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Sample GSM805232 Query DataSets for GSM805232
Status Public on Jul 11, 2012
Title colon germ-free t=0d_rep11
Sample type RNA
 
Source name colon from germ-free mouse (day 0), replicate 11
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: colon
gender: male
days of conventionalized: 0
age at start of experiment: 10 wks
Treatment protocol After 2 weeks of acclimatization and diet adaptation, a subset of GF mice were randomly assigned to sacrifice by oral anesthesia using isoflurane (t=d0, GF). The remaining GF mice were conventionalized by oral gavage with 0.5ml of mixed fecal suspension derived from 0.2g of freshly obtained fecal material of conventionally raised mice (C57 BL/6) diluted 100-folds in Brain Heart infusion (BHI) broth. Conventionalized mice were sacrificed at days (d) d1, d2, d4, d8, d16 and d30 after conventionalization. Small intestine (SI; jejunum, and ileum), and large intestine (LI; colon) from each mouse were removed. The 2 segments of the SI and the entire colon were then divided into 2-cm segments that were immediately stored in RNA-later at room temperature for 1 hour prior to subsequent storage at -80°C for RNA isolation.
Growth protocol Germ free (GF) mice (male, C57 BL/6) were purchased from the Centre de Recherché, Institute National de la Recherche Agronomique (Jouy-en-Josas, France). Mice were maintained under sterile conditions. Mice had ad libitum access to sterilized water and were maintained on a commercial laboratory chow diet (UAR 1016C Laboratory Chow, UAR, Villemoisson sur Orge, France) that was sterilized by gamma irradiation (45KGy).
Extracted molecule total RNA
Extraction protocol Total mouse RNA was obtained from a 2-cm segment of jejunum, ileum and colon by extraction with TRIzol reagent (Invitrogen, Carlsbad, CA), followed by DNAse treatment and column purification using the RNeasy mini kit (Qiagen, Hilden, Germany). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.
Label biotin
Label protocol The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.
 
Hybridization protocol The Affymetrix GeneChip Mouse Gene 1.1 ST arrays are peg arrays arranged into the standard 96 well plate format. The 144 arrays that were used in this experiment were provided as 1x 96 array plate and 3x 24 array plate. Array hybridization, washing and scanning 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' (v1.16.0). The SI samples were normalzed together, separately from the colon samples.
 
Submission date Sep 30, 2011
Last update date Jul 11, 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)
GSE32513 Identification of the core gene-regulatory network that governs the dynamic adaptation of intestinal homeostasis during conventionalization in mice

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

Data table
ID_REF VALUE
10338001 11.29509386
10338002 5.131609
10338003 9.390917463
10338004 8.594948307
10338005 2.722948865
10338006 3.014225112
10338007 3.208418489
10338008 3.559277883
10338009 7.375443303
10338010 2.752662818
10338011 4.726423073
10338012 2.85292461
10338013 2.582287564
10338014 2.646601519
10338015 2.589754633
10338016 6.208719855
10338017 12.34900237
10338018 5.608462732
10338019 4.23946702
10338020 7.026359377

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM805232.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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