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Pre-Collaborative Cross lung gene expression after allergen challenge

ABSTRACT: The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. These mice were initially described in the following reference. Genome Research 2011 Aug;21(8):1213-22 (PMID: 21406540). The goal of this specific project was to identify gene expression QTL using lung tissue from pre-CC mice that were sensitized and challenged with house dust mite allergen (namely, Der p 1).

ORGANISM(S): Mus musculus

PROVIDER: GSE51768 | GEO | 2013/11/15

SECONDARY ACCESSION(S): PRJNA225021

REPOSITORIES: GEO

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Pre-Collaborative Cross lung gene expression after allergen challenge

Project description:The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. These mice were initially described in the following reference. Genome Research 2011 Aug;21(8):1213-22 (PMID: 21406540). The goal of this specific project was to identify gene expression QTL using lung tissue from pre-CC mice that were sensitized and challenged with house dust mite allergen (namely, Der p 1). We analyzed whole lung RNAs from 138 pre-Collaborative Cross mice using Illumina WG6v2 arrays. Pre-Collaborative Cross (CC) mice are partially inbred strains created by intercrossing eight founder (parental) strains: 129S1/SvImJ, (129S1), A/J (AJ), C57BL/6J (B6), CAST/Ei (CAST), NOD/LtJ (NOD), NZO/H1LtJ (NZO), PWK/Ph (PWK), and WSB/Ei (WSB). Sister-brother mating in 220 families was done for 5-12 generations. One animal was sampled from 138 unique pre-CC strains, each designated by the prefix OR which denotes Oak Ridge National Laboratory as the original source of these mice. The parental strains are not part of this submission. Hybridizations were performed at the National Human Genome Research InstituteM-bM-^@M-^Ys Gene Expression Core Facility.The resulting data were initially processed using Illumina Genome Studio software and then imported into R (v2.9.2) for post-processing. Normalization was conducted using RMA with quantile normalization and log2 transformation.

2013-11-15 | E-GEOD-51768 | biostudies-arrayexpress

Pre-Collaborative Cross liver gene expression

2010-12-01 | GSE22297 | GEO

Pre-Collaborative Cross liver gene expression

Project description:The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. The genetic profile of these emerging lines reveals high diversity, balanced allele frequencies, and well-distributed recombination – all ideal qualities for a mapping panel. We have mapped white spot, a discrete trait; body weight, a highly polygenic complex trait; and more than 11,000 liver gene expression traits. These analyses provide a glimpse of the potential mapping power and resolution of the CC. The goal of this project was to identify eQTLs for genome-wide gene expression from liver tissue in pre-CC mice. Gene expression profiling from liver tissue from pre-CC males. Pre-Collaborative Cross (CC) mice are partially inbred strains created by intercrossing eight founder (parental) strains: 129S1/SvImJ, (129S1), A/J (AJ), C57BL/6J (B6), CAST/Ei (CAST), NOD/LtJ (NOD), NZO/H1LtJ (NZO), PWK/Ph (PWK), and WSB/Ei (WSB). Sister-brother mating in 220 families was done for 4-11 generations. One animal was sampled from 157 pre-CC strain. Hybridizations were performed at the Gene Expression Core Facility at The Jackson Laboratory. Samples were divided in six batches of about 11 to 24 samples. Two batches were performed per day. Probe-level data was summarized by a custom CDF file based on Ensembl genes (NCBI 37, Ensembl 49; htttp://brainarray.mbni.med.umich.edu). The parental strains are not part of this submission.

2010-12-01 | E-GEOD-22297 | biostudies-arrayexpress

Collaborative Cross founder strain lung miRNA expression after allergen challenge

2015-03-01 | GSE63954 | GEO

Collaborative Cross founder strain lung miRNA expression after allergen challenge

Project description:The goal of this project was to identify strain-dependent expression of miRNAs in lung tissue from Collaborative Cross founder strains that were sensitized and challenged with house dust mite allergen (Der p 1). We analyzed whole lung RNAs from the eight Collaborative Cross founder strains (n=4/strain, all males) using Affymetrix miRNA 2.0 arrays

2015-03-01 | E-GEOD-63954 | biostudies-arrayexpress

RNA-seq on periodontal tisuues of susceptible and resistant collaborative cross mice after periodontal infection

Project description:We assessed alveolar bone changes of Collaborative cross (CC) lines in response to a mixed oral infection with a well-known periodontal pathogen. The CC lines showed significant variation in their response to the mixed infection. We then carried out RNA-seq analysis on periodontal tisuues of resistant CC lines, susceptible CC lines and two CC lines that showed bone formation after oral bacterial infection.

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Transcriptomic Profiling of Collaborative Cross Founder Mouse Embryonic Fibroblasts stimulated with IFN-g and IL28

Project description:Collaborative Cross (CC) mouse embryonic fibroblasts (MEF) cells obtained from the eight Founder animals [PWK/PhJ, NZO/HILtJ, NOD/ShiLtJ, WSB/EiJ, A/J, CAST, C57BL/6J, and 129/SvlmJ] were immortalized and the cell lines used to assess differences in transcriptional responses following treatment with mouse recombinant IFNg and IL28. We collected transcriptome profiles for 8 CC MEF cell lines stimulated with either IFNg or IL28 for a total of 16 different biological conditions. Treated and mock samples were collected at 18 hr post-treatment and RNAs extracted and subjected to microarray.

2016-05-26 | E-MTAB-4690 | biostudies-arrayexpress

Influenza H3N2 infection of the Collaborative Cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice (lung)

Project description:To determine if genetic background can modulate severity of an infection, we studied the host responses to influenza infections in the eight genetically highly diverse Collaborative Cross (CC) founder mice.

2015-12-31 | GSE74074 | GEO

Influenza H3N2 infection of the Collaborative Cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice (blood)

2015-12-31 | GSE74073 | GEO

Additional Collaborative Cross Genomes

Project description:Whole genome sequencing and progress towards full inbreeding of the mouse Collaborative Cross population

| PRJEB31495 | ENA