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Sample GSM1462533 Query DataSets for GSM1462533
Status Public on Jul 25, 2015
Title M7_vs_M0_rep2_dye_swap
Sample type RNA
 
Channel 1
Source name caecum
Organism Mus musculus
Characteristics tissue: caecum
strain: C57BL6J
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 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 Nlrp12-/-
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 Nlrp12-deficient C57BL6J mouse at day 7 (test) versus non-infected Nlrp12-deficient 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 -0.159336 0.15933586
A_51_P100034 0.204 -0.204000302
A_51_P100052 1.10053 -1.100529632
A_51_P100063 -0.328974 0.328974393
A_51_P100084 -0.37497 0.37497
A_51_P100099 -0.380706 0.380706168
A_51_P100155 0.0556241 -0.05562412
A_51_P100174 0.455136 -0.45513601
A_51_P100181 0.144706 -0.144705759
A_51_P100218 0.0866372 -0.086637214
A_51_P100227 0.431736 -0.431736143
A_51_P100238 0.339606 -0.339605591
A_51_P100246 0.479023 -0.479023217
A_51_P100289 -0.112361 0.112360852
A_51_P100298 0.381925 -0.381925415
A_51_P100309 0.556206 -0.556205751
A_51_P100327 1.48012 -1.480122114
A_51_P100347 0.386601 -0.386601292
A_51_P100379 0.138066 -0.13806591
A_51_P100428 0.0131672 -0.013167221

Total number of rows: 41174

Table truncated, full table size 1400 Kbytes.




Supplementary file Size Download File type/resource
GSM1462533_10-H5-vs-K3_b4.txt.gz 11.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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