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Sample GSM999053 Query DataSets for GSM999053
Status Public on Dec 19, 2012
Title colon control repl3
Sample type RNA
Source name colon of mouse, after 14 days on a Westernized high fat (control) diet, replicate 3
Organism Mus musculus
Characteristics backgroud: C57BL/6J
gender: male
age: 11 weeks
tissue: colon
diet: Westernized high fat (control) 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
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
VALUE RMA signal (as log2)

Data table
10338001 11.54065761
10338002 4.732225175
10338003 9.855481441
10338004 8.978994786
10338005 2.488075447
10338006 2.787444215
10338007 2.944500572
10338008 3.322319511
10338009 6.584494033
10338010 2.553467498
10338011 4.31794902
10338012 2.612263868
10338013 2.357427131
10338014 2.420138764
10338015 2.364164471
10338016 5.618105738
10338017 12.56631834
10338018 5.028605232
10338019 3.772372317
10338020 6.265717052

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.

Supplementary file Size Download File type/resource
GSM999053_G067_G05_03_20A_CTRL.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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