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Sample GSM1462543 Query DataSets for GSM1462543
Status Public on Jul 25, 2015
Title WT7_vs_WT0_rep2_dye_swap
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: non-infected wild-type
treatment: day 0
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 Wild-type mouse at day 7 (test) versus non-infected Wild-type mice replicate 2 by dye swap color (reference)
Biological replicate 2 of 2
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.
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
INV_VALUE normalized log10 cy5/cy3 ratio representing reference/test

Data table
ID_REF VALUE INV_VALUE
A_51_P100021 0.154532 -0.154531877
A_51_P100034 0.155486 -0.15548648
A_51_P100052 0.291322 -0.291322089
A_51_P100063 -0.842718 0.842717778
A_51_P100084 -0.32532 0.32532022
A_51_P100099 -0.0748546 0.074854596
A_51_P100155 0.12177 -0.12176977
A_51_P100174 0.477697 -0.47769658
A_51_P100181 -0.069229 0.069228978
A_51_P100218 -0.127342 0.127341676
A_51_P100227 0.537662 -0.537662234
A_51_P100238 -0.524521 0.524521035
A_51_P100246 0.278095 -0.278094663
A_51_P100289 -0.666567 0.666566994
A_51_P100298 0.313221 -0.313221468
A_51_P100309 0.416008 -0.416008059
A_51_P100327 1.31048 -1.310479383
A_51_P100347 -0.0868364 0.08683643
A_51_P100379 0.141542 -0.141542465
A_51_P100428 0.230775 -0.230775253

Total number of rows: 41174

Table truncated, full table size 1401 Kbytes.




Supplementary file Size Download File type/resource
GSM1462543_20-B5-vs-E3_b4.txt.gz 11.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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