Ontology highlight
ABSTRACT:
PROVIDER: PRJNA814427 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18286485.fastq.gz | Fastqsanger.gz | |||
| SRR18286486.fastq.gz | Fastqsanger.gz | |||
| SRR18286487.fastq.gz | Fastqsanger.gz | |||
| SRR18286488.fastq.gz | Fastqsanger.gz | |||
| SRR18286489.fastq.gz | Fastqsanger.gz |
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Phenotyping, stability and functional analyses for iTregs induced under these conditions are available in Schmidt A et al., PLoSONE 2016, PMID: 26886923). In the publication associated to this dataset, the time-course proteomic profiling during human Treg differentiation is presented and integrated with RNA-Seq data from the same cells (including additional iTreg culture conditions and 2h time points for RNA-Seq). The data underwent clustering, network analysis and disease enrichment, which revealed many known regulators of Tregs along with novel candidate genes putatively involved in FOXP3 induction, the biological importance of which was validated with a targeted shRNA screen.
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Project description:<p>RNA sequencing (RNAseq) of peripheral blood lymphocytes was used to develop a means to assess immune function in a way that can be used in discovery science and applied to patients individually in clinical settings. The premise is that profiles of RNA present in immune cells is reflective of the combined influence of genetic and environmental variation on immune potential of individuals and that this potential can be tapped to understand human immunity in a variety of biological contexts. CD4+ cells were isolated from fresh whole blood via positive magnetic bead selection and cell lysates were prepared using Qiazol (QIAGEN) and stored at -80ºC for 3 to 8 months. RNA was extracted in batches for cDNA library preparation and RNA-Seq. For this study, we developed standard operating procedures for handling human blood samples and determined: a) the best way to enrich for CD4+ T cells from whole blood and yield high quality RNA, b) the sensitivity of this RNA profiling strategy, and c) the reproducibility of generated immune profiles from healthy subjects. We then developed bioinformatics processes to establish immune response signatures and immune response phenotypes within cohorts of individuals.</p>
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