|
| Status |
Public on Nov 18, 2006 |
| Title |
PTEN_mutant_3_intestinal_polyp_30_days |
| Sample type |
RNA |
| |
|
| Source name |
PTEN mutant 3 intestinal polyp, polyI:C, 30 days
|
| Organism |
Mus musculus |
| Characteristics |
Strain: mixed genetic background, predominantly (>87.5%) C57BL/6 with some CD1. Genotype: PTEN mutant = Mx1-Cre positive: PTENfx/fx. Sex: Female. Age: Eight and a half weeks (at tissue isolation). Tissue: Intestinal polyp from small intestine (jejunum/ileum region).
|
| Biomaterial provider |
Linheng Li Lab, Stowers Institute for Medical Research
|
| Treatment protocol |
PTEN mutant and control animals were injected a total of five times with polyinosinic-polycytidylic acid (Poly I:C), with single injections of 250 micrograms/mouse/day given every other day. Injections were performed on days 21, 23, 25, 27, 29. Mice were analyzed 30 days after the final Poly I:C injection.
|
| Growth protocol |
Animals were maintained under specific pathogen free conditions in vivarium with a 12 hour light/12 hour dark cycle. Animals had food and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Trizol Reagent (Invitrogen) according to manufacturer's protocol. Quality and quantity of the total RNA was assessed using a Bioanalyzer (Agilent).
|
| Label |
Biotin, detected with Strepavidin R-phycoerythrin
|
| Label protocol |
Biotin-labeled cRNA was prepared from 6 micrograms of total RNA using the Affymetrix One-cycle protocol. (Affymetrix Cat. #900493). Quantity and quality of unfragmented cRNA and fragmented cRNA was assessed using a Bioanalyzer (Agilent).
|
| |
|
| Hybridization protocol |
Hybridization to Affymetrix mouse Genome 430 2.0 arrays using GeneChipFluidics Station450. 20 micrograms of fragmented cRNA was used for each chip hybridization. Hyridization and wash protocols were as described in Affymetrix Technical Manual, "GENE EXPRESSION MONITORING, GeneChip®
Expression Analysis" 701021 Rev. 5. Hybridization buffer was 100 mM MES(2-(N-Morpholino)ethanesulfonic acid sodium salt), 1M [Na+], 20 mM EDTA, 0.01% Tween-20. Hybridization was performed at 45 celsius for 16 hours.
|
| Scan protocol |
Affymetrix GeneChip Scanner 3000 with GCOS GeneChip Operating software Version 1.2.0.037
|
| Description |
The study examines the effect of conditional PTEN deletion in the small intestine. Deletion of the PTEN exon 5 (encoding the phosphatase motif) was accomplished using the interferon-inducible Mx1-Cre, induced by five injections of polyinosinic-polycytidylic acid. The experiment compared the gene expression profiles of polyp regions from three PTEN mutant animals with intestines from two control animals. Genes were considered up-regulated or down-regulated if all of the following conditions were met: 1) There was at least a two-fold change in the average values measured between controls and mutants; 2) There was no overlap between the range of mutant and control data; and 3) The control mean was outside the 95% confidence interval of the PTEN-mutant mean.
|
| Data processing |
Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE= RAW SIGNAL * 100/(105.83+ 4.6698*LN(RAW_SIGNAL))
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| |
|
| Submission date |
Oct 18, 2006 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Linheng Li |
| E-mail(s) |
lil@stowers-institute.org
|
| Phone |
816-926-4081
|
| URL |
http://www.stowers-institute.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Street address |
1000 East 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE6078 |
PTEN-deficient intestinal stem cells initiate intestinal polyposis |
|
| Relations |
| Reanalyzed by |
GSE119085 |
