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Series GSE11 Query DataSets for GSE11
Status Public on Nov 21, 2001
Title NOD model of type 1 diabetes
Organism Mus musculus
Experiment type Expression profiling by array
Summary We used high density oligonucleotide arrays to measure the relative expression levels of >39,000 genes and ESTs in the NOD mouse (a murine model of T1D and other autoimmune conditions), four NOD-derived diabetes resistant congenic strains and two nondiabetic control strains. Owing to the importance of T cells in the development of T1D we decided to target two organs, the spleen and thymus. We profiled gene expression in thymi from four week old female mice and spleens from three month old female mice. For each of the 14 strain-tissue combinations (7 strains x 2 tissues) we performed two independent replicate experiments, making the total number of hybridizations performed 28. In each case, an RNA population from a pool of two or three organs was generated to minimize the chances of within strain variation masking genuine variation between the strains. To minimize any variation introduced during target preparation, all samples within a given replicate group were processed in parallel. Three samples from group two (spleen: B10.H2g7_S2 http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/query/acc.cgi?acc=gsm594 (GSM594); thymus: B10.H2g7_T2 http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/query/acc.cgi?acc=gsm608 (GSM608), B10.H2g7 Idd3_T2 http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/query/acc.cgi?acc=gsm609 (GSM609)) and one from group one (spleen B10.H2g7_S1 http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/query/acc.cgi?acc=gsm587 (GSM587) failed a preliminary quality control check. Consequently, the steps involved in preparing labelled cRNA from the initial starting material had to be repeated for these four samples at a later date. A subsequent comparison of the variation seen between samples within the same replicate group (samples processed in parallel) versus samples in distinct replicate groups (samples processed at different times) revealed that the variation between the two groups (i.e. owing to independent sample preparation) was higher than the small amount of variation between the closely matched strains. Ignoring the variability introduced during sample preparation was therefore likely to result in spurious changes being detected and genuine strain-specific differences in gene expression being masked. Consequently, we decided to exclude the four samples that had had to be prepared independently owing to failing initial quality control.
Keywords = NOD, diabetes, congenic
Keywords: other
 
Web link http://www-gene.cimr.cam.ac.uk/todd/
 
Contributor(s) Eaves IA, Wicker LS, Ghandour G, Lyons PA, Peterson LB, Todd JA, Glynne RJ
Citation(s) 11827943
Submission date Nov 19, 2001
Last update date Feb 23, 2012
Contact name Iain Eaves
E-mail(s) iain@gene.cimr.cam.ac.uk
Phone ++44 (0)1223 762105
Fax ++44 (0)1223 762102
URL http://www-gene.cimr.cam.ac.uk/todd/
Organization name Cambridge Institute for Medical Research
Department Medical genetics
Lab JDRF/WT Diabetes and Inflammation Laboratory
Street address Hills Road
City Cambridge
ZIP/Postal code CB2 2XY
Country United Kingdom
 
Platforms (1)
GPL24 EOSS002A
Samples (28)
GSM582 NOD_S1
GSM583 Idd3_S1
GSM584 Idd5_S1
Relations
BioProject PRJNA84479

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