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An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes

ABSTRACT: An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes

PROVIDER: PRJEB6329 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR505201_1.fastq.gz	Fastqsanger.gz
	ERR505201_2.fastq.gz	Fastqsanger.gz
	ERR505202_1.fastq.gz	Fastqsanger.gz
	ERR505202_2.fastq.gz	Fastqsanger.gz
	ERR505203.fastq.gz	Fastqsanger.gz

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An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes

Project description:PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.

2015-05-14 | E-MTAB-2582 | biostudies-arrayexpress

An atlas of mouse CD4(+) T cell transcriptomes.

Project description:BackgroundCD4(+) T cells are key regulators of the adaptive immune system and can be divided into T helper (Th) cells and regulatory T (Treg) cells. During an immune response Th cells mature from a naive state into one of several effector subtypes that exhibit distinct functions. The transcriptional mechanisms that underlie the specific functional identity of CD4(+) T cells are not fully understood.ResultsTo assist investigations into the transcriptional identity and regulatory processes of these cells we performed mRNA-sequencing on three murine T helper subtypes (Th1, Th2 and Th17) as well as on splenic Treg cells and induced Treg (iTreg) cells. Our integrated analysis of this dataset revealed the gene expression changes associated with these related but distinct cellular identities. Each cell subtype differentially expresses a wealth of 'subtype upregulated' genes, some of which are well known whilst others promise new insights into signalling processes and transcriptional regulation. We show that hundreds of genes are regulated purely by alternative splicing to extend our knowledge of the role of post-transcriptional regulation in cell differentiation.ConclusionsThis CD4(+) transcriptome atlas provides a valuable resource for the study of CD4(+) T cell populations. To facilitate its use by others, we have made the data available in an easily accessible online resource at www.th-express.org.

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FoxP3 mRNA-seq in mouse CD4+T cells

Project description:FoxP3 mRNA-seq in mouse CD4+T cells

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CD4+ cell transcriptional profiling by RNA sequencing

Project description:<p>We use next generation sequencing to investigate the different transcriptomes of closely related CD4+ T-cells from healthy human donors to elucidate the genetic programs that underlie their specialized immune functions. Six cell types were included: Regulatory T-cells (CD25hiCD127low/neg with >95% FOXP3+ purity), regulatory T-cells activated using PMA/ionomycin, CD25-CD45RA+ ('naive' helper T-cells), CD25-CD45RO+ ('memory' helper T-cells), activated Th17 cells (>98% IL17A+ purity) and activated IL17-CD4+ T-cells (called 'ThPI'). Poly-T capture beads were used to isolate mRNA from total RNA, and fragment sizes of ~200 were sequenced from both ends on Illumina's genome analyzer. We confirm many of the canonical signature genes of T-cell populations, but also discover new genes whose expression is limited to specific CD4 T-cell lineages, including long non-coding RNAs. Additionally, we find that genes encoded at loci linked to multiple human autoimmune diseases are enriched for preferential expression upon T-cell activation, suggesting that an aberrant response to T-cell activation is fundamental to pathogenesis.</p>

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Project description:We used state of the art mass spectrometry (MS) and RNA sequencing (RNA-Seq) to provide the first integrated proteomic, phosphoproteomic and transcriptomic atlas of the animal model Mus musculu . We measured 66 murine pancreatic ductal adenocarcinoma cell lines (66 proteomes and 66 phosphoproteome) and 41 healthy tissues (41 proteomes, 41 phosphoproteome, and 29 transcriptomes). The employed MS-based and bioinformatics strategy identified >17,000 proteins and >50,000 phosphorylation sites, providing expression evidence for ~76% of the 22,437 protein-coding genes reported in UniProtKB. The RNA-Seq strategy resulted in the quantification of 21,261 unique gene that were expressed in at least one of the 29 sequenced tissue.

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Project description:Cis-regulatory atlas of primary human CD4+ T cells

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E-MTAB-2582

Project description:An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes

2015-07-29 | E-MTAB-2582 | ExpressionAtlas

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Project description:The composition of intrahepatic immune cells in primary sclerosing cholangitis (PSC) and their contribution to disease pathogenesis is widely unknown. We here generated a single-cell atlas of intrahepatic T cells in PSC, a type of immune cells that has previously been involved in the pathogenesis of PSC. This atlas provides a valuable data source to the field. Using that atlas, we identified a population of liver-resident naive-like CD4+ T cells which are expanded in livers of patients with PSC compared to healthy and other liver diseases. Trajectory inference suggest that these cells have a propensity to acquire TH17-associated effector functions. Using blood-derived cells naive CD4+ T cells we experimentally prove this propensity. Since TH17-polarized cells are considered to contribute to the development of PSC, our findings point towards a so far underestimated role of naive T cells in PSC.

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