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Sample GSM1081157 Query DataSets for GSM1081157
Status Public on Feb 01, 2016
Title Liver_Maternal_Separation_5
Sample type RNA
 
Source name Liver, Maternal Separation, replicate 5
Organism Rattus norvegicus
Characteristics gender: female
strain: Wistar
age: 10 days
tissue: liver
treatment: maternal separation
Treatment protocol At 10 days post-partum female Wistar rats from at least 3 different litters were separated from their mothers for 4 hours (MS=maternal separation) or not (CT=controls). The animals were put back with their mothers for 24h prior to microarray analysis of their livers.
Growth protocol Litters of Wistar rats and their mothers were housed at 23+/-1°C on a 12 hour light/dark cycle. The in vivo study was conducted under the European Union Guidelines for the use and care of laboratory animals and were approved by an independent ethics committee.
Extracted molecule total RNA
Extraction protocol Immediately following euthanasia, liver was removed and an approx. 100mg fragment was snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from frozen liver samples with TRIzol reagent (Invitrogen) following manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies) and assayed at 260nm on a Nanodrop ND-1000 spectrophotometer (Thermo Scientific).
Label Cy3
Label protocol For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-color Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Courtaboeuf, France). Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray 4x44K v3 (design 028282) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).
Scan protocol Slides were scanned immediately after washing on an Agilent High Resolution C Scanner (G2565CA)
Data processing The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028282_D_F_20110906). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0 okFoundGreen<-x$gIsFound==1 okPos=x$gIsPosAndSignif==1 okWellAbove<- x$gIsWellAboveBG==1 as.numeric(okType & okFoundGreen & okPos & okWellAbove)} We selected the spots with a weight of 1 for at least 8 out of 9 microarrays or with a weight of 1 in 4 microarrays from at least one experimental group. The filtered data were then stored as an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 17604 rows each corresponding to a unique ProbeName (provided as data Matrix).
 
Submission date Feb 11, 2013
Last update date Feb 01, 2016
Contact name Pascal GP Martin
E-mail(s) [email protected]
Organization name INRAE
Department UMR1332 BFP
Lab FDFE
Street address 71 avenue Edouard Bourlaux
City Villenave d'Ornon
ZIP/Postal code 33140
Country France
 
Platform ID GPL14746
Series (1)
GSE44241 A short-term maternal separation in early neonate rats markedly increases intestinal permeability, induces bacterial translocation to systemic organs and impacts gene expression in the liver

Data table header descriptions
ID_REF
VALUE log2 quantile normalized signal

Data table
ID_REF VALUE
A_42_P453055 8.127522967
A_42_P453171 10.13495462
A_42_P453894 11.55015944
A_42_P453935 14.17808684
A_42_P453976 8.121852672
A_42_P454206 8.363892515
A_42_P454301 11.80437389
A_42_P454311 9.358236103
A_42_P455785 12.30826017
A_42_P455802 11.4383993
A_42_P456155 14.39206623
A_42_P456701 10.52313591
A_42_P457003 9.914932906
A_42_P457692 10.60504714
A_42_P457773 12.51366056
A_42_P457783 7.940060275
A_42_P457895 9.807389471
A_42_P458075 11.91516345
A_42_P458137 7.246412488
A_42_P458494 6.798764233

Total number of rows: 17604

Table truncated, full table size 427 Kbytes.




Supplementary file Size Download File type/resource
GSM1081157_US10463851_252828210709_S01_GE1_1010_Sep10_1_2.txt.gz 8.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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