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Unknown,Transcriptomics,Genomics,Proteomics

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Single-cell transcriptome sequencing from mouse mTECs

ABSTRACT: Promiscuous gene expression (pGE) of tissue-restricted antigens in medullary thyme ephitelial cells (mTECs) is essential for self-tolerance induction and to prevent autoimmunity. We sequenced single mTEC transcriptomes to explore gene expression heterogeneity and to discover patterns of regulation of pGE.

INSTRUMENT(S): Illumina HiSeq 2500, Illumina MiSeq

ORGANISM(S): Mus musculus

SUBMITTER: Alejandro Reyes

PROVIDER: E-MTAB-3346 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells.

Brennecke Philip P Reyes Alejandro A Pinto Sheena S Rattay Kristin K Nguyen Michelle M Küchler Rita R Huber Wolfgang W Kyewski Bruno B Steinmetz Lars M LM

Nature immunology 20150803 9

Expression of tissue-restricted self antigens (TRAs) in medullary thymic epithelial cells (mTECs) is essential for the induction of self-tolerance and prevents autoimmunity, with each TRA being expressed in only a few mTECs. How this process is regulated in single mTECs and is coordinated at the population level, such that the varied single-cell patterns add up to faithfully represent TRAs, is poorly understood. Here we used single-cell RNA sequencing and obtained evidence of numerous recurring ...[more]

PMID: 26237553

Similar Datasets

Single-cell transcriptome sequencing from mouse mTECs (additional data)

Project description:Promiscuous gene expression (pGE) of tissue-restricted antigens in medullary thyme ephitelial cells (mTECs) is essential for self-tolerance induction and to prevent autoimmunity. We sequenced single mTEC transcriptomes to explore gene expression heterogeneity and to discover patterns of regulation of pGE. This data set complements what's submitted earlier, under ArrayExpress accession E-MTAB-3346 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3346/ ).

2015-08-03 | E-MTAB-3624 | biostudies-arrayexpress

mRNA expression profile of medullary thymic epithelial cells-mTECs- of BALBc mice

Project description:The medullary thymic epithelial cells (mTECs) express virtually all autoantigens of the body. This phenomenon was then termed promiscuous gene expression (PGE). A large set of autoantigen genes (but not all) is controlled by the transcriptional modulator Autoimmune regulator (Aire) in mTECs. These autoantigens represent all tissues and organs in the thymus and it is implicated in the negative selection of autoreactive thymocytes, and consequantly preventing autoreactive autoimmune reactions and autoimmune diseases (e.g. type 1 diabetes mellitus, systemic lupus erythematosus). Thus, we are looking at gene expression in thse cells because it is very important to better understand the molecular basis of central immune tolerance to normal tissues and organs. The aim of this study is to evaluate the possible link between the expression of the transcriptional regulator Aire, the genetic background of mouse strains and the promiscuous gene expression in mTECs.

2014-04-18 | E-MEXP-3881 | biostudies-arrayexpress

Single-cell RNA sequencing of OT-I CD8+ T cells after stimulation with different affinity ligands

Project description:Activation of CD8+ T cells depends exquisitely on the affinity of the T cell receptor (TCR) for a peptide MHC (pMHC) ligand complex. Here, we activated OT-I transgenic CD8+ T cells with pure peptide and examined early activation responses by single-cell RNA-sequencing. T cells were activated with the high affinity OT-I cognate peptide (N4=SIINFEKL) for 1, 3 or 6 hours, or with reduced affinity peptides (T4=SIITFEKL and G4=SIIGFEKL) or the non-binding peptide (NP68=ASNENMDAM) for 6 hours. Cells were then sorted into 96-well plates by FACS and RNA was sequenced following an adapted Smart-Seq2 protocol.

2018-06-25 | E-MTAB-6051 | biostudies-arrayexpress

Aire secures the transcription of polycomb marked genes to complete a comprehensive program of promiscuous gene expression in the thymic epithelial cell lineage

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

2014-09-04 | E-GEOD-53111 | biostudies-arrayexpress

Single cell RNA-sequencing of murine endothelial and stromal populations at embryonic day 17 (E17)

Project description:The origin of bone marrow stromal cells (BMSCs) is not completely understood. We have identified a rare population of cells with a transcriptional profile consistent with endothelial to mesenchymal transition (Endo-MT) in human fetal development. Therefore, we hypothesized that Endo-MT contributes to bone marrow niche formation in mammals. Here, we sought to determine whether Endo-MT cells could be identified in murine bone marrow during embryonic development. We isolated bone marrow and collagenased bone fraction from long bones of 9 fetuses at embryonic day 17 (E17) and FACS purified endothelial cells and BMSCs for single cell RNA sequencing.

