Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling by array of spleen samples from male and female BWF1 lupus-prone mice to investigate sex hormone regulated genes

ABSTRACT: Goal of experiment: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference).

ORGANISM(S): Mus musculus

SUBMITTER: Melanie Gubbels

PROVIDER: E-GEOD-2336 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of candidate genes that influence sex hormone-dependent disease phenotypes in mouse lupus.

Gubbels Bupp M R MR Jørgensen T N TN Kotzin B L BL

Genes and immunity 20071129 1

Ninety percent of systemic lupus erythematosus patients are female, and gender differences in lupus susceptibility are also observed in (New Zealand Black x New Zealand White)F1 (BWF1) lupus-prone mice. We followed orchiectomized, intact male and female BWF1 mice for lupus-like disease for 1 year. A comparative gene expression analysis was then used to identify candidate genes potentially responsible for gender-dependent differences in lupus susceptibility. Seven genes encoded on the sex chromos ...[more]

PMID: 18046341

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Project description:Background: Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to identify significant breed-by-probe interactions. Results: Gene specific linear mixed models were fit to each of the log2 transformed probe intensities on these arrays, using fixed effects for breed, probe, breed-by-probe interaction, and a random effect for array. After surveying the day 25 placental transcriptome, 789 probes with a q-value â¤ 0.05 and |fold change| â¥ 2 for the breed-by-probe interaction were identified as candidates containing SFP. To address the quality of the bioinformatics approach, universal pyrosequencing assays were designed from Affymetrix exemplar sequences to independently assess polymorphisms within a subset of probes. Of those probes sampled from high-, medium-, and low-ranking categories, 20 of 27 were confirmed by pyrosequencing to contain SFPs. In most cases, the 25-mer probe sequence printed on the microarray diverged from Meishan, not occidental crosses. This analysis was used to define a set of highly reliable predicted SFPs according to their probability scores. Conclusions: By this method we detected transition and transversion single nucleotide polymorphisms, as well as insertions/deletions. These results demonstrate that this approach can identify polymorphisms between two breeds and/or lines of any species for which a short oligonucleotide array is available, and can be used to rapidly develop markers for genetic mapping and association analysis in species where high density genotyping platforms are otherwise unavailable. SNPs and INDELS discovered by this approach have been publicly deposited in NCBIâs SNP repository dbSNP. This method is an attractive bioinformatics tool for uncovering breed-by-probe interactions, for rapidly identifying expressed SNPs, for investigating potential functional correlations between gene expression and breed polymorphisms, and is robust enough to be used on any Affymetrix gene expression platform. Keywords: Transcriptional profiling of Day 25 porcine placentas 6 samples: Breed (Meishan, Occidental) Placental Tissue, Day 25

Dataset Information

Transcription profiling by array of spleen samples from male and female BWF1 lupus-prone mice to investigate sex hormone regulated genes

Publications

Identification of candidate genes that influence sex hormone-dependent disease phenotypes in mouse lupus.

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