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Sample GSM999055 Query DataSets for GSM999055
Status Public on Dec 19, 2012
Title colon heme repl1
Sample type RNA
 
Source name colon of mouse, after 14 days on a Westernized high fat (heme) diet, replicate 1
Organism Mus musculus
Characteristics backgroud: C57BL/6J
gender: male
age: 11 weeks
tissue: colon
diet: Westernized high fat (heme) diet
Treatment protocol Male control and heme-fed mice were maintained on a high fat-low calcium diet (with or without heme) for 2 weeks. After 2 weeks diet intervention all mice were sacrificed and colons were taken out. Mesenteric fat was removed. Colons were cut open longitudinally, washed in PBS, and epithelial cells were scraped off.
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 Dec 19, 2012
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)
GSE40672 Dietary heme alters microbiota and mucosa of mouse colon without functional changes in host-microbe cross-talk.

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

Data table
ID_REF VALUE
10338001 11.34095702
10338002 4.913896157
10338003 9.597713594
10338004 8.714457507
10338005 2.524302769
10338006 2.829487303
10338007 3.016845071
10338008 3.409650062
10338009 6.791208748
10338010 2.54402793
10338011 4.488868798
10338012 2.639387179
10338013 2.373113653
10338014 2.439089624
10338015 2.353352838
10338016 5.838219799
10338017 12.4853423
10338018 5.307430431
10338019 3.921724558
10338020 6.543227097

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM999055_G067_G09_05_2C_HEME.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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