Journal: Cancer immunology research

Article Title: Prostate cancer cells express more androgen receptor (AR) following androgen deprivation, improving recognition by AR-specific T cells

doi: 10.1158/2326-6066.CIR-16-0390

Figure Lengend Snippet: 22Rv1 cultured in either androgen-replete (FCS, F) or androgen-deprived (CSS, C) medium for greater than six months were analyzed for mRNA gene expression differences (HTG EdgeSeq). (A) relative mRNA quantities for all genes significantly upregulated (left) or downregulated (right) in androgen-deprived medium compared with full medium. Heatmap shows relative expression per gene between FCS and CSS groups (green=low expression, red = high expression), and ranked top to bottom by fold change for all significantly differentially expressed genes. (B) The gene ontology subsets and (C) specific genes associated with immune function.(D)Data for selected genes associated with immune recognition and antigen presentation.* indicates P<0.05 by Studentt-test. (HVEM – herpesvirus entry mediator (TNFRSF14); TAP – transporter associated with antigen processing; CALR – calreticulin; NAIP – baculoviral IAP repeat-containing protein 1).

Article Snippet: 22Rv1 cells cultured in medium containing 10% complete fetal calf serum (FCS) or charcoal-stripped serum (CSS) were evaluated in triplicate for differences in gene expression of a panel of 2568 genes by high-throughput mRNA quantitation (HTG EdgeSeq Oncology Biomarker Panel, HTG Molecular, Tucson, AZ).

Techniques: Cell Culture, Expressing

Journal: Theranostics

Article Title: Improved cardiovascular risk prediction in patients with end-stage renal disease on hemodialysis using machine learning modeling and circulating microribonucleic acids

doi: 10.7150/thno.46123

Figure Lengend Snippet: Study flowchart. Among the 2776 patients included in the AURORA trial, blood samples were available from 2141 subjects. In Phase I (matching), 205 cases were matched with 205 controls. Patients with missing blood samples, patients whose plasma samples were used for other experimental procedures and patients in which miRNA quantification did not pass the quality control were excluded. The study population in phase I was composed of 379 patients (189 cases, 190 controls). Among the population of unmatched patients with blood sample available (n=1731), 200 cases and 200 controls were randomly drawn (Phase II). One low-quality sample was excluded. The study population in phase II was composed of 399 patients (200 cases, 199 controls).

Article Snippet: The HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA) (HTG Molecular, Tucson, AZ, USA) was applied to detect miRNAs differentially expressed in plasma samples from 10 cases and 10 matched controls.

Techniques: Clinical Proteomics, Control

Journal: Theranostics

Article Title: Improved cardiovascular risk prediction in patients with end-stage renal disease on hemodialysis using machine learning modeling and circulating microribonucleic acids

doi: 10.7150/thno.46123

Figure Lengend Snippet: Plasma microRNA levels in cases and controls from Phases I and II.

Article Snippet: The HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA) (HTG Molecular, Tucson, AZ, USA) was applied to detect miRNAs differentially expressed in plasma samples from 10 cases and 10 matched controls.

Techniques: Clinical Proteomics, Control

Journal: Theranostics

Article Title: Improved cardiovascular risk prediction in patients with end-stage renal disease on hemodialysis using machine learning modeling and circulating microribonucleic acids

doi: 10.7150/thno.46123

Figure Lengend Snippet: Association between plasma microRNA levels and the endpoint in Phase I.

Article Snippet: The HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA) (HTG Molecular, Tucson, AZ, USA) was applied to detect miRNAs differentially expressed in plasma samples from 10 cases and 10 matched controls.

Techniques: Clinical Proteomics

Journal: Theranostics

Article Title: Improved cardiovascular risk prediction in patients with end-stage renal disease on hemodialysis using machine learning modeling and circulating microribonucleic acids

doi: 10.7150/thno.46123

Figure Lengend Snippet: Association between plasma microRNA levels and the endpoint in Phase II.

Article Snippet: The HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA) (HTG Molecular, Tucson, AZ, USA) was applied to detect miRNAs differentially expressed in plasma samples from 10 cases and 10 matched controls.

Techniques: Clinical Proteomics

Journal: Theranostics

Article Title: Improved cardiovascular risk prediction in patients with end-stage renal disease on hemodialysis using machine learning modeling and circulating microribonucleic acids

doi: 10.7150/thno.46123

Figure Lengend Snippet: Discrimination ability of plasma microRNAs in Phase II.

Article Snippet: The HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA) (HTG Molecular, Tucson, AZ, USA) was applied to detect miRNAs differentially expressed in plasma samples from 10 cases and 10 matched controls.

Techniques: Clinical Proteomics

Journal: Theranostics

Article Title: Improved cardiovascular risk prediction in patients with end-stage renal disease on hemodialysis using machine learning modeling and circulating microribonucleic acids

doi: 10.7150/thno.46123

Figure Lengend Snippet: Performance of the regression tree model. A) Kaplan-Meier estimations and hazard ratios for the eight final nodes defined by the regression tree model including microRNAs. Data showed as hazard ratios (HR) and their 95% confidence intervals (CI); B) Variable Importance for the variables included in the regression tree model.

Article Snippet: The HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA) (HTG Molecular, Tucson, AZ, USA) was applied to detect miRNAs differentially expressed in plasma samples from 10 cases and 10 matched controls.

Techniques: