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Sample GSM234917 Query DataSets for GSM234917
Status Public on Dec 01, 2007
Title Normal_colon_22_13April05
Sample type RNA
 
Source name colorectum, cecum
Organism Homo sapiens
Characteristics Tissue: Colorectal mucosa
Location: (as per 'SOURCE')
Biomaterial provider Flinders Medical Centre in collaboration with CSIRO P-Health Flagship
Treatment protocol The colorectal specimens in this set were collected from a tertiary referral
hospital tissue bank in metropolitan Adelaide, Australia (Repatriation General Hospital and Flinders Medical Centre). The tissue bank and this project were approved by the Research and Ethics Committee of the Repatriation General Hospital and patient consent was received for each tissue studied. Following surgical resection, specimens were placed in a sterile receptacle and collected from theatre. The time from operative resection to collection from theatre was variable but not more than 30 minutes. Samples, approximately 125mm3 (5x5x5mm) in size, were taken from the macroscopically normal tissue as far from pathology as possible, defined both by colonic region as well as by distance either proximal or distal to the pathology. Tissues were placed in cryovials, then immediately immersed in liquid nitrogen and stored at -150degC until processing.

Extracted molecule total RNA
Extraction protocol Frozen samples were processed by the authors using standard protocols and commercially available kits. Briefly, frozen tissues were homogenized using a carbide bead mill (Mixer Mill MM 300, Qiagen, Melbourne, Australia) in the presence of chilled Promega SV RNA Lysis Buffer (Promega, Sydney, Australia) to neutralize RNase activity. Homogenized tissue lysates for each tissue were aliquoted to convenient volumes and stored -80degC. Total RNA was extracted from tissue lysates using the Promega SV Total RNA system according to manufacturers instructions and integrity
was assessed visually by gel electrophoresis.
Label biotin
Label protocol To measure relative expression of mRNA transcripts, tissue RNA samples were analyzed using Affymetrix HG U133 Plus 2.0 GeneChips (Affymetrix, Santa Clara, CA USA) according to the manufacturers protocols. Biotin labeled cRNA was prepared using 5ug (1.0 ug/uL) total RNA
(approx. 1 ug mRNA) with the One-Cycle cDNA kit (incorporating a T7-oligo(dT) primer) and the GeneChip IVT labeling kit. In vitro
transcribed cRNA was fragmented (20ug) and analyzed for quality control purposes by spectrophotometry and gel electrophoresis prior to hybridization.
 
Hybridization protocol An hybridization cocktail was prepared with 15ug of cRNA (0.5 ug/uL) and hybridized to HG U133 Plus 2.0 microarrays for 16h at 45degC in an Affymetrix Hybridization Chamber 640. Each cRNA sample was spiked with standard prokaryotic hybridization controls for
quality monitoring.
Scan protocol Hybridized microarrays were stained with streptavidin phycoerytherin and washed with a solution containing biotinylated anti-streptavidin antibodies using the Affymetrix Fluidics Station 450. Finally, the stained and washed microarrays were scanned with the
Affymetrix Scanner 3000.
Description Normal_colon_22_13April05.csv
Data processing The Affymetrix software package was used to transform raw microarray image files to digitized format. As for the Discovery set above, gene expression levels for the this data set were calculated using MAS 5.0 (Affymetrix), scaled to 100 for quality control purposes and with the RMA normalization algorithm for expression data.
 
Submission date Oct 06, 2007
Last update date Aug 28, 2018
Contact name Lawrence C LaPointe
E-mail(s) larry@clinicalgenomics.com
Organization name Clinical Genomics
Street address 11 Julius Ave
City North Ryde
State/province NSW
ZIP/Postal code 2113
Country Australia
 
Platform ID GPL570
Series (1)
GSE9254 Normal human colorectal mucosa, cecum, ascending, transverse, sigmoid and rectum
Relations
Reanalyzed by GSE39923
Reanalyzed by GSE64985
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE RMA normalized expression levels

Data table
ID_REF VALUE
1007_s_at 8.83650701224041
1053_at 3.36182775172803
117_at 3.60648658956681
121_at 5.8304799077437
1255_g_at 2.86928771373051
1294_at 5.73539278231993
1316_at 3.78445685328006
1320_at 3.64629143228259
1405_i_at 6.9064001466816
1431_at 2.90932177531713
1438_at 3.86450580498447
1487_at 6.50798768295598
1494_f_at 3.88633519150841
1552256_a_at 5.80109950870673
1552257_a_at 6.94198342622408
1552258_at 3.35366756941982
1552261_at 3.46561376190228
1552263_at 3.85276405941397
1552264_a_at 4.38234880301321
1552266_at 3.11162165720488

Total number of rows: 54675

Table truncated, full table size 1480 Kbytes.




Supplementary file Size Download File type/resource
GSM234917.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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