|
| Status |
Public on Aug 02, 2007 |
| Title |
TAp63 alpha 24h induction s3 |
| Sample type |
RNA |
| |
|
| Source name |
TET-on Human lung carcinoma H1299
|
| Organism |
Homo sapiens |
| Characteristics |
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
| Treatment protocol |
1 μg/ml doxycycline for 24 hours
|
| Extracted molecule |
cytoplasmic RNA |
| Extraction protocol |
Total RNA (ttlRNA) was extracted and
purified from stably transfected H1299 cell lines with the Concert
Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
with a Bioanalyzer (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
|
| |
|
| Hybridization protocol |
Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
(20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
by the manufacturer (Affymetrix Inc.).
|
| Scan protocol |
GeneChip Fluidics station 400
(Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
|
| Description |
None
|
| Data processing |
DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
Probe set intensities were obtained by means of GCRMA, a robust
multiarray analysis method.
The full data set was normalized according to the
quantiles method.
|
| |
|
| Submission date |
Aug 01, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Raffaele A Calogero |
| E-mail(s) |
[email protected]
|
| Phone |
++39 0116706454
|
| Organization name |
University of Torino
|
| Department |
Molecular Biotechnology Center
|
| Lab |
Bioinformatics and Genomics Unit
|
| Street address |
Via Nizza 52
|
| City |
Torino |
| State/province |
To |
| ZIP/Postal code |
10126 |
| Country |
Italy |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE8646 |
The Hay Wells Syndrome-Derived TAp63alphaQ540L Mutant Has Impaired Transcriptional and Cell Growth Regulatory Activity |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
