Unknown,Transcriptomics,Genomics,Proteomics

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T cell receptors repertoire sequencing of the human CD8+ naive subsets (CXCR3-,CXCR3+)

ABSTRACT: The presented data corresponds to the analysis of two discrete subsets of human CD8+ naive T cells, defined by positive and negative expression of the chemokine receptor CXCR3 (TNR3-, TNR3+). In this study we demonstrated that these subsets have different potential to generate fully-differentiated effector T cells following antigen-specific stimulation. The performed systematic immune repertoire analysis (T cell receptor beta chain (TRB)) of the sorted cell subsets revealed diverse physico-chemical properties of TRB CDR3 sequences suggesting enhanced TCR self-reactivity in human TNR3+ cells. In total, we analyzed 74 samples (from 11 patients, 3 replicates of each cell subset (excluding one missing replicate) and additionally for 3 patients CD8+ memory T cells in 3 replicates). We used the Human TCR Profiling Kit (MiLaboratory LLC) for sequencing libraries preparation and Illumina NextSeq 550 sequencing (150+150bp) followed by the demultiplexing procedure using MIGEC software (https://github.com/mikessh/migec).

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Homo sapiens

SUBMITTER: Alexey Davydov

PROVIDER: E-MTAB-7638 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Triclocarban (TCC) is a widely used antimicrobial agent that is routinely detected in surface waters. The present study was designed to examine TCC’s efficacy and mode of action as a reproductive toxicant in fish. Reproductively mature Pimephales promelas were continuously exposed to either 1 or 5 μg TCC/L, 0.5 μg 17β-trenbolone (TRB)/L or a mixture (MIX) of 5 μg TCC and 0.5 μg TRB/L for 22 d and a variety of reproductive and endocrine-related endpoints were examined. The data were evaluated to answer several key questions: first, whether exposure to TCC could be linked with an ecologically-relevant adverse outcome, i.e., impaired reproduction; second, whether the present study provided additional support for augmentation of androgen action as an endocrine-disrupting mode of action for TCC; and third, whether there were any novel and/or plausible linkages between changes in the ovarian transcriptome and the apical responses observed in females that could support adverse outcome pathway development and/or further hypothesis-driven testing. Fathead minnows were randomly paired (one male, one female) and placed in tanks at a density of two pairs per tank with six replicate tanks per treatment. Pairs were separated by a water permeable mesh divider and each pair had its own breeding substrate. The fish were held in the test system, receiving UV-treated, filtered Lake Superior (control) water only, for a 21 d acclimation period during which the fecundity and fertility of each pair were assessed daily. After 21 d, exposures were initiated with pairs that had spawned successfully during acclimation. Fish were exposed continuously to target test concentrations of 0 (Lake Superior control), TCC (1 and 5 µg/L), TRB (0.5 μg/L), or a mixture of the two chemicals (5 μg TCC and 0.5 μg TRB/L) for 22 d. Water concentrations of TCC and TRB were determined in stock solutions and all exposure tanks every two to three days. General water quality characteristics (mean ± SD) measured regularly over the course of the Experiment were: temperature, 24.8 ± 0.7 oC; pH, 7.87 ± 0.04; dissolved oxygen, 6.8 ± 0.35 mg/L. Ovary RNA samples from twenty four fish (n=5 for all treatments except TRB alone; n=4) were selected for microarray analysis.

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T cell receptors repertoire sequencing of the human CD8+ naive subsets (CXCR3-,CXCR3+)

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