Unknown,Transcriptomics,Genomics,Proteomics

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RNA sequencing of primary Naive CD4+ T cells and Activated Naive CD4+ T cells

ABSTRACT: RNA sequencing of the chromatin associated RNA and nucleoplasm associated RNA of Naive CD4+ T cells to identify novel chromatin associated RNAs containing TEs. RNA sequencing of Naive CD4+ T cells or Activated Naive CD4+ T cells treated with Scr or LINE1 antisense oligonucleotides (ASO).

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Beatrice Bodega

PROVIDER: E-MTAB-9574 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Naive CD4+ T cells are the common precursors of multiple effector and memory T cell subsets and possess a high plasticity in terms of differentiation potential. This stem-cell like character is important for cell therapies aiming at regeneration of specific immunity. Cell surface proteins are crucial for recognition and response to signals mediated by other cells or environmental changes. Knowledge of cell surface proteins of human naive CD4+ T cells and their changes during the early phase of T cell activation is urgently needed for a guided differentiation of naive T cells and may support the selection of pluripotent cells for cell therapy.<br>Periodate oxidation and aniline-catalyzed oxime ligation (PAL) technology was applied with subsequent quantitative LC-MS/MS (PAL-qLC-MS/MS) to generate a dataset describing the surface proteome of human naive CD4+ T cells and to monitor dynamic changes during the early phase of activation. This led to the identification of 173 N-glycosylated surface proteins, of which 24 were previously not known to be expressed on human naive CD4+ T cells or have no defined role within T cell activation. To independently confirm the proteomic dataset and to analyse the cell surface by an alternative technique a systematic phenotypic expression analysis of surface antigens via flow cytometry was performed. This screening expanded the previous dataset, resulting in 229 surface proteins which are expressed on naive unstimulated and activated CD4+ T cells. Furthermore, we generated a surface expression atlas based on transcriptome data, experimental annotation and predicted subcellular localization, and correlated the proteomics result with this transcriptional dataset.<br>This extensive surface atlas provides an overall naive CD4+ T cell surface resource and will enable future studies aiming at a deeper understanding of mechanisms of T cell biology allowing the identification of novel immune targets usable for the development of therapeutic treatments.

Dataset Information

RNA sequencing of primary Naive CD4+ T cells and Activated Naive CD4+ T cells

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