|
| Status |
Public on Mar 31, 2011 |
| Title |
cDNA from HBEC after transcfection with noncoding siRNA |
| Sample type |
RNA |
| |
|
| Source name |
RNA from human bronchial epithelia cells immortalized with hTERT and CDK4
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human bronchial epithelia cells
cell line: HBEC
transcfection: non coding siRNA
|
| Treatment protocol |
cells were transfected with siRNA using Lipofectamine 2000 for 96 hours
|
| Growth protocol |
cells were cultured in K-SFM media (Invitrogen, Carlsbad, CA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNAeasy purification kit
|
| Label |
Biotin
|
| Label protocol |
Standard Affymetrix Protocol, as described in GeneChip Whole Transcript Sense Target Labeling Assay Manual, Version 4 (available at http://www.affymetrix.com/support/technical/product_updates/wt_1_1_assay.affx)
|
| |
|
| Hybridization protocol |
The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Mouse Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.
|
| Scan protocol |
Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.
|
| Description |
Expressional changes associated with noncoding siRNA transfection in HBEC
|
| Data processing |
Transcript level expression was summarized by RMA method implemented in Partek Genomic Suite
|
| |
|
| Submission date |
Dec 14, 2010 |
| Last update date |
Mar 31, 2011 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE26020 |
Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription |
| GSE26038 |
Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuEx-1_0-st, transcript] |
|
