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Sample GSM158580 Query DataSets for GSM158580
Status Public on Jan 31, 2007
Title CAS-1
Sample type RNA
 
Source name rat mammary epithelial cells
Organism Rattus norvegicus
Characteristics Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of casein based diet (CAS )
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 #4 mammary gland from 2 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 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4chips 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 Value column are raw signal intensity generated from MAS 5.0.
 
Submission date Jan 26, 2007
Last update date Jan 30, 2007
Contact name Ying Su
E-mail(s) [email protected]
Phone 501-364-2033
Fax 501-364-3161
Organization name UAMS
Department physiology
Street address 1120 Marshall St. South Campus
City Little Rock
State/province AR
ZIP/Postal code 72202
Country USA
 
Platform ID GPL341
Series (1)
GSE6879 Dietary effect of SPI or Genistein alters rat mammary epithelial global gene expression profiles

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
1367452_at 2343.4 P
1367453_at 2013.8 P
1367454_at 1190.3 P
1367455_at 2601.5 P
1367456_at 5309.7 P
1367457_at 1376.8 P
1367458_at 342.1 P
1367459_at 6160.7 P
1367460_at 5295.1 P
1367461_at 1474.8 P
1367462_at 2621.5 P
1367463_at 1683.1 P
1367464_at 770.6 P
1367465_at 1850.2 P
1367466_at 1059.7 P
1367467_at 1316.7 P
1367468_at 592.3 P
1367469_at 4789.6 P
1367470_at 3215.6 P
1367471_at 844.7 P

Total number of rows: 15923

Table truncated, full table size 292 Kbytes.




Supplementary file Size Download File type/resource
GSM158580.CEL.gz 2.4 Mb (ftp)(http) CEL

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