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Sample GSM358107 Query DataSets for GSM358107
Status Public on Jan 08, 2009
Title HCC, biological rep 5
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 7.825697319
1053_at 6.171295142
117_at 5.840291041
121_at 8.892765157
1255_g_at 4.227410745
1294_at 7.572871101
1316_at 5.92739958
1320_at 5.141508773
1405_i_at 7.144722891
1431_at 13.03271582
1438_at 6.146492151
1487_at 7.486800437
1494_f_at 12.07103388
1598_g_at 8.795687711
160020_at 7.809222928
1729_at 7.180278019
1773_at 5.686281995
177_at 5.59901876
179_at 9.552631011
1861_at 5.944023863

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM358107.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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