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Sample GSM449772 Query DataSets for GSM449772
Status Public on Sep 11, 2009
Title HCV+cirrhosis with HCC 12
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 6.746198267
1053_at 5.433747834
117_at 5.37740281
121_at 7.409167581
1255_g_at 4.080744902
1294_at 6.544724709
1316_at 5.422823189
1320_at 4.870485374
1405_i_at 6.7425049
1431_at 12.76024116
1438_at 5.256889541
1487_at 6.898890503
1494_f_at 10.98580501
1598_g_at 7.493428072
160020_at 6.398082467
1729_at 6.598233842
177_at 4.935931107
1773_at 4.680018331
179_at 8.309341653
1861_at 5.417886328

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM449772_DC-388.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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