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Sample GSM2702094 Query DataSets for GSM2702094
Status Public on Jul 05, 2018
Title liver - female - control - rep1
Sample type RNA
 
Source name liver
Organism Mus musculus
Characteristics gender: female
treatment: control
age: 68 weeks
Treatment protocol The experimental work on animals was conducted in the Toxalim Unit, INRA, Toulouse (France), followed the European Union guidelines for laboratory animal use and care, and was approved by an independent ethics committee. Eight weeks-old female and male C57 BL/6J mice were purchased from Janvier Laboratories, France. Mean body weights were 18.9 and 23.1g for females and males respectively. The animals were allowed to acclimatise to laboratory conditions for 2 weeks before starting the experiment.
Extracted molecule total RNA
Extraction protocol Thirty-six males and 36 females were housed in the laboratory animal room (23 ± 2 ºC) and segregated into 2 groups, each including 18 females and 18 males, fed the pesticides-enriched or the control diet for 52 weeks.
Label Cy3
Label protocol For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809) 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 a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software
Data processing The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). 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 minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 34183 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R 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 31532 rows each corresponding to a unique ProbeName (provided as data Matrix).
 
Submission date Jul 13, 2017
Last update date Jul 05, 2018
Contact name laurence Gamet-Payrastre
E-mail(s) laurence.payrastre@inra.fr
Organization name INRA ToxAlim
Department Human alimentation
Lab Team research Integrative toxicology and metabolism
Street address 180 chemin de Tournefeuille
City Toulouse
ZIP/Postal code 31027
Country France
 
Platform ID GPL21163
Series (1)
GSE101405 In vivo metabolic disorders induced by a pesticide cocktail at the Acceptable Daily Intake level

Data table header descriptions
ID_REF
VALUE log2 normalized signal

Data table
ID_REF VALUE
A_51_P399985 11.74871921
A_55_P2419483 7.021892814
A_55_P2739683 9.79513995
A_51_P211903 10.10437166
A_51_P226429 8.006856785
A_55_P2737159 12.00801214
A_55_P2728466 7.596848415
A_55_P2101526 7.953701784
A_52_P1132414 5.677389766
A_66_P135936 15.96071364
A_55_P2805396 8.647358845
A_55_P2717104 6.849853802
A_55_P2909714 12.73929643
A_55_P2744310 7.756660669
A_52_P83363 6.003032687
A_55_P2091691 12.00305517
A_66_P106200 6.959299779
A_66_P137157 13.4645119
A_51_P389543 6.664729183
A_55_P2084656 14.87293445

Total number of rows: 31532

Table truncated, full table size 783 Kbytes.




Supplementary file Size Download File type/resource
GSM2702094_US10463851_257480911443_S01_GE1_1010_Sep10_1_2.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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