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Sample GSM1098824 Query DataSets for GSM1098824
Status Public on Dec 19, 2013
Title TCR_Low_13890596
Sample type RNA
 
Channel 1
Source name TCR_Low
Organism Sus scrofa
Characteristics animal: R_0416
group: Low
tissue: peripheral blood
sample type: test
Extracted molecule total RNA
Extraction protocol Total RNA extracted using PAXgene blood RNA Kid (Qiagen, France) following manufacturer's instructions
Label Cy3
Label protocol 5 µg ofRNA from both blood and reference samples were reverse transcribed to cDNAand fluorescent-labelled by Cy3 and Cy5, respectively, using the ChipShotTM Direct Labeling System (Promega, Charbonnieres, France). The CyDye-labelled cDNA were purified usingChipShotTMMembrane Clean-Up System (Promega, USA), and 750 ng each of Cy3-labeled and Cy5-labeled cDNA targets were combined for slide hybridization with a freshly prepared solution of 1% BSA, 2 x SSC, 0.1% SDS over 30 min at 50°C. After automatic washing according to manufacturer’sinstructions, the slides were hybridized for 17h at 60ºC.
 
Channel 2
Source name reference
Organism Sus scrofa
Characteristics reference: pooling of total RNAs from different porcine tissues
Extracted molecule total RNA
Extraction protocol Total RNA extracted using PAXgene blood RNA Kid (Qiagen, France) following manufacturer's instructions
Label Cy5
Label protocol 5 µg ofRNA from both blood and reference samples were reverse transcribed to cDNAand fluorescent-labelled by Cy3 and Cy5, respectively, using the ChipShotTM Direct Labeling System (Promega, Charbonnieres, France). The CyDye-labelled cDNA were purified usingChipShotTMMembrane Clean-Up System (Promega, USA), and 750 ng each of Cy3-labeled and Cy5-labeled cDNA targets were combined for slide hybridization with a freshly prepared solution of 1% BSA, 2 x SSC, 0.1% SDS over 30 min at 50°C. After automatic washing according to manufacturer’sinstructions, the slides were hybridized for 17h at 60ºC.
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Scan protocol Detection of the fluorescence signals was made with a laser scanner (GenePix 4000A from Axon Instruments, CA) keeping a constant PMT gain fro each channel. The images were analysed with GenePixTM Pro 6.0 software (Axon instruments, Inc., Union City, CA).
Description 13890596
Data processing All microarray analysis, including pre-processing, normalization and statistical analysis was carried out using Bioconductor packages in R programming language (version 2.14). The centring was preformed by “Lowes fitness”to take into account the intensity dependence of the fluorescence bias.
 
Submission date Mar 15, 2013
Last update date Dec 19, 2013
Contact name Nuria Mach
E-mail(s) nuria.mach@inra.jouy.fr
Organization name INRA
Department Animal Genetics and Integrative Biology (GABI)
Lab Laboratory of Animal Genetics
Street address Rue de Vilvert
City Jouy-en-Josas
State/province Ile de France
ZIP/Postal code 78350
Country France
 
Platform ID GPL7151
Series (1)
GSE45196 The peripheral blood transcriptome reflects variations in immunity traits in swine: toward identification of biomarkers
Relations
Reanalyzed by GSM1099079

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy3/Cy5) representing test/reference

Data table
ID_REF VALUE
SS00000707 -0.230410714
SS00000701 0.585127432
SS00000683 -0.404804383
SS00000677 0.855904232
SS00000375 -0.393677051
SS00000369 -0.074517586
SS00000351 -0.466335
SS00000345 -0.135554033
SS00000327 0.276524021
SS00000321 0.294226255
SS00000303 0.739736089
SS00000297 1.009657528
SSNC000006 -0.581858692
SS00004130 0.667152873
SSNC000006.2 -0.541775496
SS00004130.2 0.49354708
SSNC000006.3 -0.521989737
SS00004130.3 0.500125452
SSNC000006.4 -0.539758235
SS00004130.4 0.66761057

Total number of rows: 19200

Table truncated, full table size 447 Kbytes.




Supplementary file Size Download File type/resource
GSM1098824_13890596.gpr.gz 1.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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