Journal: Journal of Experimental & Clinical Cancer Research : CR

Article Title: Downregulation of lncRNA ZNF582-AS1 due to DNA hypermethylation promotes clear cell renal cell carcinoma growth and metastasis by regulating the N(6)-methyladenosine modification of MT-RNR1

doi: 10.1186/s13046-021-01889-8

Figure Lengend Snippet: ZNF582-AS1 expression was regulated by DNA methylation in ccRCC. a Detection of CpG islands in ZNF582-AS1 promoter and design of MSP primers. The horizontal axis of the curved lines represents the input sequence of ZNF582-AS1, and the vertical axis of the curved lines represents GC percentage. TSS: Transcription Start Sites. b MSP analysis of ZNF582-AS1 promoter DNA methylation status in ccRCC cell lines. c MSP analysis of ZNF582-AS1 promoter DNA methylation status in ccRCC tissues. d Detection of 38 CpG sites in ZNF582-AS1 promoter. e Quantitative detection of DNA methylation level of 38 CpG sites in ZNF582-AS1 promoter using Sequenom MassARRAY quantitative DNA methylation analysis. f and g Comparison of the DNA methylation levels of 38 CpG sites in ccRCC and adjacent normal renal tissues. h Treatment with 5-aza-dC and TSA demethylated ZNF582-AS1 promoter and increased ZNF582-AS1 expression in OSRC2 and Caki-1 cells. T refers to Tumor tissue of ccRCC, N refers to Adjacent normal kidney tissue. M = Methylated, U = Unmethylated

Article Snippet: The detailed primers information of qRT-PCR, MSP, Sequenom MassARRAY quantitative methylation analysis and MeRIP-qRT-PCR.

Techniques: Expressing, DNA Methylation Assay, Sequencing, Comparison, Methylation

Journal: medRxiv

Article Title: RT-PCR/MALDI-TOF diagnostic target performance reflects circulating SARS-CoV-2 variant diversity in New York City

doi: 10.1101/2021.12.04.21267265

Figure Lengend Snippet: (A) Heatmap depicting the proportion of SARS-CoV-2-positive specimens that have detectable RT-PCR/MALDI-TOF targets (N1, N2, N3, ORF1A, ORF1AB) by week from April 11 through August 28, 2021. The total number of SARS-CoV-2-positive specimens and the number of SARS-CoV-2-positive specimens sequenced by pathogen surveillance are depicted above each week (column). Grey boxes indicate weeks where no specimens were positive for SARS-CoV-2 on this platform. (B) Stacked area plots depicting frequencies of SARS-CoV-2 variants reported by publicly-available NYC Department of Health surveillance data within the same timeframe.

Article Snippet: We utilized publicly-available primer/probe sequences of the Agena MassARRAY ® SARS-CoV-2 Panel and a deidentified dataset from clinical specimens that included individual target detection data and whole-genome sequencing to generate a snapshot of virus sequence diversity at each target PBS and to determine the extent to which polymorphisms are associated with individual target performance.

Techniques: Reverse Transcription Polymerase Chain Reaction

Journal: medRxiv

Article Title: RT-PCR/MALDI-TOF diagnostic target performance reflects circulating SARS-CoV-2 variant diversity in New York City

doi: 10.1101/2021.12.04.21267265

Figure Lengend Snippet: (A) Stacked bar plots depict the composition of SARS-CoV-2 variants in 254 MSHS genomes tested by RT-PCR/MALDI-TOF. Bar plots reflect absolute number of genomes with N2 target dropout (left) and those with N2 target detection (right). Variant groups are color-coded and genomes with the G28916U polymorphism are depicted by a hatched pattern. (B) Stacked bar plot of publicly-available sequences (GISAID, see methods) from the same timeframe of this study depicting absolute numbers of variant genomes and presence or absence of the G28916U polymorphism. Color-coding and patterns are the same as in (A).

Article Snippet: We utilized publicly-available primer/probe sequences of the Agena MassARRAY ® SARS-CoV-2 Panel and a deidentified dataset from clinical specimens that included individual target detection data and whole-genome sequencing to generate a snapshot of virus sequence diversity at each target PBS and to determine the extent to which polymorphisms are associated with individual target performance.

Techniques: Reverse Transcription Polymerase Chain Reaction, Variant Assay