|
| Status |
Public on Sep 29, 2014 |
| Title |
EC_TNF_1 |
| Sample type |
RNA |
| |
|
| Source name |
HUVEC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary endothelium
|
| Treatment protocol |
Cells were stimulated with human TNFalpha (25 ng/mL, hr) in the presence or absence of JQ1 (500 nM, 2 hour pretreatment)
|
| Growth protocol |
M199 + 20% FBS + 0.1% heparin + 50 micrograms/mL endothelial cell growth factors (ECGF).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.
|
| Label |
biotin
|
| Label protocol |
Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.
|
| Description |
gene expression of 1 hour TNF alpha treated endothelium
|
| Data processing |
A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf. The data were analyzed with Bioconductor using the MAS5 nomalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.
|
| |
|
| Submission date |
Jan 10, 2014 |
| Last update date |
Sep 29, 2014 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL16043 |
| Series (2) |
| GSE53999 |
NF-kB coordinates rapid, BRD4-dependent remodeling of proinflammatory super-enhancers [Affymetrix] |
| GSE54000 |
NF-kB coordinates rapid, BRD4-dependent remodeling of proinflammatory super-enhancers |
|
