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Sample GSM1462536 Query DataSets for GSM1462536
Status Public on Jul 25, 2015
Title M7_vs_WT7_rep2
Sample type RNA
 
Channel 1
Source name caecum
Organism Mus musculus
Characteristics tissue: caecum
strain: C57BL6J
genotype: infected wild-type
treatment: day 7
Treatment protocol Nlrp12-deficient and wild type C57BL6/J mice were infected or not with 1x10^9 colony-forming units of C. rodentium
Growth protocol RNA was isolated from the caecum of Nlrp12-deficient and wild type mice at day 0 and 7 post C. rodentium infection
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Rneasy Mini kit- Qiagen following manufacturer's instructions
Label cy3
Label protocol 500 ng of total RNA were labeled using Quick-amp labeling kit 2 colors, following manufacturer's informations
 
Channel 2
Source name caecum
Organism Mus musculus
Characteristics strain: C57BL6J
tissue: caecum
genotype: infected Nlrp12-/-
treatment: day 7
Treatment protocol Nlrp12-deficient and wild type C57BL6/J mice were infected or not with 1x10^9 colony-forming units of C. rodentium
Growth protocol RNA was isolated from the caecum of Nlrp12-deficient and wild type mice at day 0 and 7 post C. rodentium infection
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Rneasy Mini kit- Qiagen following manufacturer's instructions
Label cy5
Label protocol 500 ng of total RNA were labeled using Quick-amp labeling kit 2 colors, following manufacturer's informations
 
 
Hybridization protocol 850 ng of each linearly amplified cRNA per cyanine were cohybridized on microarrays ( Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F) using Agilent Gene Expression Hybridization Kit , and enclosed in Agilent SureHyb-enabled hybridization chambers during 17 hours at 65°C rotated at 10 rpm . After hybridization, slides were washed sequential
Scan protocol Scanned on an Innoscan 700 scanner ( Innopsys )
Images were quantified using Mapix Software (version 3.2.1).
Description C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus C rodentium infected Wild-type mouse at day 7 replicate 2 (reference)
Biological replicate 2 of 3
Data processing A specific script on R was used ( limma library ) for LOWESS normalization within slide and between slides.
 
Submission date Jul 30, 2014
Last update date Jul 25, 2015
Contact name Mathias Chamaillard
E-mail(s) mathias.chamaillard@inserm.fr
Organization name Inserm
Department Center for Infection and Immunity of Lille
Lab Nods-like receptors in infection and immunity
Street address 1, rue Prof A. Calmette
City Lille
ZIP/Postal code 59019
Country France
 
Platform ID GPL7202
Series (1)
GSE59940 The Nlrp12 inflammasome negatively regulates NOD2-mediated adjuvanticity, endotoxic shock and host defence afforded by an immunomodulatory muropeptide.

Data table header descriptions
ID_REF
VALUE normalized log10 ratio representing test/reference

Data table
ID_REF VALUE
A_51_P100021 0.082434061
A_51_P100034 0.134348546
A_51_P100052 0.048344996
A_51_P100063 -0.22283308
A_51_P100084 0.002999282
A_51_P100099 -0.12167485
A_51_P100155 0.018910028
A_51_P100174 0.398951499
A_51_P100181 0.006215902
A_51_P100218 -0.309905022
A_51_P100227 0.21003098
A_51_P100238 -0.730321442
A_51_P100246 -0.17132364
A_51_P100289 0.38884431
A_51_P100298 -0.306630457
A_51_P100309 0.149580826
A_51_P100327 0.286747837
A_51_P100347 -0.545561752
A_51_P100379 0.205661607
A_51_P100428 -0.953131091

Total number of rows: 41174

Table truncated, full table size 1019 Kbytes.




Supplementary file Size Download File type/resource
GSM1462536_13-E3-vs-K5_b1.txt.gz 11.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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