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Sample GSM358108 Query DataSets for GSM358108
Status Public on Jan 08, 2009
Title HCC, biological rep 6
Sample type RNA
 
Source name liver tissue with HCC
Organism Homo sapiens
Characteristics Tissue: HCC
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 21, 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 GPL96
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 7.848547518
1053_at 5.22496538
117_at 5.934255564
121_at 9.12805444
1255_g_at 4.59495197
1294_at 7.619599271
1316_at 6.394186093
1320_at 5.068361032
1405_i_at 6.072648292
1431_at 10.87011986
1438_at 6.406758329
1487_at 7.298942839
1494_f_at 9.37390473
1598_g_at 9.189348337
160020_at 7.924110653
1729_at 7.481159016
1773_at 5.209996243
177_at 5.326600802
179_at 9.088326244
1861_at 5.20767256

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM358108.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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