|
| Status |
Public on Jun 01, 2010 |
| Title |
Esophageal Adenocarcinoma MRC/OEA0635CJ4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Stratagene Universal Human Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Reference RNA Pool
|
| Treatment protocol |
Human tissue specimens were surgically excised and snap frozen in liquid nitrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 10x 15 μm sections using Trizol™ according to Invitrogen's instructions
|
| Label |
Cy3
|
| Label protocol |
Custom automated version of the aminoallyl MessageAmp II kit from Ambion. Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.
|
| |
|
| Channel 2 |
| Source name |
HumanEsophagealAdenocarcinoma_MRC/OEA0635CJ4
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human esophageal adenocarcinoma
patient id: MRC/OEA0635CJ4
gender: Female
survival days: 578
positive nodes: 6
tumor histology: Gastric adenocarcinoma
tumor differentiation: Poor
tumour length cm: 4
tumour width cm: 4
tumor volume mm3: 32000
|
| Treatment protocol |
Human tissue specimens were surgically excised and snap frozen in liquid nitrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 10x 15 μm sections using Trizol™ according to Invitrogen's instructions
|
| Label |
Cy5
|
| Label protocol |
Custom automated version of the aminoallyl MessageAmp II kit from Ambion. Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.
|
| |
|
| |
| Hybridization protocol |
Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber
|
| Scan protocol |
Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.
|
| Description |
Individual esophageal adenocarcinoma tissue specimen
|
| Data processing |
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
|
| |
|
| Submission date |
Dec 10, 2009 |
| Last update date |
Dec 11, 2009 |
| Contact name |
Paul Grosu |
| Organization name |
Microsoft/Merck
|
| Street address |
33 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL4372 |
| Series (1) |
| GSE19417 |
Human esophageal adenocarcinomas |
|
