NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM362969 Query DataSets for GSM362969
Status Public on Dec 01, 2010
Title Liver Non-Tumor Tissue LCS-102B
Sample type RNA
 
Source name LCS-102B
Organism Homo sapiens
Characteristics Tissue: Liver Non-Tumor Tissue
Disease state: Hepatocellular carcinoma (HCC)
Individual: 02-323B
Extracted molecule total RNA
Extraction protocol TRIzol Extraction Protocol
Other: Total RNA was isolated from microdissected fresh frozen tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Biotinylated cRNA Labeling for HT Arrays
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, For HT Array Plates Using the GeneChip® Array Station, P/N 702063 Rev. 2, Affymetrix).
 
Hybridization protocol Hybridization Protocol
Other: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Scan protocol Scanning Protocol for HT Arrays
Other: GeneChips were scanned using GeneChip® HT Array Plate Scanner by Affymetrix.
Description No additional information.
Data processing Data Processing Protocol
Calculation Method: 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 22, 2009
Last update date Dec 18, 2009
Contact name Xin Wei Wang
E-mail(s) xw3u@nih.gov
Phone 240-760-6858
Organization name National Cancer Institute
Department Laboratory of Human Carcinogenesis
Lab Liver Carcinogenesis Unit
Street address 37 Convent Drive
City Bethesda
State/province MD
ZIP/Postal code 20892-4255
Country USA
 
Platform ID GPL3921
Series (1)
GSE14520 Gene expression data of human hepatocellular carcinoma (HCC)

Data table header descriptions
ID_REF Affymetrix ID
VALUE log2 of RMA-calculated Signal intensity

Data table
ID_REF VALUE
1007_s_at 6.605
1053_at 3.849
117_at 4.348
121_at 6.265
1255_g_at 3.255
1294_at 6.197
1316_at 3.945
1320_at 3.745
1405_i_at 5.626
1431_at 12.160
1438_at 3.781
1487_at 6.441
1494_f_at 11.429
1598_g_at 7.629
160020_at 4.800
1729_at 5.641
1773_at 3.710
177_at 4.537
179_at 6.794
1861_at 3.769

Total number of rows: 22268

Table truncated, full table size 368 Kbytes.




Supplementary file Size Download File type/resource
GSM362969.CEL.gz 2.4 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap