Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation

ABSTRACT: We present high quality deep read-depth single cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. All cell types include genes with high variability in expression, in a tissue-specific manner. We also find evidence that single cell variability of neuronal genes in mice is correlated with that in rats consistent with the hypothesis that levels of variation may be conserved. From an initial 143 cells we identified 107 high quality samples with deep genic coverage, including 13 brown adipocytes, 19 cardiomyocytes, 19 cortical pyramidal neurons and 18 hippocampal pyramidal neurons from embryonic mouse, 8 cortical pyramidal neurons and 8 hippocampal pyramidal neurons from embryonic rat, and 22 serotonergic neurons from adult mouse. While mouse data is collected from three strains of mice at different ages, each cell type dataset is internally consistent. There are no technical replicates of single-cell samples. We additionally prepared 30 control samples, amplifications of bulk total cardiomyocyte RNA diluted to single cell quantities.

ORGANISM(S): Mus musculus

SUBMITTER: Junhyong Kim

PROVIDER: E-GEOD-56638 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Five allotetraploid cotton species have adapted, through their transcriptional responses, to unique environments with distinct levels of inherent abiotic stresses. The transcriptional responses of leaf and root tissue in five allotetraploid cotton species (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii) under salt stress have been investigated in this study using cotton long oligonucleotide microarrays. Physiological responses to salinity such as stomatal conductance, ion and osmoprotectant contents were also measured as indicators of imposed stress. Accessions from these five cotton species were hydroponically grown and gradually introduced to a NaCl treatment (15 dS m-1). The microarray results identified 2721 and 2460 differentially expressed genes under salt stress that were significant in leaf and root tissue, respectively. Many of these genes were classified under gene ontology (GO) categories that suggest abiotic stress. These allotetraploid cottons shared transcriptional responses to salinity, but also showed responses that were species-specific. No consistent differences in transcriptional response among the previously estimated phylogenetic branches were found. Stomatal conductance, ion accumulation, and betaine, trigonelline, and trehalose contents also indicated salt stress. This global assessment of transcriptional and physiological responses to salt stress of these cotton species may identify possible gene targets for crop improvement and evolutionary studies of cotton. Keywords: CEGC Cotton oligo salt stress The transcriptional responses of leaf and root tissue in five allotetraploid cotton species (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii) under salt stress have been investigated in this study using cotton long oligonucleotide microarrays. Physiological responses to salinity such as stomatal conductance, ion and osmoprotectant contents were also measured as indicators of imposed stress. Accessions from these five cotton species were hydroponically grown and gradually introduced to a NaCl treatment (15 dS m-1).

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Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation

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