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Sample GSM358116 Query DataSets for GSM358116
Status Public on Jan 08, 2009
Title cirrhosisHCC, match HCC rep 12
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 7.15844017
1053_at 6.394077261
117_at 5.276531395
121_at 7.575210289
1255_g_at 4.142775046
1294_at 7.202931361
1316_at 5.537078845
1320_at 4.975288398
1405_i_at 7.632876757
1431_at 12.99399552
1438_at 5.571293149
1487_at 7.241738971
1494_f_at 11.66848591
1598_g_at 7.734395435
160020_at 6.614688139
1729_at 6.804779193
1773_at 5.043898166
177_at 5.389422564
179_at 8.356651124
1861_at 6.178377752

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM358116.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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