RNase project - preparatory work

Check in data from others

Check in Transcriptome data whether SARS-CoV2 results in specific RNA degradation

priority: (pmid: 34106002) timescaled, gene-comparable transcriptome of SARS-CoV-2. Sequencing data were archived at the NCBI Sequence Read Archive (SRA) under accession number SRP324059.

(pmid: 32995793) - Single cell sequencing of OC43 - can this data be used to see whether certain mRNAs go down?

(pmid: 33630927 2021) hCoV229E - transcriptomic changes

publically available transcriptome datasets

from (pmid: 33802569) GEO dataset GSE147507 contains data from cell lines infected with SARS-CoV-2, including Calu-3 adenocarcinoma cells and A549 cells supplemented with a vectorexpressing ACE2. GEO dataset GSE139516 contains data from the Calu3 cell line infectedwith Middle East respiratory syndrome coronavirus (MERS-CoV), while GEO datasetGSE148729 contains data from the Calu3 cell line infected with SARS-CoV-1 and SARS-CoV-2. Raw sequence data from BALF of COVID-19 patients were retrieved from theGenome Sequence Archive (https://bigd.big.ac.cn/, accessed on 2 February 2021), Bei-jing Institute of Genomics (accession number CRA002390) [28]. RNA-seq data for BALFfrom healthy control samples were downloaded from the NCBI SRA database (accessionnumbers SRR10571724, SRR10571730, and SRR10571732). Data from mock-treated cellswere provided for eachin vitrogroup (N= 3 per group).