Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ChIP-seq of H3K4me1, me2 and me3 on mouse salivary gland cancer cells cultured in either adherent or non-adherent conditions

ABSTRACT: Investigating how the Wnt-driven Mll1 epigenome regulates salivary gland and head and neck cancer. We performed mRNA-seq and ChIP-seq of H3K4me1, me2 and me3 on mouse salivary gland cancer cells that are kept in two different growth conditions, adherent culture and non-adherent sphere culture. Mouse salivary gland cancer cells were isolated from salivary gland of transgenic mouse that harbor K14-Cre-induced Wnt/β-catenin gain-of-function and Bmpr1a loss-of-function mutations. Anti-H3K4me1 (C15410194), -me2 (C15410035) and -me3 (C15410003-50) antibodies were purchased from Diagenode. ChIP-seq was performed according to the protocols provided by Diagenode using the iDeal ChIP-seq kit for histones and the iDeal library preparation kit. For mRNA-seq, mRNA was extracted according to the standard TRIzol protocol (Invitrogen) and subjected to library preparation using the TruSeq stranded mRNA library preparation kit. Sequencing was performed with the TruSeq SBS Kit v3-HS (2 X 200 cycles) on an Illumina HiSeq 2000 sequencer.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Ramon Oliveira Vidal

PROVIDER: E-MTAB-7514 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In addressing R. microplus - A. marginale interactions, we propose and test three linked hypotheses. The first is that the tick gene response is organ specific: the midgut gene regulation is unique during feeding and during acquisition of A. marginale as compared to the salivary gland. This distinction is relevant as the two organs serve very different roles in the transmission biology of A. marginale with early survival and replication within the midgut epithelium, composed of highly phagocytic cells, required for initial colonization while a second round of replication in the salivary gland acini, composed of highly secretory cells, is required for transmission of an infectious dose in the saliva. Importantly, both the midgut epithelium and salivary glands have been identified as separate and distinct barriers for transmission of A. marginale and thus represent two potential sites where transmission could be blocked. The second hypothesis to be tested is that the salivary gland transcriptome is temporally dynamic. Initiation of tick attachment and feeding involves secretion of a virtual pharmacopeia including lytic enzymes, anticoagulants, and inhibitors of the mammalian innate immune and nocioceptive systems. Concomitantly, the acini provide an environment where A. marginale replicates >100 fold and are secreted into the saliva. Prior studies show that duration of feeding is a critical component of transmission efficiency, with increased efficiency positively correlated with time of tick feeding. The third hypothesis to be tested is that A. marginale colonization does not significantly modulate the tick midgut and salivary gland transcriptome. This hypothesis is based on observations by ourselves and others that tick infection does not impart a significant fitness cost on the vector. This is in contrast to other bacterial and protozoal pathogens that have dramatic effects on success of tick attachment, engorgement, and survival. A. marginale, similar to other tick-borne pathogens in the Family Anaplasmataceeae, is believed to have evolved from an arthropod-specific bacterium with relatively late adaptation to specific niches in mammalian hosts. Consequently, we predict that A. marginale is well adapted to its tick vector and utilizes the normal signaling pathways of the feeding tick with few, if any, effects on the midgut and salivary gland transcriptome. In this manuscript, we report the testing of these three hypotheses and present the results in context of the vector-pathogen-mammalian host interaction at the time of transmission. A Roche NimbleGen high-density gene expression microarray was custom designed based on the expressed sequence tag (EST) database, B. microplus Gene Index Version 2 (BmiGI V2) for R. microplus. The expression level of 14,447 R. microplus genes was analyzed from total RNA extracted from 10 different tick tissue samples; 30 arrays were included since triplicates of each different sample were analyzed as follow: unfed (midgut and salivary glands), blood feeding (2 days midgut and 2, 6 and 9 days salivary glands), A. marginale-infected blood feeding (2 days midgut and 2, 6 and 9 days salivary glands).

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ChIP-seq of H3K4me1, me2 and me3 on mouse salivary gland cancer cells cultured in either adherent or non-adherent conditions

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