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Sample GSM141509 Query DataSets for GSM141509
Status Public on Oct 26, 2006
Title Proximal colon whey 3
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
E-mail(s) xiaorijin@uams.edu
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
ID_REF
VALUE SIGNAL (See Affymetrix Literature)
ABS_CALL Presence (P), Marginal (M) or Absence (A) of gene transcript

Data table
ID_REF VALUE ABS_CALL
AFFX-MurIL2_at 21.8 A
AFFX-MurIL10_at 19.4 A
AFFX-MurIL4_at 12.3 A
AFFX-MurFAS_at 17.6 A
AFFX-BioB-5_at 597.1 P
AFFX-BioB-M_at 1561.8 P
AFFX-BioB-3_at 487 P
AFFX-BioC-5_at 2225.4 P
AFFX-BioC-3_at 1528.8 P
AFFX-BioDn-5_at 1747.1 P
AFFX-BioDn-3_at 8924.7 P
AFFX-CreX-5_at 16308.6 P
AFFX-CreX-3_at 17439.8 P
AFFX-BioB-5_st 77.2 A
AFFX-BioB-M_st 22.3 A
AFFX-BioB-3_st 14.1 A
AFFX-BioC-5_st 35.6 A
AFFX-BioC-3_st 10.3 A
AFFX-BioDn-5_st 315 A
AFFX-BioDn-3_st 237 P

Total number of rows: 8799

Table truncated, full table size 178 Kbytes.




Supplementary file Size Download File type/resource
GSM141509.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM141509.EXP.gz 493 b (ftp)(http) EXP
Raw data provided as supplementary file

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