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

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

PROVIDER: PRJNA607278 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11101625.fastq.gz	Fastqsanger.gz
	SRR11101626.fastq.gz	Fastqsanger.gz
	SRR11101627.fastq.gz	Fastqsanger.gz
	SRR11101628.fastq.gz	Fastqsanger.gz
	SRR11101629.fastq.gz	Fastqsanger.gz

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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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Collaborative Cross founder strain lung miRNA expression after allergen challenge

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Project description:To accurately identify the unique transcriptional signatures in collaborative cross mice after exposure to West Nile Virus (or mock/no virus) , RNA isolated from spleen tissue and was analyzed using the nanostring immunology panel.

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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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