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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Felix Krueger

PROVIDER: E-GEOD-74535 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity [Bisulfite-Seq]

Project description:We report scM&T-seq, a method for parallel single-cell genome-wide methylome and transcriptome sequencing, allowing discovery of associations between transcriptional and epigenetic variation. Profiling of 61 mouse embryonic stem cells confirmed known links between DNA methylation and transcription. Notably, the method reveals novel associations between heterogeneous methylation of distal regulatory elements and transcriptional heterogeneity of key pluripotency genes. E14 ES cells were grown in either serum/LIF or 2i culture conditions and separated into single cells. RNA-Seq or Bisulfite-Seq libraries were prepared. This Series includes only the Bisulfite-Seq data. The list of 61 samples that passed QC in both BS-seq and RNA-seq is included in "Supplementary Table 1" of the associated manuscript.

2015-12-24 | E-GEOD-68642 | biostudies-arrayexpress

Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity [RNA-seq]

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Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

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ATAC-seq of primary mesenchymal stem cell (MSC)-derived osteoblasts (differentiated with BMP2) from 4 human donors

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ATAC-seq of human non-tumourigenic breast epithelial cell line MCF10A

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Differential Regulation of Th17 and Th1 Cells in mouse by Glutaminase-Dependent Metabolism and Chromatin Remodeling

Project description:Activated T cells differentiate into functional subsets which require distinct metabolic programs. Glutaminase (GLS) converts glutamine to glutamate to provide substrate for the tricarboxylic acid cycle and epigenetic reactions and here we identify a key role for GLS in T cell activation and specification. Though GLS-deficiency diminished T cell activation, proliferation and impaired differentiation of Th17 cells, loss of GLS also increased Tbet and Interferon-γ expression and CD4 Th1 and CD8 CTL effector cell differentiation. These changes were mediated by differentially altered gene expression and chromatin accessibility, leading to increased sensitivity of Th1 cells to IL-2 mediated mTORC1 signaling. In vivo, GLS-null T cells failed to drive a Th17 mediated Graft-vs-Host Disease model. Transient inhibition of GLS, however, increased Th1 and CTL T cell numbers in viral and chimeric antigen receptor models. Glutamine metabolism thus has distinct roles to promote Th17 but constrain Th1 and CTL effector cell differentiation.

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