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Sample GSM141508 Query DataSets for GSM141508
Status Public on Oct 26, 2006
Title Proximal colon whey 2
Sample type RNA
Source name Rat Proximal colon
Organism Rattus norvegicus
Characteristics Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet (CAS), proximal colon
Extracted molecule total RNA
Extraction protocol TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
Label biotin
Label protocol Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
Hybridization protocol Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
Scan protocol GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
Description Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
Data processing To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.
Submission date Oct 23, 2006
Last update date Oct 25, 2006
Contact name Rijin Xiao
Phone 501-364-2790
Fax 501-364-3161
Organization name Nutrition Center, Arkansas Chidren's Hospital
Street address 2020 Marshall Street
City Little Rock
State/province AR
ZIP/Postal code 72202
Country USA
Platform ID GPL85
Series (1)
GSE6102 Dietary exposure to soy or whey proteins alters colonic global gene expression profiles during rat colon tumorigenesis

Data table header descriptions
VALUE SIGNAL (See Affymetrix Literature)
ABS_CALL Presence (P), Marginal (M) or Absence (A) of gene transcript

Data table
AFFX-MurIL2_at 9.2 A
AFFX-MurIL10_at 16 A
AFFX-MurIL4_at 27.6 A
AFFX-MurFAS_at 14.6 A
AFFX-BioB-5_at 609 P
AFFX-BioB-M_at 1629.7 P
AFFX-BioB-3_at 601.7 P
AFFX-BioC-5_at 2062.5 P
AFFX-BioC-3_at 1768.7 P
AFFX-BioDn-5_at 2285.8 P
AFFX-BioDn-3_at 10519.1 P
AFFX-CreX-5_at 23309.1 P
AFFX-CreX-3_at 28237.6 P
AFFX-BioB-5_st 52.3 A
AFFX-BioB-M_st 34.5 A
AFFX-BioB-3_st 16.3 A
AFFX-BioC-5_st 11.7 A
AFFX-BioC-3_st 5.6 A
AFFX-BioDn-5_st 198.6 A
AFFX-BioDn-3_st 226.1 P

Total number of rows: 8799

Table truncated, full table size 178 Kbytes.

Supplementary file Size Download File type/resource
GSM141508.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM141508.EXP.gz 493 b (ftp)(http) EXP
Raw data provided as supplementary file

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