1x bio rad ddpcr supermix  (Bio-Rad)

Journal: medRxiv

Article Title: Circulating Tumor Cells Are Detectable and Independent of PSA and PSMA-PET Metrics in Localized High-Risk and Biochemically Recurrent Prostate Cancer

doi: 10.1101/2025.07.09.25331014

Figure Lengend Snippet: (A) Proportion of patients with detectable EpCAM expression assessed by ddPCR across the combined cohorts. (B) Distribution of EpCAM expression levels (copies/µL) in individual patients, shown for both combined and individual cohorts. The red line indicates the threshold for EpCAM positivity. (C) Frequency of EpCAM-positive cases in HR group (Cohort 1) (left panel) and BCR group (Cohort 2) (right panel).

Article Snippet: This was followed by ddPCR on the Bio-Rad QX200 Droplet Digital PCR System with standard thermal cycling parameters (50 °C for 2 min; 95 °C for 10 min followed by 40 cycles of 95 °C for 15 s and 60 °C for 1 min) in a 22 μL total reaction volume using Bio-Rad ddPCR supermix for probes and exon spanning TaqManTM assays (EpCAM Hs00158980_m; PSMA Hs00379515_m1; Life Technologies).

Techniques: Expressing

Journal: medRxiv

Article Title: Circulating Tumor Cells Are Detectable and Independent of PSA and PSMA-PET Metrics in Localized High-Risk and Biochemically Recurrent Prostate Cancer

doi: 10.1101/2025.07.09.25331014

Figure Lengend Snippet: (A) Proportion of patients with detectable PSMA expression assessed by ddPCR across the combined cohorts. (B) Distribution of PSMA expression levels (copies/µL) in individual patients, shown for both combined and individual cohorts. The red line indicates the threshold for PSMA positivity. (C) Frequency of PSMA-positive cases in HR group (Cohort 1) (left panel) and BCR group (Cohort 2) (right panel). (D) Venn diagram illustrating the distribution of EpCAM-positive, PSMA-positive, and dual EpCAM+PSMA+ patients within the ddPCR cohort.

Article Snippet: This was followed by ddPCR on the Bio-Rad QX200 Droplet Digital PCR System with standard thermal cycling parameters (50 °C for 2 min; 95 °C for 10 min followed by 40 cycles of 95 °C for 15 s and 60 °C for 1 min) in a 22 μL total reaction volume using Bio-Rad ddPCR supermix for probes and exon spanning TaqManTM assays (EpCAM Hs00158980_m; PSMA Hs00379515_m1; Life Technologies).

Techniques: Expressing

Journal: medRxiv

Article Title: Circulating Tumor Cells Are Detectable and Independent of PSA and PSMA-PET Metrics in Localized High-Risk and Biochemically Recurrent Prostate Cancer

doi: 10.1101/2025.07.09.25331014

Figure Lengend Snippet: ( A ) Comparison of EpCAM-positive CTC counts between patients with no clinical progression and those with progression in the flow group. The dotted line indicates the CTC positivity threshold (≥3). (B) Comparison of expression levels of EpCAM (measured by ddPCR) in CD45-depleted cells, between patients with no clinical progression and those with progression in the ddPCR group. (C) Comparison of expression levels of PSMA (measured by ddPCR) in CD45-depleted cells between patients with no clinical progression and those with progression in the ddPCR group

Article Snippet: This was followed by ddPCR on the Bio-Rad QX200 Droplet Digital PCR System with standard thermal cycling parameters (50 °C for 2 min; 95 °C for 10 min followed by 40 cycles of 95 °C for 15 s and 60 °C for 1 min) in a 22 μL total reaction volume using Bio-Rad ddPCR supermix for probes and exon spanning TaqManTM assays (EpCAM Hs00158980_m; PSMA Hs00379515_m1; Life Technologies).

Techniques: Comparison, Expressing

Journal: bioRxiv

Article Title: microRNA-206 is a reproducibly sensitive and specific plasma biomarker of amyotrophic lateral sclerosis

doi: 10.1101/2025.06.27.662023

Figure Lengend Snippet: A) Graphical illustration of discovery cohort project workflow. In short, samples were processed through a high-throughput NGS workflow optimized to reduce bias in biomarker discovery, and validation was performed using ddPCR. B) Residuals from a linear regression of hsa-miR-206 log(counts per million) versus sample covariates (see Methods) are plotted for controls (“CTL”) and ALS from this study. P-value from t-test of regression coefficient (null model coefficient equals zero) is shown. C) Same as B but for data from Magen et al. (see Methods). D) For analytes passing filters in both sets (median counts greater than 50 and at least one count in every sample, n = 187) the t -statistic is plotted for each set.

Article Snippet: After droplet generation, samples immediately underwent 40 cycles of endpoint PCR, according to Bio-Rad ddPCR Supermix for Probes (No dUTP) manufacturer’s instructions.

Techniques: High Throughput Screening Assay, Biomarker Discovery

Journal: bioRxiv

Article Title: microRNA-206 is a reproducibly sensitive and specific plasma biomarker of amyotrophic lateral sclerosis

doi: 10.1101/2025.06.27.662023

Figure Lengend Snippet: A) ROC curve displaying the ability of hsa-miR-206 to distinguish ALS from healthy controls in the discovery cohort based on ddPCR absolute quantification. The red dot represents the optimal threshold of sensitivity and specificity in the discovery cohort. B) Z-scored hsa-miR-206 ddPCR expression data, dashed lines represent the optimal threshold as shown in panel A. C-D) Same as A-B, but in the NEALS replication cohort. E-F) Same as A-B, but with the SFC Parkinson’s cohort included.

Article Snippet: After droplet generation, samples immediately underwent 40 cycles of endpoint PCR, according to Bio-Rad ddPCR Supermix for Probes (No dUTP) manufacturer’s instructions.

Techniques: Quantitative Proteomics, Expressing

Journal: bioRxiv

Article Title: microRNA-206 is a reproducibly sensitive and specific plasma biomarker of amyotrophic lateral sclerosis

doi: 10.1101/2025.06.27.662023

Figure Lengend Snippet: A) Z-scored hsa-miR-206 expression in all samples analyzed by ddPCR. The p-value was computed from a t-test of the regression coefficient, testing the association between hsa-miR-206 expression and sex. B) ROC curve displaying the ability of hsa-miR-206 to distinguish ALS from healthy controls in the discovery cohort based on ddPCR absolute quantification, with sex included in the analysis.

Article Snippet: After droplet generation, samples immediately underwent 40 cycles of endpoint PCR, according to Bio-Rad ddPCR Supermix for Probes (No dUTP) manufacturer’s instructions.

Techniques: Expressing, Quantitative Proteomics