|
| Status |
Public on Sep 01, 2010 |
| Title |
Appendicitis induction followed by appendicectomy after 1 week No. 3 |
| Sample type |
RNA |
| |
|
| Source name |
Most distal colon from 5 -week old Male BALB/c mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
age: 5 weeks
tissue: Most distal colon
protocol: Appendicitis-Appendicectomy (AA)
batch: 2
|
| Treatment protocol |
Appendicitis induction followed by appendicectomy after 1 week OR 1st Sham surgery followed by 2nd sham surgery after 1 week.
|
| Growth protocol |
5 -week old Male BALB/c mice maintained at Standard PC2 Animal Storage Facility at the 5th Floor, Wallace Wurth Building, UNSW, Sydney.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted (TRIzol®) from 4 individual colonic samples per group (AA group vs. SS group) with each sample taken independently through Affymetrix® microarray hybridization.
|
| Label |
biotin
|
| Label protocol |
100 ng of RNA from each sample was labelled using the Whole Transcript Sense Target Labelling Assay, following manufacturers instructions
|
| |
|
| Hybridization protocol |
The standard hybridization protocol was used as recommended by Affymetrix
|
| Scan protocol |
GeneChips were scanned using a Affymetrix GCS3000 7G four-colour Gene Array scanner with autoloader (Affymetrix) at the Ramaciotti Centre for Gene Function Analysis, UNSW, Australia
|
| Description |
Sample name: AA3
CEL file (original name): RC_MG6_(MoGene-1_0-st-v1).CEL
|
| Data processing |
Raw data from 8 CEL files was normalisd in a single batch using RMA in Partek 6.4, with default settings, excluding the control probesets. Batch effects in the normalised data due to date of processing were removed using the batch removal tool in partek (essentially using the residuals from an ANOVA fitted to batch effect). Probesets not detected on any array were excluded. Probeset detection based upon the detected above background procedure from affymetrix power tools, where detected means DABG P=10^-5 in at least one sample
probe group file: MoGene-1_0-st-v1.r3.pgf
|
| |
|
| Submission date |
Sep 01, 2010 |
| Last update date |
Sep 01, 2010 |
| Contact name |
Rajkumar Cheluvappa |
| E-mail(s) |
[email protected]
|
| Phone |
+61 0406 0406 20
|
| Organization name |
University of New South Wales
|
| Department |
St George Clinical School
|
| Lab |
Inflammation and nfection Research Centre
|
| Street address |
Inflammation and Infection Research Centre, School of Medical Sciences, Wallace Wurth Building, University of New South Wales, Gate 9 High Street, Sydney, NSW 2052, Australia.
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE23914 |
Gene expression study identifies important protective pathways utilized by appendicitis and appendectomy for ameliorating colitis |
|
