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Sample GSM449752 Query DataSets for GSM449752
Status Public on Sep 11, 2009
Title HCV+cirrhosis with HCC 7
Sample type RNA
 
Source name liver tissue
Organism Homo sapiens
Characteristics disease state: HCV + cirrhosis with HCC
tissue: liver
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 RMA method in the R affy package was used to obtain probe set expression summaries.
 
Submission date Sep 04, 2009
Last update date Sep 10, 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)
GSE17967 RMA expression data for liver samples from subjects with HCV cirrhosis with and without concomitant HCC

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

Data table
ID_REF VALUE
1007_s_at 7.054745941
1053_at 5.705360666
117_at 5.202754299
121_at 7.515429906
1255_g_at 4.066277899
1294_at 7.467927616
1316_at 5.439106257
1320_at 4.752325856
1405_i_at 6.906166119
1431_at 12.44382586
1438_at 5.240445916
1487_at 7.097535315
1494_f_at 9.880585934
1598_g_at 7.963872169
160020_at 7.067553289
1729_at 6.470377568
177_at 5.478709058
1773_at 4.776149479
179_at 8.22291614
1861_at 5.104655815

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM449752_D-332.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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