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Transcriptomics analysis of heart, kidney, and liver tissues from 58 Collaborative Cross strains

ABSTRACT: Transcriptomics analysis of heart, kidney, and liver tissues from 58 Collaborative Cross strains

PROVIDER: PRJNA821207 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18520700.fastq.gz	Fastqsanger.gz
	SRR18520800.fastq.gz	Fastqsanger.gz
	SRR18520900.fastq.gz	Fastqsanger.gz
	SRR18521000.fastq.gz	Fastqsanger.gz
	SRR18521100.fastq.gz	Fastqsanger.gz

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Transcriptomics analysis of heart, kidney, and liver tissues from 58 Collaborative Cross strains

Project description:We report transcriptomic profiling from bulk heart, kidney, and liver tissues for 58 strains of the inbred mouse Collaborative Cross (CC). Each strain is represented by a male/female pair. Reads were first aligned to the pooled transcriptomes of the eight founder strains of the CC and then total gene counts were quantified using the EMASE and GBRS software tools. Total read counts can be further normalized for use in differential gene expression analysis, expression quantitative trait locus (eQTL) analysis, and integrative analyses with other -omic data sets measured on the same samples, including proteomics and phosphoproteomics.

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Project description:RNA-Seq was performed on all 8 mouse founder strains of the Collaborative Cross to obtain a comprehensive splicing landscape of each strain.

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Project description:The data was used for eQTL analysis of cecum gene expression in the Collaborative Cross Breeding Population.

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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

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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.

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

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Collaborative Cross Genomes Project

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