Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq time-course of Calu-3 cells infected with SARS-CoV-2 early-lineage and Alpha variant viruses

ABSTRACT: Emergence of SARS-CoV-2 variants of concern (VOCs), including the globally successful Alpha (B.1.1.7) variant, suggests viral adaptation to enhance human-to-human transmission. Although much effort has focused on characterisation of spike changes, Alpha mutations outside spike likely contribute to adaptation. Here we used RNAseq as well as viral replication assays to show that Alpha isolates more effectively suppress innate immune responses (ISGs as assessed by RNA) in airway epithelial cells, compared to first wave isolates. We found that Alpha has dramatically increased subgenomic RNA and protein levels of N, Orf9b and Orf6, all known innate immune antagonists.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Mehdi Bouhaddou

PROVIDER: E-MTAB-11275 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant.

Thorne Lucy G LG Bouhaddou Mehdi M Reuschl Ann-Kathrin AK Zuliani-Alvarez Lorena L Polacco Ben B Pelin Adrian A Batra Jyoti J Whelan Matthew V X MVX Ummadi Manisha M Rojc Ajda A Turner Jane J Obernier Kirsten K Braberg Hannes H Soucheray Margaret M Richards Alicia A Chen Kuei-Ho KH Harjai Bhavya B Memon Danish D Hosmillo Myra M Hiatt Joseph J Jahun Aminu A Goodfellow Ian G IG Fabius Jacqueline M JM Shokat Kevan K Jura Natalia N Verba Klim K Noursadeghi Mahdad M Beltrao Pedro P Swaney Danielle L DL Garcia-Sastre Adolfo A Jolly Clare C Towers Greg J GJ Krogan Nevan J NJ

bioRxiv : the preprint server for biology 20210607

Emergence of SARS-CoV-2 variants, including the globally successful B.1.1.7 lineage, suggests viral adaptations to host selective pressures resulting in more efficient transmission. Although much effort has focused on Spike adaptation for viral entry and adaptive immune escape, B.1.1.7 mutations outside Spike likely contribute to enhance transmission. Here we used unbiased abundance proteomics, phosphoproteomics, mRNA sequencing and viral replication assays to show that B.1.1.7 isolates more eff ...[more]

PMID: 34127972

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Project description:Transcript profiling is crucial to study biological systems and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the characteristics of the CATMA microarray designed for Arabidopsis thaliana transcriptome analysis, and compared it with two commercial platforms from Agilent and Affymetrix. The CATMA array consists of gene-specific sequence tags of 150 to 500 base pairs, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (TIGR release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled target derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. A total of fourteen cDNA clones were thus selected and used as templates to synthesize bona fide polyadenylated spike RNAs. Each spike RNA was calibrated then mixed in equal amount with one of the other spike RNAs to obtain seven pairs at equal concentration. These seven spike RNA pairs were then combined systematically to construct seven complex spike mixes in a design similar to an ordered Latin square, each mix containing six of the seven spike pairs in staggered concentrations covering five logs. To prevent loss of spike RNA through adsorption to the plastic ware, the spike mixes were prepared in 0.5 Âµg/Âµl Col RNA, resulting in a range of concentration from 0.1 to 10,000 copies per cellular equivalent (cpc), assuming that the total RNA contained 1% polyadenalated mRNA and that a cell contained on average 300,000 transcripts. These seven RNA samples included equal amounts of combined spike RNA . To convert the spike hybridization signals to ratios, an eighth sample was prepared, called the reference sample, consisting of the base Col RNA completed with all spike RNAs at a concentration of 100 cpc. The results from the eight experiments using the Affymetrix gene chips (ATH1) are available for analysis or download from this site.

Dataset Information

RNA-seq time-course of Calu-3 cells infected with SARS-CoV-2 early-lineage and Alpha variant viruses

Publications

Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant.

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