SARS-CoV-2 Probe Design Protocol

SARS-CoV-2 probes were designed as described [74 ], with probes designed based on the reference transcriptome Wuhan-Hu-1 isolate Sars_cov_2.ASM985889v3, Ensembl build 101 (https://covid-19.ensembl.org/Sars_cov_2/Info/Index) and were not designed for other strains or mutation patterns. Probes were designed to target the SARS-CoV-2 genes Surface glycoprotein (S), Envelope protein (E), Membrane glycoprotein (M), ORF1ab, ORF3a, ORF7a, ORF7b, ORF8, Nucleocapsid phosphoprotein (N), and ORF10 (Additional file 2: Table S1, Additional file 12: Table S12, Additional file 13: Table S13) (10X Genomics).

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Sounart H., Lázár E., Masarapu Y., Wu J., Várkonyi T., Glasz T., Kiss A., Borgström E., Hill A., Rezene S., Gupta S., Jurek A., Niesnerová A., Druid H., Bergmann O, & Giacomello S. (2023). Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections. Genome Biology, 24, 237.

Publication 2023

Covid 19 Envelope protein Genes Membrane glycoprotein Mutation Nucleocapsid Phosphoprotein Sars cov 2 Strains Transcriptome

Corresponding Organization :

Other organizations : KTH Royal Institute of Technology, Science for Life Laboratory, Semmelweis University, 10X Genomics (United States), Karolinska Institutet, TU Dresden

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Variable analysis

independent variables

Probes designed based on the reference transcriptome Wuhan-Hu-1 isolate Sars_cov_2.ASM985889v3, Ensembl build 101

dependent variables

SARS-CoV-2 genes targeted by the probes: Surface glycoprotein (S), Envelope protein (E), Membrane glycoprotein (M), ORF1ab, ORF3a, ORF7a, ORF7b, ORF8, Nucleocapsid phosphoprotein (N), and ORF10

control variables

Not explicitly mentioned

positive controls

Not specified

negative controls

Not specified

Annotations

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