NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM452643 Query DataSets for GSM452643
Status Public on Feb 04, 2010
Title patient 044, normal, homogenized
Sample type RNA
 
Source name surgically resected material
Organism Homo sapiens
Characteristics metastasis: none
tissue: normal, homogenized
Treatment protocol Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
Label biotin
Label protocol cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
Description Gene expression profile of surgically resected material
Data processing The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
 
Submission date Sep 14, 2009
Last update date Aug 28, 2018
Contact name Kaoru Mogushi
E-mail(s) [email protected]
Phone +81-3-5802-1797
Organization name Juntendo University
Department Intractable Disease Research Center
Street address 2-1-1 Hongo
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-8421
Country Japan
 
Platform ID GPL570
Series (2)
GSE18105 Stage II and stage III colorectal cancer
GSE22598 Clinical significance of UNC5B Expression in Colorectal Cancer
Relations
Reanalyzed by GSM800756
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
1007_s_at 10.71017055
1053_at 6.286325039
117_at 5.567601372
121_at 8.281772809
1255_g_at 3.674720969
1294_at 8.257710482
1316_at 6.423776432
1320_at 4.934232886
1405_i_at 7.79166943
1431_at 3.652104106
1438_at 6.945410356
1487_at 9.704971529
1494_f_at 6.329109442
1552256_a_at 8.976914357
1552257_a_at 9.821909665
1552258_at 4.479556965
1552261_at 4.897130652
1552263_at 6.694059897
1552264_a_at 6.121773551
1552266_at 4.273701445

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM452643.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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