|
| Status |
Public on Dec 30, 2012 |
| Title |
U2OS_NS_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
U2OS cells treated with non-specific siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
protocol: control
gender: female
tissue: bone
cell line: U2OS cells (originated from 15 year old female)
disease state: osteosarcoma
|
| Treatment protocol |
RNAi was conducted by two separate transfections, at intervals of 48 h, with 40 nM non-specific or SRp20 siRNA in the presence of Lipofectamine 2000.
|
| Growth protocol |
Dulbecco’s modified Eagle medium (DMEM, Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS) (HyClone, Logan, UT), 2 mM L-glutamine, 100U/ml penicillin, and 100µg/ml streptomycin (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cell RNA was prepared from the cells using TRIzol (Invitrogen) following the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
the FL-Ovation cDNA Biotin Module v2 (NuGen, Inc., part # ‘s 4200-60)
|
| |
|
| Hybridization protocol |
Standard methods following recommendations of the manufacturer were used to hybridize the samples to the SpliceArrays. The arrays were washed and stained using the FS450-0001 Fluidics protocol.
|
| Scan protocol |
Affymetrix GeneChip® Scanner 3000 7G
|
| Description |
N/A
|
| Data processing |
The .CEL files were imported into Partek® Genomics Suite and the data was processed using the Robust Multichip Average (RMA) method which only utilizes the PM values to correct background. Quantile normalization was performed across all arrays, and then data was median polished for probeset summarization. ANOVA analysis was performed to identify probes that are differentially expressed between the sample groups specified. For ease of analysis and interpretation, the “evidenced” and “discovery” probes (for known or unknown splice events) were input separately for the analysis. A false discovery rate (FDR) was applied to the ANOVA p-values to select significant probes for comparison of the sample types.
The results files titled, SpliceArray Analysis Results_ALL (Evidenced or Discovery) Probesets.txt contain the ANOVA data for all probes on the array, as well as probeset-specific annotation information. These files are linked as supplementary files on the Series GSE22149 record.
|
| |
|
| Submission date |
Jun 04, 2010 |
| Last update date |
Dec 30, 2012 |
| Contact name |
Zhi-Ming Zheng |
| E-mail(s) |
[email protected]
|
| Phone |
3018467634
|
| Organization name |
National Cancer Institute
|
| Department |
HIV DRP Program
|
| Lab |
Tumor Virus RNA Biology Section
|
| Street address |
Bldg. 560, Rm. 11-86
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL7884 |
| Series (1) |
| GSE22149 |
SRp20 regulates Genome-wide Alternative RNA splicing events in U2OS cells |
|