2021-01-21 | E-MTAB-9994 | biostudies-arrayexpress

Gene expression in thymic epithelial cells [RNA-seq]

Project description:This study set out to assay the (polyA+) transcriptomes of specific FACS sorted populations of mouse thymic epithelial cells (TEC). Two biological replicates of each of seven murine TEC populations were FACS sorted and sequenced.

2014-09-04 | E-GEOD-53110 | biostudies-arrayexpress

Whole exome sequencing analyses of human, IDH2-mutated, acute myeloid leukemia samples from patients before or during treatment with Enasidenib.

Project description:Mutations in isocitrate dehydrogenase 2 (IDH2) occur in many cancers including Acute Myeloid Leukemia (AML). In preclinical models mutant IDH2 causes partial hemopoietic differentiation arrest. Recently, we showed that single agent Enasidenib, a first-in-class, selective mutant IDH2 inhibitor, produces a 40% response in relapsed/refractory AML patients by promoting differentiation. Yet, the rate, extend and duration of the clinical benefits of Enasidenib vary from one patient to another. To investigate how the genetic mutational landscape, at baseline or at relapse, contributes in modulating response to Enasidenib, WES analyses on FACS-sorted blasts from baseline, best response and/or relapse samples from 16 Enasidenib-treated patients were performed. WES analyses were also performed on the CD3+ cells from the same patients, which may be used as germinal control samples.

2018-08-13 | E-MTAB-6299 | biostudies-arrayexpress

BASIC: B-cell receptor (BCR) assembly from single cell RNA-seq

Project description:The B-cell receptor (BCR) enables individual B cells to identify diverse antigens, including bacterial and viral proteins. While advances in RNA-seq have enabled high throughput profiling of transcript expression in single cells, the unique task of assembling the full-length heavy and light chain sequences from single cell RNA-sequencing (scRNA-seq) in B cells has been largely unstudied. We developed a new software tool, BASIC, which allows investigators to use scRNA-seq for assembling BCR sequences at single cell level. To demonstrate the utility of our software, we subjected single B cells from a human donor to scRNA-seq, assembled the full-length heavy and the light chains, and experimentally confirmed these results by using single cell primer based nested PCRs and Sanger sequencing.

2016-06-02 | E-MTAB-4745 | biostudies-arrayexpress

FACS-sorted cells from Young Adults Vaccinated with Influenza TIV or LAIV Vaccines during 2008/09 Flu Season

Project description:Systems vaccinology has emerged as an interdisciplinary field that combines systems wide measurements and network and predictive modeling applied to vaccinology. Here we used the systems vaccinology approach to study the molecular mechanisms underlying the innate responses to the trivalent inactivated influenza (TIV) and live attenuated influenza (LAIV) vaccination in humans, and to identify early gene signatures that predict the magnitude of the antibody responses to influenza vaccination. During the 2008 influenza season, healthy adults were vaccinated with TIV (6 vaccinees) or LAIV (6 vaccinees), and blood samples isolated at day 0 and at day 7 post-vaccination. Cell subsets (B cells, Monocytes, mDCs and pDCs) were FACS-sorted from frozen PBMCs. Microarrays were performed using amplified total RNA.

2011-07-10 | E-GEOD-29618 | biostudies-arrayexpress

EOMES interacts with RUNX3 and BRG1 to promote innate memory cell formation through epigenetic reprogramming

Project description:Memory CD8+ T cells have the ability to provide lifelong immunity against pathogens. Although memory features generally arise after challenge with a foreign antigen, naïve CD8 single positive (SP) thymocytes may acquire phenotypic and functional characteristics of memory cells in response to cytokines such as interleukin-4. This process is associated with the induction of the T-box transcription factor Eomesodermin (EOMES). However, the underlying molecular mechanisms remain ill-defined. Using epigenomic profiling, we show that these innate memory CD8SP cells acquire only a portion of the active enhancer repertoire of conventional memory cells. This reprograming is secondary to EOMES recruitment, mostly to RUNX3-bound enhancers. Furthermore, EOMES is found within chromatin-associated complexes containing BRG1 and promotes the recruitment of this chromatin remodelling factor. Also, the in vivo acquisition of EOMES-dependent program is BRG1-dependent. In conclusion, our results support a strong epigenetic basis for the EOMES-driven establishment of CD8+ T cell innate memory program.

2019-06-06 | PXD014142 | Pride

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