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Sample GSM999028 Query DataSets for GSM999028
Status Public on Aug 03, 2015
Title colon_control_with Abx_repl1
Sample type RNA
 
Source name colon of mouse, after 14 days on a Westernized high fat (control) diet and Abx, replicate 1
Organism Mus musculus
Characteristics backgroud: C57BL/6J
gender: male
age: 11 weeks
tissue: colon
diet: 14 days on a Westernized high fat (control) diet and Abx
Treatment protocol Mice were fed a Westernized high fat control diet, or the same diet supplemented with 0.5 µmol heme/g diet. One group of control and one group of heme mice received a mixture of broad spectrum Antibiotics (Abx) (ampicilin, neomycin and metronidazole) in their drinking water. After 14 days of intervention, mice were killed and the colon was taken out. Mesenteric fat was removed from the colon. Colons were cut open longitudinally, washed in PBS, and scraped. RNA was isolated from scrapings and analysed by microarray.
Growth protocol C57BL/6J mice were purchased from Harlan (Horst, the Netherlands), and housed in a light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle, 20±2 °C). Mice had free access to feed and water.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from colonic scrapings using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
Label biotin
Label protocol One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).
 
Hybridization protocol Hybridization, washing and scanning of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument.
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).
 
Submission date Sep 06, 2012
Last update date Aug 03, 2015
Contact name Guido Hooiveld
E-mail(s) guido.hooiveld@wur.nl
Organization name Wageningen University
Department Div. Human Nutrition & Health
Lab Nutrition, Metabolism & Genomics Group
Street address HELIX, Stippeneng 4
City Wageningen
ZIP/Postal code NL-6708WE
Country Netherlands
 
Platform ID GPL11533
Series (1)
GSE40670 Microbiota facilitates dietary heme-induced epithelial hyperproliferation and hyperplasia by breaking the mucus barrier

Data table header descriptions
ID_REF
VALUE RMA signal (as log2)

Data table
ID_REF VALUE
10338001 11.13905637
10338002 4.635670337
10338003 9.565272287
10338004 8.529424058
10338005 2.329341795
10338006 2.59432828
10338007 2.778673881
10338008 3.122674509
10338009 6.835545032
10338010 2.355666848
10338011 4.363176761
10338012 2.419345058
10338013 2.187193795
10338014 2.220023019
10338015 2.1794251
10338016 5.743018194
10338017 12.38208675
10338018 5.073194262
10338019 3.756435059
10338020 6.516284966

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM999028_G026_C05_05_32Aplus_CTRL_ANTIB.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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