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