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| Status |
Public on Dec 10, 2014 |
| Title |
ASC_Day-2 |
| Sample type |
SRA |
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| Source name |
Pre-adipocytes from liposuction material, cultured, undifferentiated, proliferating, 2 days before adipogenic stimulation.
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Pre-adipocytes
passages: Cells in passage 5-7
treatment: control
time: 2 days before adipogenic stimulation (Day -2)
differentiation state: Proliferating, undifferentiated
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| Treatment protocol |
Cells were cultured as described under Growth protocol. 10e6 cells were cultured to the indicated stages for total RNA isolation.
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| Growth protocol |
Primary ASCs isolated from liposuction material were cultured in T175 flasks under proliferative conditions in high-glucose DMEM (4.5 g/l; Life Technologies-BRL) containing 20% FBS and 2 ng/ml basic fibroblast growth factor (Sigma-Aldrich). Cells at passage 5-7 were used for adipogenic induction. When cells reached confluency, adipogenic differentiation was induced by replacing growth medium with DMEM/F12 containing 10% FBS and by addition of 0.5 µM 1-methyl-3 isobutylxanthine (Dumex Alpharma), 1 µM dexamethasone (Dumex Alpharma), 10 µg/ml insulin (Novo Nordisk) and 100 µM (Dumex Alpharma) indomethacin for up to 9 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation.
RNAseq library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
reads aligned with tophat v2.0.8b with parameter –-b2-very-sensitive,
transcript abundance estimated with cufflinks v2.1.1 with parameter -–GTF-guide
reference gtf with cuffmerge v2.1.1 with parameters -g, -s
diffrential expression analysis with cuffdiff v2.1.1 with parameters -b, -s, -u
csv file created from columns 5,10,14,18,22 from cuffdiff output file genes.fpkm_tracking
Genome_build: hg19
Supplementary_files_format_and_content: csv with two columns; gene_short_name and fpkm value
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| Submission date |
Aug 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Philippe Collas |
| Organization name |
University of Oslo
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| Department |
Institute of Basic Medical Sciences
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| Street address |
PO Box 1112 Blindern
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| City |
Oslo |
| ZIP/Postal code |
0317 |
| Country |
Norway |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE60237 |
A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules |
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| Relations |
| BioSample |
SAMN02979007 |
| SRA |
SRX672348 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1468492_ASC_Day-2_fpkm.csv.gz |
160.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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