|
| Status |
Public on Nov 01, 2016 |
| Title |
B2_Beer_029_GEJAC |
| Sample type |
RNA |
| |
|
| Source name |
gastroesophageal junction adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
patient disease state: esophageal adenocarcinoma
sample type: esophagectomy specimen
tissue: gastroesophageal junction adenocarcinoma
tumor stage: IV
age: 31 yr
gender: male
racial group: white American
|
| Treatment protocol |
Samples were immediately fresh-frozen in liquid nitrogen and stored at -80oC until use.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from primary tissues were isolated using Trizol reagent from Invitrogen and the RNeasy mini kit from QIAGEN following the manufacturers' instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (WT Expression Kit User Manual, 2010, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 20 hr at 48C on GeneChip Human Gene 2.1 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.
|
| Description |
Esophagectomy specimen with no preoperative chemoradiation therapy.
|
| Data processing |
Data was analyzed with R/Bioconductor software and normalized using RMA. The arrays were run in two batches, the first batch holding 8 NE, 5 NG, and 35 GEJAC, while the second batch consisted of 52 tEAC and an additional 35 GEJAC. We adjusted log2-transformed data for batch effects by adding constants (one per probe-set) to the values of each probe-set in the second batch to make the mean for the GEJAC's in batch 2 agree with the GEJAC mean in batch 1. When fitting a one-way analysis of variance (ANOVA) model with means for each of the four tissue types, we reduce the degrees of freedom in the mean-squared-error and F-tests by 1 to account for this batch adjustment. Analyses were restricted to the 26,613 coding and non-coding genes for which annotation details were available, including HUGO Gene Nomenclature Committee (HGNC) approved gene symbol and Entrez Gene ID.
|
| |
|
| Submission date |
Oct 30, 2015 |
| Last update date |
Nov 01, 2016 |
| Contact name |
Derek John Nancarrow |
| E-mail(s) |
dnancarr@med.umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Department of Surgery
|
| Lab |
Thoracic Surgery Cancer Biology Laboratory
|
| Street address |
1500 E. Medical Center Dr.
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL17692 |
| Series (1) |
| GSE74553 |
Genomic Similarity between Gastroesophageal Junction and Esophageal Barrett's Adenocarcinomas |
|
