cap analysis of gene expression  (Human Protein Atlas)

Journal: bioRxiv

Article Title: Novel Herpesvirus Transcripts with Putative Regulatory Roles in DNA Replication and Global Transcription

doi: 10.1101/2023.03.25.534217

Figure Lengend Snippet: Techniques applied for the generation of novel sequencing data, including infection of the cells with various viruses, library preparation, sequencing and bioinformatics. The workflow of the qPCR validations of several transcripts is also illustrated. Abbreviations: PA: polyadenylated RNAs; T: Terminator-handled samples; RD: ribodepleted RNAs; dcDNA: direct cDNA-seq; CAGE: Cap Analysis Gene Expression-Seq; dRNA: direct RNA-Seq; qRNA: short-read RNA-Seq (library generated by qRNA-seq kit); acDNA: amplified cDNA-Seq.

Article Snippet: Additionally, Cap Analysis of Gene Expression (CAGE) sequencing (CAGE-Seq, running on Illumina platform) was used for defining the TSS landscape in EHV-1 and KSHV ( ).

Techniques: Sequencing, Infection, Expressing, RNA Sequencing Assay, Generated, Amplification

Journal: bioRxiv

Article Title: Novel Herpesvirus Transcripts with Putative Regulatory Roles in DNA Replication and Global Transcription

doi: 10.1101/2023.03.25.534217

Figure Lengend Snippet: TSS distributions are illustrated in the following genomic regions of EHV-1 and KSHV: A. EHV-1 OriL; B. EHV-1 OriS of the IRS; C. KSHV OriLyt-R; D. KSHV OriLyt-L; E. KSHV OriLyt-L – here a higher resolution is used for the better visibility of the low-abundance TSSs. It can be seen that CTO-S transcript is at a high level (A), whereas NOIR-1 is a group of transcripts expressed in a relative low level. Smoothed density plots of the 5′ ends in the CAGE data. Here, y-axis shows the result of the probability estimation of the 5′ ends using a probability density function (details are described in the Materials and Methods section). Coding sequence (CDS) annotations for the respective genomes (shown with the accession number at the right) were visualized in the lower part. The coverage of the positive strand and the CDS annotation are shown in red while these were illustrated in blue in the negative strand. The Ori regions in EHV-1 are illustrated in black whereas in KSHV they are depicted in green – in the latter case, an accompanying white box shows the 20-nt binding site for the DNA replication origin-binding protein.

Article Snippet: Additionally, Cap Analysis of Gene Expression (CAGE) sequencing (CAGE-Seq, running on Illumina platform) was used for defining the TSS landscape in EHV-1 and KSHV ( ).

Techniques: Sequencing, Binding Assay