|
| Status |
Public on Mar 30, 2012 |
| Title |
BE-rep2 |
| Sample type |
RNA |
| |
|
| Source name |
BE
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Barrett's
|
| Treatment protocol |
Samples were snap frozen in liquid nitrogen at the time of collection
|
| Growth protocol |
N/A - samples were biopsies collected at the time of endoscopy from the normal oesophagus, Barrett's oesophagus and gastric cardia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biopsies were homogenised in Trizol using the Precellys. A standard Trizol extraction method was used.
|
| Label |
biotin
|
| Label protocol |
WT Expression Kit (Ambion) was used to obtain ss cDNA which was then labelled and fragmented using Affymetrix WT Terminal Labelling Kit according to manufacturing instructions
|
| |
|
| Hybridization protocol |
Samples were hybridized to Affymetrix Human GeneChip 1.0ST arrays using Affymetrix Hybridization Kit following manufacturer's instructions for the 49/64 format array. Wash and stain of arrays was carried out on geneChip Fluidics 450 Workstation using protocol FS450_0007
|
| Scan protocol |
Arrays were scanned on Affymetrix GeneChip GCS3000
|
| Data processing |
Softwares/Tools used for the data processing were Affymetrix GeneChip Command Console Software (AGCC), and Partek Genomic Suite 6.5. For the creation of the summarized log-signal, the Robust Multichip Average (RMA) with Quantile normalisation and Median Polish for Probe set summarisation were used
|
| |
|
| Submission date |
Dec 21, 2011 |
| Last update date |
Mar 30, 2012 |
| Contact name |
Massimiliano di Pietro |
| E-mail(s) |
[email protected]
|
| Organization name |
MRC Cancer Cell Unit
|
| Street address |
Hills Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0XZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE34619 |
Gene expression profile in Barrett's esopahgus |
|
