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Sample GSM913533 Query DataSets for GSM913533
Status Public on Apr 11, 2012
Title BE_07B
Sample type RNA
 
Source name Esophagectomy specimen with no preoperative chemoradiation therapy.
Organism Homo sapiens
Characteristics disease state: Barrett’s esophageal tissues
age: 52
gender: M
ethnicity: Caucasian
Stage: NA
tissue: esophagectomy specimen
Treatment protocol N/A
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. Total RNA was isolated using the RNeasy mini kit from Qiagen, following the manufacturer’s instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Affymetrix 3000 GeneChip Scanner.
Description Gene expression data from Barrett’s esophageal tissues.
Data processing Data was analyzed using the affy Bioconductor package implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.
 
Submission date Apr 11, 2012
Last update date Apr 11, 2012
Contact name David G Beer
E-mail(s) dgbeer@umich.edu
Phone 734-763-0325
Fax 734-615-6033
Organization name University of Michigan Medical School
Department Surgery
Lab Thoracic Surgery Cancer Biology Lab
Street address 1500 E Medical Center Dr. CCGC 6431
City Ann Arbor
State/province Michigan
ZIP/Postal code 48109
Country USA
 
Platform ID GPL96
Series (2)
GSE37200 Gene expression profiling of Barrett’s esophageal tissues and esophageal adenocarcinoma specimens
GSE37203 Barrett's esophageal tissues and esophageal adenocarcinoma specimens

Data table header descriptions
ID_REF
VALUE Log2 Transformed RMA signal

Data table
ID_REF VALUE
1007_s_at 10.82280628
1053_at 6.6525377
117_at 6.851268686
121_at 9.583135289
1255_g_at 4.992243563
1294_at 8.450552307
1316_at 6.402039381
1320_at 5.547122256
1405_i_at 7.071639705
1431_at 4.729128916
1438_at 8.399899999
1487_at 8.831550478
1494_f_at 7.260007805
1598_g_at 10.09660951
160020_at 8.940795068
1729_at 8.569055155
177_at 6.431182913
1773_at 6.749833445
179_at 9.436054868
1861_at 6.461916323

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM913533_Beer_07B.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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