|
| Status |
Public on Feb 28, 2012 |
| Title |
HNRPA2B1_KD_1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: siRNA transfection (set 1)
|
| Growth protocol |
MDA-MB-231 cells at 80% confluency were transfected with siRNA (Dharmacon) and control oligo (Invitrogen) using Lipofectamin 2000 reagent (Invitrogen) according to manufacturer’s recommendations. Experiments were performed in duplicates for each set.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Forty-eight hours post-transfection, total RNA was extracted using Norgen Biotek Total RNA Purification Kit.
|
| Label |
Cy3
|
| Label protocol |
200ng of total RNA were labeled using Low Input Quick Amp Labeling Kits per manufacturer's instructions
|
| |
|
| Channel 2 |
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: BLOCK-it control transfection
|
| Growth protocol |
MDA-MB-231 cells at 80% confluency were transfected with siRNA (Dharmacon) and control oligo (Invitrogen) using Lipofectamin 2000 reagent (Invitrogen) according to manufacturer’s recommendations. Experiments were performed in duplicates for each set.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Forty-eight hours post-transfection, total RNA was extracted using Norgen Biotek Total RNA Purification Kit.
|
| Label |
Cy5
|
| Label protocol |
200ng of total RNA were labeled using Low Input Quick Amp Labeling Kits per manufacturer's instructions
|
| |
|
| |
| Hybridization protocol |
Agilent Gene Expression Hybridization Kit was used to gybridize labeled samples.
|
| Scan protocol |
Scanned on an Agilent G2505B scanner.
Images were quantified using Agilent Feature Extraction Software (version 9).
|
| Description |
set 1 of 3.
|
| Data processing |
Agilent Feature Extraction Software (v 9) was used for background subtraction and LOWESS normalization. In house scripts were then used for downstream processing of the data. GSE35757_HNRNPA2B1_KD_processed.txt: Average LOWESS-normalized log10 ratio (siRNA/BLOCK-it control)
|
| |
|
| Submission date |
Feb 13, 2012 |
| Last update date |
Feb 28, 2012 |
| Contact name |
Hani Goodarzi |
| Organization name |
UCSF
|
| Department |
Biochemistry and Biophysics
|
| Street address |
600 16th St, GH S312D
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE35757 |
siRNA-mediated HNRPA2B1 knock-down in MDA-MB-231 cells |
| GSE35800 |
Systematic Discovery of Structural Elements Governing Mammalian mRNA Stability |
|
