|
| Status |
Public on Feb 15, 2012 |
| Title |
Untreated cells rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
A549_untreated_unstimulated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: A549
sirna: No siRNA
stimulation: Unstimulated
|
| Treatment protocol |
For siRNA treatments, cells were transfected using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen) according to the manufacturer’s instructions. siRNA pools targeted to either human PAF1 (L-020349-01, Dharmacon), CHD1 (L-008529-00, Dharmacon) or a control non-targeting pool (D-001810-10-05, Dharmacon) were transfected at a final siRNA concentration of 50 nM. Transfected cells were stimulated with the appropriate stimuli 48 hours post transfection. Gene knockdown efficiency was determined by quantitative PCR and/or Western blotting. For stimulations, cells were infected with A/Puerto Rico/8/1934(ΔNS1) (PR8/∆NS1) at MOI 1 or stimulated with recombinant human IFN beta 1a (IFNβ1) (11415-1, PBL Interferon Source). Where cells were stimulated with IFNβ1, a concentration of 500 units/mL of cytokine was used. For Poly(I:C) stimulations, cells were transfected with Poly(I:C) at a final concentration of 2 µg/ml using the Lipofectamine2000 reagent (Invitrogen).
|
| Growth protocol |
Standard culture techniques
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN Rneasy mini kit
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled RNA was prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems)
|
| |
|
| Hybridization protocol |
Standard Illumina protocol
|
| Scan protocol |
Standard Illumina protocol
|
| Description |
untreated_unstimulated_rep_2
Replicate 2
|
| Data processing |
Data was analysed using Genespring GX11.0 . To analyze gene expression changes from hPAF1 siRNA treatment, raw data were subject to quantile normalization and baseline transformation was performed to the median of all unstimulated samples. non_normalized.txt = log2-transformed; normalized data matrix = After quantile normalization and baseline transformation performed in Genespring GX11.0
|
| |
|
| Submission date |
Jan 23, 2012 |
| Last update date |
May 17, 2012 |
| Contact name |
ivan marazzi |
| E-mail(s) |
imarazzi@rockefeller.edu
|
| Phone |
2123278265
|
| Fax |
2123278258
|
| Organization name |
rockefeller univeristy
|
| Lab |
epigenetic and immune signaling
|
| Street address |
1230 York Avenue
|
| City |
new york |
| State/province |
ny |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE35267 |
Analysis of global gene expression profiles of hPAF1 deficient A549 cells during stimulation with PR8/∆NS1 influenza virus, IFNβ1 or Poly(I:C) |
| GSE35268 |
Analysis of global gene expression profiles of hPAF1 deficient A549 cells |
|
| Relations |
| Reanalysis of |
GSM864718 |
