|
| Status |
Public on May 01, 2012 |
| Title |
control knockdown, biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
HEK293 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: control
length of knockdown: 72 hours
|
| Treatment protocol |
shRNA constructs were transiently transfected using Lipofectamine 2000 (Invitrogen), incubated for 4 hours and removed. Cells grew for 72 hours under knockdown conditions.
|
| Growth protocol |
HEK293 cells grown in DMEM + 10%FBS + L-glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All samples were separated for RNA and protein level analysis. Total RNA was isolated using Trizol reagent (Invitrogen). RNA samples were treated with Dnase and subsequently phenol-chloroform extracted prior to labeling.
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
n/a
|
| Data processing |
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HJAY_r2.pgf
meta-probeset file: HJAY_r2.full.mps
|
| |
|
| Submission date |
Feb 24, 2012 |
| Last update date |
May 01, 2012 |
| Contact name |
Erik S Anderson |
| E-mail(s) |
esa2@ucla.edu
|
| Organization name |
UCLA
|
| Department |
MBIDP
|
| Lab |
Douglas Black
|
| Street address |
6-567 MRL, 675 Charles E. Young Drive South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL15106 |
| Series (1) |
| GSE36069 |
shRNA mediated knockdown of TRA2B and SRSF3 in HEK293 cell line |
|
