|
Status |
Public on Jan 01, 2016 |
Title |
RNA-seq at 24 h EtOH, replicate C |
Sample type |
SRA |
|
|
Source name |
monocytic cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: THP-1 treatment: Ethanol treatment time: 24 h
|
Treatment protocol |
cells were either treated with 100 nM of the natural VDR ligand 1,25-dihydroxyvitamin D3 (Sigma-Aldrich) or with the solvent Ethanol
|
Growth protocol |
THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.
|
Extracted molecule |
total RNA |
Extraction protocol |
total RNA was extracted from the cells Standard protocol as suggested by the manufacturer for RNA-seq libraries as utilized at the EMBL Gene Core in Heidelberg, Germany
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer II |
|
|
Data processing |
Alignment to hg19 using Bowtie v1.0 with the following parameters: -n 1 – k 1 -m 1 -l 32 -t -q –best Visualization as tdf in Integrative Genomics Viewer via conversion from sam to sorted bam (using samtools) and then to tdf (using igvtools) Differential gene expression using Cuffdiff with FDR < 0.05, and three replicates for each time
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|
|
Submission date |
May 27, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Carsten Carlberg |
E-mail(s) |
carsten.carlberg@uef.fi
|
Organization name |
University of Eastern Finland
|
Department |
Institute of Biomedicine
|
Street address |
Yliopistonranta 1D
|
City |
Kuopio |
ZIP/Postal code |
70211 |
Country |
Finland |
|
|
Platform ID |
GPL9115 |
Series (2) |
GSE69284 |
RNA-seq 1,25(OH)2D3 time course in THP-1 cells |
GSE69303 |
1,25(OH)2D3 time course in THP-1 cells |
|
Relations |
BioSample |
SAMN03737814 |
SRA |
SRX1040873 |