|
| Status |
Public on Jan 24, 2013 |
| Title |
Parental HCET control, biological rep2 [gene-level] |
| Sample type |
RNA |
| |
|
| Source name |
Parental HCET cell
|
| Organism |
Homo sapiens |
| Characteristics |
shRNA: parental
|
| Treatment protocol |
Parental HCET (control), shRNA-PNN HCET knock down, shRNA-ESRP1 HCET knock down cells with/without doxycycline treatment
|
| Growth protocol |
HCET cells were cultured in DMEM/F12 medium containing 5% FBS , 5 μg/mL insulin, 0.1 μg/mL cholera toxin, 10 ng/mL human epidermal growth factor (hEGF) and 0.5% dimethyl sulfoxide (DMSO). The stable cells were selected and maintained with 2 ug/ml of puromycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the RNeasy Plus Mini Kit and treated with RNase-free DNase I (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the Affymetrix GeneChip WT Terminal Labeling Kit protocol from 100 ng total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix hGlue3_0 transcriptome array. GeneChips were washed and stained in the Affymetrix Fluidics Station.
|
| Scan protocol |
The arrays were scanned using Affymetrix Fluidics Station FS450 and GeneChip Scanner 30007G.
|
| Description |
Gene expression data from parental HCET cell
|
| Data processing |
Affymetrix Power Tools (APT) was applied for data processing. Arrays were RMA-background-corrected, quantile-normalized and summarized into exon/gene expression using median-polish approaches. The probe group file is hGlue3_0.r1.pgf, and the meta-probeset file is hGlue3_0.r1.TC.mps
|
| |
|
| Submission date |
Nov 02, 2012 |
| Last update date |
Jan 24, 2013 |
| Contact name |
Jian-Liang Li |
| Organization name |
NIEHS
|
| Street address |
111 TW Alexander Dr
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL16238 |
| Series (1) |
| GSE41996 |
Transcriptomic Analysis of PNN- and ESRP1-regulation in Human Corneal Epithelial Cells |
|
| Relations |
| Alternative to |
GSM1032658 (exon-level analysis) |
