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Sample GSM1462525 Query DataSets for GSM1462525
Status Public on Jul 25, 2015
Title M0_vs_WT0_rep1_dye_swap
Sample type RNA
 
Channel 1
Source name caecum
Organism Mus musculus
Characteristics tissue: caecum
strain: C57BL6J
genotype: 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 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 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 Nlrp12-deficient C57BL6J mouse at day 0 (test) versus Wild-type mouse at day 0 both infected by Citrobacter rodentium replicate 1 by dye swap color (reference)
Biological replicate 1 of 3
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 -0.491692 0.491691589
A_51_P100034 -0.114257 0.114257018
A_51_P100052 0.0788149 -0.078814927
A_51_P100063 -0.529893 0.529892569
A_51_P100084 -0.00873259 0.008732595
A_51_P100099 0.0966243 -0.096624342
A_51_P100155 0.10693 -0.106930356
A_51_P100174 0.146231 -0.146231099
A_51_P100181 0.533669 -0.533669289
A_51_P100218 0.702658 -0.702657974
A_51_P100227 0.690404 -0.690403805
A_51_P100238 -0.132019 0.132018965
A_51_P100246 0.431544 -0.431544166
A_51_P100289 -0.396429 0.396428957
A_51_P100298 -0.0804685 0.080468483
A_51_P100309 0.719101 -0.719100964
A_51_P100327 0.178944 -0.178943835
A_51_P100347 0.232662 -0.232662347
A_51_P100379 -0.003606 0.003605997
A_51_P100428 -0.662497 0.662497012

Total number of rows: 41174

Table truncated, full table size 1404 Kbytes.




Supplementary file Size Download File type/resource
GSM1462525_02-A5-vs-G3_b2.txt.gz 11.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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