|
| Status |
Public on Jun 12, 2013 |
| Title |
Colon |
| Sample type |
RNA |
| |
|
| Source name |
Normal colon
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Normal colon
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
|
| Label |
biotin
|
| Label protocol |
In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
|
| |
|
| Hybridization protocol |
10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
|
| Scan protocol |
Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
|
| Description |
Normal colon
|
| Data processing |
Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm with target intensity=100.
|
| |
|
| Submission date |
Jan 08, 2013 |
| Last update date |
Jun 12, 2013 |
| Contact name |
Atsushi Kaneda |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Tokyo
|
| Department |
RCAST
|
| Lab |
Genome Science Division
|
| Street address |
4-6-1 Komaba
|
| City |
Meguro-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
153-8904 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE43346 |
Gene repression with H3K27me3 modification in human small cell lung cancer |
| GSE99316 |
Gene repression and ChIP-seq in Human Small Cell Lung Cancer |
|
