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Sample GSM3101215 Query DataSets for GSM3101215
Status Public on May 09, 2018
Title colon, control diet, age 12 months, rep09
Sample type RNA
 
Source name scraping from colonic mucosa and submucosa, control diet, age 12 months
Organism Mus musculus
Characteristics Sex: male
mouseid: A2_09
diet group: C
diet (full name): control
age at sacrifice (months): 12M
mouse number: 09
tissue: colon
strain: C57BL/6J
Treatment protocol Prior to sacrifice, each mouse was first fasted for 4 hours after which they received an intragastric gavage of 400ul of 0.5% carboxymethyl cellulose, then fasted again for another 6 hours. During the sacrifice, after sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), colon tissue was removed, whereafter the mucosa and submucosa was scraped-off, snap-frozen and stored at -80C until further analysis.
Growth protocol The design of the study and experimental procedures have been described in detail previously (PMID: 25504628). Briefly, male C57BL/6J mice (age: 7 weeks) were purchased from Janvier (Cedex, France) and were housed in pairs of two in the light and temperature (20C)-controlled animal facility of Wageningen University (12-hour light/dark cycle, lights on at 04.00). The mice received standard AIN-93G (Research Diet Services, Wijk bij Duurstede, The Netherlands) for 2 weeks upon arrival. At the age of 9 weeks, mice were individually housed and randomized to different dietary regimens. For the current analyses, we only considered mice that were lifelong fed ad libitum a semi-synthetic control diet consisting of 10E% of fat (C; control). Mice were sacrificed at 6, 12, 24 or 28 months of age.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the scrapings using TRIzol Reagent according to the manufacturer’s instructions (Invitrogen, Breda, The Netherlands). Isolated RNA was purified using RNeasy Micro columns (Qiagen, Venlo, The Netherlands) and total RNA yield (Nanodrop ND-1000, Nanodrop Products, Maarssen, The Netherlands) and RNA integrity (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) were assessed. 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 Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).
 
Hybridization protocol Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).
 
Submission date Apr 17, 2018
Last update date May 10, 2018
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)
GSE113257 Integrative analysis of gut microbiota composition, host colonic gene expression and intraluminal metabolites in aging C57BL/6J mice

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

Data table
ID_REF VALUE
10338001 11.69705817
10338002 4.851322188
10338003 9.876984882
10338004 9.184644925
10338005 2.35833018
10338006 2.592257388
10338007 2.839712818
10338008 3.285045526
10338009 6.681917627
10338010 2.347615185
10338011 4.512673032
10338012 2.451243874
10338013 2.125897452
10338014 2.174444302
10338015 2.155818196
10338016 5.744356419
10338017 12.81316776
10338018 5.142278848
10338019 4.014585331
10338020 6.343134498

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM3101215_068_A2-09_G160_D10.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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