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Sample GSM358174 Query DataSets for GSM358174
Status Public on Jan 08, 2009
Title cirrhosisHCC, match HCC rep 40
Sample type RNA
 
Source name liver tissue with cirrhosisHCC
Organism Homo sapiens
Characteristics Tissue: cirrhosisHCC
Treatment protocol Five mm frozen section slides were made and stained with H&E for Pathologist evaluation to determine tumor content. After Pathologist evaluation, normal/necrotic tissue was macrodissected. Twenty 20 mm sections were performed in a 15 ml tube with 10 ml of Trizol.
Growth protocol Fresh tissue specimens were collected from the consented patients in the operating room and processed immediately after extraction to minimize RNA degradation. Liver tissue samples were collected in liquid nitrogen or RNA later solution (Ambion, Inc, Austin, TX), and stored at -80°C until use.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.The precipitated product was further purified using RNeasy Mini Kit (Qiagen, CA).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using GeneChip® Scanner 3000 by Affymetrix.
Description Gene expression using RMA method
Data processing The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.
 
Submission date Jan 07, 2009
Last update date Jan 07, 2009
Contact name Kellie J. Archer
E-mail(s) archer.43@osu.edu
Phone (614) 247-6167
Organization name Ohio State University
Department Division of Biostatistics
Street address 1841 Neil Ave
City Columbus
State/province OH
ZIP/Postal code 43210
Country USA
 
Platform ID GPL571
Series (1)
GSE14323 RMA expression data for liver samples from subjects with HCV, HCV-HCC, or normal liver

Data table header descriptions
ID_REF
VALUE Robust multiarray average (RMA)

Data table
ID_REF VALUE
1007_s_at 6.564762456
1053_at 6.156565188
117_at 5.72030275
121_at 7.378238338
1255_g_at 4.311734497
1294_at 7.222438346
1316_at 5.647821269
1320_at 5.146427742
1405_i_at 7.005149386
1431_at 12.7358795
1438_at 5.483086013
1487_at 7.252990562
1494_f_at 12.27879395
1598_g_at 8.025370742
160020_at 6.501361397
1729_at 6.497083686
1773_at 4.50367492
177_at 5.528948776
179_at 8.019484776
1861_at 5.822235937

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM358174.CEL.gz 3.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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