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Sample GSM297551 Query DataSets for GSM297551
Status Public on Aug 01, 2008
Title colon_24h_rep2
Sample type RNA
 
Source name DA rat colon treated 24 h
Organism Rattus norvegicus
Characteristics Gender: female
Age: 10 weeks
Treatment protocol Rats received a single intraperitoneal injection of irinotecan while under light halothane anaesthetic (2% in 1.5 L O2). At the specified time point, rats were killed by exsanguination and cervical dislocation. The GIT was removed immediately and flushed with chilled isotonic saline. Sections of whole stomach, jejunum and colon were snap frozen in LN2 and stored at -70C until extraction.
Growth protocol Rats were housed individually with free access to food and water
Extracted molecule total RNA
Extraction protocol Extraction of RNA was carried out by NucleoSpin RNA II kit (Machery Nagel, Germany) as per manufacturer's instructions. Rat total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.
Label biotin
Label protocol A total of 7ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millenium Sciences cat no. 900431). The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371). Biotin was incorporated into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449). After the IVT process, the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol. Samples were then prepared for hybridisation to the Rat 230 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO.
 
Hybridization protocol A total hybridisation volume of 300ul was prepared for each sample and 200ul loaded into a Rat 230 version 2.0 GeneChip. The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm. After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.
Scan protocol Chips were scanned using the Affymetrix GeneChip Scanner 3000. The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which is used for generating subsequent CEL and CHP files for analysis.
Description Gene expression data from large intestine treated with irinotecan
Data processing Data was normalised using robust multiarray average approach with additional background adjustment using sequence information to estimate probe affinity for nonspecific binding
 
Submission date Jun 09, 2008
Last update date Jun 09, 2008
Contact name Joanne Marie Bowen
E-mail(s) joanne.bowen@imvs.sa.gov.au
Organization name Royal Adelaide Hospital
Department Medical Oncology
Lab Mucositis Research
Street address North Terrace
City Adelaide
State/province South Australia
ZIP/Postal code 5000
Country Australia
 
Platform ID GPL1355
Series (1)
GSE11722 Irinotecan-induced gene expression changes in the rat intestine

Data table header descriptions
ID_REF
VALUE Time course profiles were evaluated using multivariate empirical Bayes statistic developed for replicated microarray data by Yu Chuan Tai and Terence P. Speed (2004) and implemented as ‘‘TimeCourse’’ package in Bioconductor. Statistical strength of differential expression for whole time course profiles was ranked with Hotelling’s T-square statistic

Data table
ID_REF VALUE
1367452_at 11.07933715
1367453_at 9.927573168
1367454_at 10.98486755
1367455_at 11.06110506
1367456_at 11.48555537
1367457_at 9.875259661
1367458_at 8.957607947
1367459_at 12.41028648
1367460_at 11.86363063
1367461_at 10.66513727
1367462_at 11.30053605
1367463_at 10.32532464
1367464_at 9.527545199
1367465_at 9.782198425
1367466_at 10.10031192
1367467_at 10.58201708
1367468_at 10.01715094
1367469_at 12.14899149
1367470_at 10.26054607
1367471_at 9.421480935

Total number of rows: 31099

Table truncated, full table size 698 Kbytes.




Supplementary file Size Download File type/resource
GSM297551.CEL.gz 2.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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