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Sample GSM228797 Query DataSets for GSM228797
Status Public on Nov 12, 2007
Title Intact jejunum, biological rep1
Sample type RNA
 
Source name Mouse jejunum
Organism Mus musculus
Characteristics Adult, male, C57Bl/6
Treatment protocol Mice were sacrificed at 8-10 weeks of age, and the jejunum was harvested. Mucosal digests were prepared using collagenase and dispase. These were then subject to SP sorting via Hoechst 33342 dye exclusion. Cells were also stained with fluorescein isothiocyanate (FITC) labeled anti-CD45 antibody (BD Pharmingen, San Diego, CA) to eliminate bone-marrow derived cells from the populations to be analyzed. Propidium iodide (PI) was used to exclude dead cells.
Growth protocol All mice for this study were housed in our animal facility under a 12-hour light/dark cycle, and all had unrestricted access to rodent Lab Chow #5001 (PMI Nutrition International, Brentwood, MO) as well as acidified tap water. The Institutional Animal Care and Use Committee of Baylor College of Medicine approved all experimental procedures.
Extracted molecule total RNA
Extraction protocol Total cellular RNA was extracted using an RNeasy Mini Kit (Qiagen, Valencia, CA) per the manufacturer’s instructions.
Label biotin
Label protocol 50 ng of total RNA was amplified using the Affymetrix Two Cycle Target Labeling Kit according to standard Affymetrix protocols (Expression Analysis Technical Manual, 2004, Affymetrix). Biotinylated cRNA were prepared from 5 mcg of total RNA.
 
Hybridization protocol Following fragmentation, 15 mcg of biotinylated cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix Mouse Genome 430 2.0 GeneChips. GeneChips were washed and stained using the Affymetrix Fluidics station 400 according to standard Affymetirx protocols.
Scan protocol Laser scanning of the chips was performed using the Affymetrix GeneChip Scanner 3000.
Description Gene expression data from mouse jejunum prior to processing
Data processing The data were analyzed using the dChip software platform (v2005).
 
Submission date Sep 11, 2007
Last update date Aug 28, 2018
Contact name Ajay S Gulati
E-mail(s) ajay_gulati@med.unc.edu
Phone (919) 966-7886
Organization name University of North Carolina at Chapel Hill
Department Pediatric Gastroenterology
Street address 130 Mason Farm Road, CD#7220
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL1261
Series (1)
GSE9013 Expression data from side-population sorted putative intestinal stem cells.
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE dChip normalized expression value.
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 165.071 P
AFFX-BioB-M_at 197.518 P
AFFX-BioB-3_at 163.912 P
AFFX-BioC-5_at 383.862 P
AFFX-BioC-3_at 399.91 P
AFFX-BioDn-5_at 1000.06 P
AFFX-BioDn-3_at 1632.69 P
AFFX-CreX-5_at 5603.02 P
AFFX-CreX-3_at 6691.47 P
AFFX-DapX-5_at 66.9014 P
AFFX-DapX-M_at 483.515 P
AFFX-DapX-3_at 1075.67 P
AFFX-LysX-5_at 22.3522 P
AFFX-LysX-M_at 89.1504 P
AFFX-LysX-3_at 347.748 P
AFFX-PheX-5_at 43.7548 P
AFFX-PheX-M_at 62.6063 P
AFFX-PheX-3_at 191.888 P
AFFX-ThrX-5_at 21.0337 P
AFFX-ThrX-M_at 74.103 P

Total number of rows: 45101

Table truncated, full table size 938 Kbytes.




Supplementary file Size Download File type/resource
GSM228797.CEL.gz 3.9 Mb (ftp)(http) CEL
GSM228797.EXP.gz 2.4 Mb (ftp)(http) EXP
Raw data provided as supplementary file
Processed data included within Sample table

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