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Sample GSM411417 Query DataSets for GSM411417
Status Public on Sep 01, 2009
Title D44N transgenic enterocytes, biological rep1
Sample type RNA
Source name D44N transgenic villi enterocytes
Organism Mus musculus
Characteristics age: 3.8 months
gender: Male
cell type: D44N transgenic enterocytes
biological replicate: 1
Treatment protocol The intestine was removed in its entirety from the abdominal cavity of mice, from the exit of the stomach to the entry into the large intestine. The intestines were then opened along their cephalocaudal axis, washed with phosphate-buffered saline, and rolled from the duodenum to the ileum. Rolls from wild-type, TAg and TAg mutant transgenic mice were then processed to isolate villi cell types by LCM. Briefly, the rolls were quickly frozen and stored at -80C. Frozen sections were cut and immediately dehydrated in graded alcohol solutions. The dried sections were examined microscopically and the top 2/3 of 50 villous segments from each section were collected using a laser capture microscope (Pix Cell II, Arcturus, Mt. View, CA).
Growth protocol The mice were held in our selected pathogen-free colony according to NIH guidelines for use of animals in research. The mice had access to food and water ad libitum, 24 hours a day.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from villi enterocytes with the PicoPure kit (Arcturus) and amplified twice with the RiboAmp kit (Arcturus).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Agilent GeneArray 3000 with 7G upgrade.
Description D44N transgenic enterocytes, biological rep1
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150. RMA was performed using BRB-Array Tools (Rich Simon, National Cancer Institute,
Submission date Jun 02, 2009
Last update date Jun 03, 2009
Contact name Daniel Clark
Organization name University of Pittsburgh
Street address 3501 Terrace St.
City Pittsburgh
ZIP/Postal code 15213
Country USA
Platform ID GPL1261
Series (1)
GSE16389 Global analysis of gene expression by SV40 T antigen in the mouse small intestine epithelium

Data table header descriptions
VALUE log2 RMA expression value

Data table
1415670_at 7.744826794 P 0.023926
1415671_at 6.885012627 P 0.000732
1415672_at 9.303154945 P 0.000244
1415673_at 4.477179527 A 0.171387
1415674_a_at 7.131054401 P 0.000244
1415675_at 6.221941948 P 0.005859
1415676_a_at 9.441438675 P 0.000244
1415677_at 9.05770874 P 0.000244
1415678_at 10.71926498 P 0.001221
1415679_at 10.12961769 P 0.000244
1415680_at 8.29067421 P 0.000244
1415681_at 8.679577827 P 0.000244
1415682_at 4.445120811 M 0.056152
1415683_at 11.31136799 P 0.000244
1415684_at 6.173021793 P 0.001953
1415685_at 4.731557369 P 0.000732
1415686_at 7.555787563 P 0.023926
1415687_a_at 7.772848606 P 0.000732
1415688_at 9.782793999 P 0.000244
1415689_s_at 6.630571365 P 0.000244

Total number of rows: 45101

Table truncated, full table size 1501 Kbytes.

Supplementary file Size Download File type/resource
GSM411417.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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