|
| Status |
Public on Feb 28, 2012 |
| Title |
HNRPA2B1_KD_2hr_1_1 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: siRNA-mediated HNRPA2B1 knock-down
protocol: growth in the presence of alpha-amanitine
time point: 2 hr
|
| Treatment protocol |
Forty-eight hours post-transfection, cells were exposed to 5ug/mL alpha-amanitine (Sigma) and total RNA was extracted using Norgen Biotek Total RNA Purification Kit at 0, 1, 2 and 4hr timepoints.
|
| 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 |
200ng of total RNA were labeled using Low Input Quick Amp Labeling Kits per manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Agilent Gene Expression Hybridization Kit was used to gybridize labeled samples.
|
| |
|
| Hybridization protocol |
Scanned on an Agilent G2505B scanner.
|
| Scan protocol |
Images were quantified using Agilent Feature Extraction Software (version 9).
|
| Description |
siRNA set
|
| 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. Upon fitting exponentia decay rates to each time-point series, a t-test based score was calculated for each transcript. This score ranging from -1 (significant reduction in decay rate in HNRPA2B1 knock-down samples) to 1 (significant increase), is calculated based on equation s*(1-p) where p is the t-test p-value between decay rates in the HNRPA2B1-KD samples and control samples and s is the sign of the difference between the average values (+1 if HNRPA2B1-KD values are greater than controls and -1 otherwise). Data provided in GSE35756_HNRNPA2B1_differential_decay_rate_processed.txt.
|
| |
|
| 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) |
| GSE35756 |
Whole-genome decay rate measurements in MDA-MB-231 cells transfected with HNRPA2B1 siRNAs versus controls |
| GSE35800 |
Systematic Discovery of Structural Elements Governing Mammalian mRNA Stability |
|
