Dataset Information

Analysis of cutaneous MRGPRD free nerve endings and C-LTMRs transcriptomes by RNA-sequencing.

ABSTRACT: The skin is the largest sensory organ that is densely innervated by highly specialized sensory neurons allowing the detection of a wide range of stimulations including light touch, temperature, itch and pain. Our knowledge of the sets of genes instructing the functional specialization of sensory neurons is just emerging. In a previous study, we have identified a new G?i inhibitory interacting protein (GINIP) that marks two distinct subsets of skin-innervating sensory neurons conveying noxious and pleasant touch: the MRGPRD-expressing C-fibers specialized in noxious touch and the TH(+)/TAFA4(+)/V-GLUT3(+) C-Low Threshold MechanoReceptors (C-LTMRs), part of neurons processing pleasant touch. In the recent study published by Reynders et al. (2015), we took advantage of GINIP(mCherry) mouse model in combination with Isolectin B4 (IB4) cell surface labeling and fluorescence activated cell sorting (FACS). We successfully purified MRGPRD(+), C-LTMRs and a heterogeneous population of sensory neurons and subjected their RNA contents RNA-deep sequencing (RNA-seq). The subsequent RNA-seq experiment led to the generation of unique sets of data representative of pure transcriptome profiles of each subset. As a result of this pioneering approach, we established the combinatorial expression of the sets of genes that could dictate the functional specializations of MRGPRD(+) neurons and C-LTMRs. Herein we provide details regarding the experimental design, the quality controls and statistical analysis of the data deposited at Gene Expression Omnibus under the accession number GSE64091.

SUBMITTER: Reynders A

PROVIDER: S-EPMC4583636 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Analysis of cutaneous MRGPRD free nerve endings and C-LTMRs transcriptomes by RNA-sequencing.

Reynders Ana A Moqrich Aziz A

Genomics data 20150530

The skin is the largest sensory organ that is densely innervated by highly specialized sensory neurons allowing the detection of a wide range of stimulations including light touch, temperature, itch and pain. Our knowledge of the sets of genes instructing the functional specialization of sensory neurons is just emerging. In a previous study, we have identified a new Gαi inhibitory interacting protein (GINIP) that marks two distinct subsets of skin-innervating sensory neurons conveying noxious an ...[more]

PMID: 26484241

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Project description:BackgroundOrgan-specific gene expression contains rich information about in vivo biological processes. This kind of information, previously gathered through microarray profiling, has been proven fruitful to the understanding of specific mutants, regulatory events, signaling, and development. With the advent of the next-generation sequencing (NGS) of RNAs, more quantitative and detailed information of gene expressions than previously available can now be collected for each organ or organ developmental stages. The combination of an object-oriented experimental design and an efficient treatment of the high volume information generated through a NGS platform may offer a powerful tool for inferring previously intractable developmental processes.ResultsWe collected transcriptomic data over a Solexa/Illumina platform on samples of Ipomoea leaf, sepal, and petals (at three developmental stages), and presented a method for analyzing transcriptomic variations within and between organs. We demonstrated that in vivo signals of transcriptomes can be retrieved de novo through the NGS techniques, proper data handling, bioinformatic tools, and the current understanding of molecular networks. We found that numbers of transcribed genes from both nuclear and chloroplast genomes decreased by the same order of leaf → sepal →petal. Petal resembled leaf in cell division patterns and abundance level of commonly expressed organelle genes. Its chloroplast transcripts constituted a subset of those in leaf. Moreover, reconstructions of multiple metabolic networks for each organ enabled inferences of substance flow, providing transcript evidence for the path of sucrose in leaf to anthocyanin synthesis in petal.ConclusionOur results attest that developmental transcriptomes are highly informative for exploring connections between morphological traits and the associated molecular networks. Significant hypotheses have been developed, including that the petal is a derived organ of leaf and that its color can be modified by fluctuations of substance flow within the associated metabolic networks among organs.

Dataset Information

Analysis of cutaneous MRGPRD free nerve endings and C-LTMRs transcriptomes by RNA-sequencing.

Publications

Analysis of cutaneous MRGPRD free nerve endings and C-LTMRs transcriptomes by RNA-sequencing.

Similar Datasets

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