tempo-seq human whole transcriptome v2.1 kit  (BioSpyder Technologies)

Journal: Toxicological Sciences

Article Title: In vitro transcriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals

doi: 10.1093/toxsci/kfac127

Figure Lengend Snippet: Comparison of estrogen receptor alpha (ERα) bioactivity and transcriptomic points of departure (tPODs) derived from the whole transcriptome analysis in MCF-7 cells ( n = 3–4 per concentration) exposed to bisphenol A and 15 alternative chemicals at a range of concentrations (0.0005–100 µM) for 48 h. ERα prediction is based on at least one concentration yielding an agonist or antagonist call. For tPOD derivation, data were prefiltered using the Williams trend test ( p ≤ .05) and a fold-change of ≥1.5 or ≤1.5. Data were also postfiltered with the following settings in BMDExpress v2.3: Best BMD/BMDL <20, Best BMDU/BMD <20, Best BMDU/BMDL <40, and Best fitPvalue >.1. tPODs representing the 25th rank ordered gene benchmark concentration (BMC) (shown in µM), the median gene BMC for the lowest pathway (at least 3 genes and 5% of pathway) as well as the median gene BMC for the ERα biomarker gene set are shown in the table and in the top panel. The chemicals are shown in decreasing order of potency based on tPODS from the 25th gene BMC.

Article Snippet: Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.0 kit (BioSpyder Technologies Inc, Carlsbad, California) as per manufacturer’s instructions and previously described ( Yeakley et al. , 2017 ).

Techniques: Comparison, Derivative Assay, Concentration Assay, Biomarker Discovery

Journal: Toxicological Sciences

Article Title: In vitro transcriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals

doi: 10.1093/toxsci/kfac127

Figure Lengend Snippet: Comparison of ERα bioactivity and tPODs derived from the whole transcriptome analysis in MCF-7 cells ( n = 3–4 per concentration) exposed to BPA and 15 alternative chemicals at a range of concentrations (0.0005–100 μM) for 48 h. ERα prediction is based on at least one concentration yielding an agonist or antagonist call. For tPOD derivation, data were prefiltered using the Williams trend test ( p ≤ .05) and a fold-change of ≥1.5 or ≤1.5. Data were also post-filtered with the following settings in BMDExpress v2.3: Best BMD/BMDL <20, Best BMDU/BMD <20, Best BMDU/BMDL <40, and Best fitPvalue >.1. tPODs representing the 25th rank ordered gene BMC (shown in μM), the median gene BMC for the lowest pathway (at least 3 genes and 5% of pathway) as well as the median gene BMC for the ERα biomarker gene set are shown in the table and in the top panel. The chemicals are shown in decreasing order of potency based on tPODS from the 25th gene BMC. 25th gene, ERα biomarker, lowest median pathway.

Article Snippet: Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.0 kit (BioSpyder Technologies Inc, Carlsbad, California) as per manufacturer’s instructions and previously described ( Yeakley et al. , 2017 ).

Techniques: Comparison, Derivative Assay, Concentration Assay, Biomarker Discovery

Journal: Archives of toxicology

Article Title: Development and Validation of the TGx-HDACi Transcriptomic Biomarker to Detect Histone Deacetylase Inhibitors in Human TK6 Cells

doi: 10.1007/s00204-021-03014-2

Figure Lengend Snippet: Quantitative RT-PCR measurements of the three HDACi indicator genes, RGL1, NEU1, and GPR183 A: The concentration-response of the three indicator genes in TK6 cells exposed to scriptaid, a reference HDACi, for 4 hours. The bars represent the averaged fold change of two technical replicates normalized to the vehicle control. Fifty µM was selected for whole transcriptome profiling. The expression profiles of all tested compounds are included in Supplementary Fig. S1 B: The fold changes in the three indicator genes measured in TK6 cells exposed to HDACi at the concentrations selected for whole transcriptome profiling.

Article Snippet: Two 96-sample TempO-Seq Human Whole Transcriptome Assay kits (BioSpyder, Carlsbad, CA) were used to generate sequencing libraries using total RNA from TK6 cells following the manufacturer’s protocols ( Yeakley et al. 2017 ).

Techniques: Quantitative RT-PCR, Concentration Assay, Control, Expressing

Journal: Archives of toxicology

Article Title: Development and Validation of the TGx-HDACi Transcriptomic Biomarker to Detect Histone Deacetylase Inhibitors in Human TK6 Cells

doi: 10.1007/s00204-021-03014-2

Figure Lengend Snippet: Heatmap of the TGx-HDACi biomarker genes in TK6 cells exposed to the reference (A) or validation (B) compounds for 4 hours. The gene expression profiles have been averaged across three replicates, except for Tac, Pra, and MTX (n=2). The biomarker genes are on the Y-axis and the chemicals are on the X-axis. Red indicates gene up-regulation and green indicates gene down-regulation in the heat maps. The bars above the heat maps show the class of the chemical and the prediction made by the biomarker in the probability analysis – HDACi in red and non-HDACi in blue.

Article Snippet: Two 96-sample TempO-Seq Human Whole Transcriptome Assay kits (BioSpyder, Carlsbad, CA) were used to generate sequencing libraries using total RNA from TK6 cells following the manufacturer’s protocols ( Yeakley et al. 2017 ).

Techniques: Biomarker Discovery, Gene Expression