|
| Status |
Public on Apr 09, 2010 |
| Title |
HEK293_5azaC-4days_rep2 [gene expression] |
| Sample type |
RNA |
| |
|
| Source name |
HEK293 cells treated with 5uM 5-azacytidine for 4 days, biological replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293 cells
agent: 5-azacytidine
dose: 5uM
time: 4 days
|
| Treatment protocol |
5-azacytidine was purchased from Sigma (cat # 2385) and dissolved in 50% acetic acid. HEK293 cells were treated with 5uM 5-azacytidine dissolved in medium for 4 days; medium was changed daily.
|
| Growth protocol |
The human HEK293 embryonal kidney cells were obtained from Dr David Segal's laboratory at the Genome and Biomedical Science Facility, UC Davis (ATCC cat# CRL-1573) and grown in DMEM, 10% FBS, 2mM L-glutamine and 1% penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from 5x10e6 cells using RNAeasy Kit (QIAGEN) following the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated RNA was prepared with the Illumina TotalPrep RNA Amplification kit (Ambion)
|
| |
|
| Hybridization protocol |
Array hybridization was performed by the Expression Analysis Core at UC Davis (http://genomecenter.ucdavis.edu/expression_analysis/) according to standard Illumina protocols
|
| Scan protocol |
Scanning was performed by the Expression Analysis Core at UC Davis (http://genomecenter.ucdavis.edu/expression_analysis/) according to standard Illumina protocols
|
| Description |
SAMPLE 6
|
| Data processing |
RNA hybridization signals were generated using BeadStudo Gene Expression Module v.3.2.3 (Illumina). To normalize gene expression data we used the R Project for Statistical Computing v.2.7.0 (http://www.r-project.org/) and Bioconductor package (http://www.bioconductor.org/) beadarray. Quantile method was used for normalization, data was log2 transformed (beadarray package).
|
| |
|
| Submission date |
Mar 23, 2010 |
| Last update date |
Apr 09, 2010 |
| Contact name |
Vitalina Komashko |
| E-mail(s) |
vitalina.komashko@sagebase.org
|
| Organization name |
Sage Bionetworks
|
| Street address |
1100 Fairview Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL6883 |
| Series (1) |
| GSE20598 |
5-azacytidine treatment reorganizes genomic histone modification patterns |
|
