|
| Status |
Public on Feb 20, 2012 |
| Title |
control 293T splicing array 3 |
| Sample type |
RNA |
| |
|
| Source name |
human 293T cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: control siRNA
cell line: 293T
|
| Treatment protocol |
Cells were transfected at 40% confluency using 5μl/ml Lipofectamine-2000 (Invitrogen) and siRNAs at a final concentration of 100nM. For hnRNP A1, A2/B1, H1, M and U, equal mixtures of multiple siRNA sequences were used and for hnRNP F only one siRNA sequence was used. Media was changed 4-6 hrs after the initial transfection, and the transfection was repeated 48 hrs later. Cells intended for RNA analysis were suspended and lysed in TRIzol (Invitrogen) 72 hrs after the first transfection.
|
| Growth protocol |
Human 293T cells were obtained from ATCC and cultured in DMEM supplemented with 10% FBS at 37 ̊C and 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol (Invitrogen) extraction of RNA was performed according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
WT Terminal Labeling Kit, Affymetrix
|
| |
|
| Hybridization protocol |
Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.
|
| Scan protocol |
Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.
|
| Description |
polyA selected RNA
|
| Data processing |
Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
|
| |
|
| Submission date |
Jan 10, 2012 |
| Last update date |
Feb 20, 2012 |
| Contact name |
Gene Yeo |
| E-mail(s) |
geneyeo@ucsd.edu
|
| Organization name |
UCSD
|
| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL15106 |
| Series (2) |
| GSE34992 |
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays) |
| GSE34996 |
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins |
|
