biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsAndrew FirthNextSeq 500RNA-seq of total RNAHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16460The purpose of the study was to investigate the dynamics of viral RNA production during astrovirus infection. Caco-2 cells were infected at MOI 5 with HAstV1, HAstV4 or VA1; Huh7.5.1 cells were infected at MOI 5 with MLB1 or MLB2. Cells were harvested at 6, 12, 18, 24 (HAstV1) or 24 (HAstV4, MLB1, MLB2, VA1) hours post-infection, and total RNA was extracted, fragmented, depleted for rRNA and sequenced.biostudies-arrayexpressSample Collection - Cells were harvested at 6, 12, 18 or 24 h as indicated.Growth Protocol - Caco-2 (ATCC) and Huh7.5.1 cells (Apath, Brooklyn, NY) were maintained at 37 °C in DMEM supplemented with 5% fetal bovine serum (FBS), 1 mM L-glutamine, 10% FBS, non-essential amino acids and antibiotics. Caco-2 cells were infected at MOI 5 with HAstV1, HAstV4 or VA1. Huh7.5.1 cells were infected at MOI 5 with MLB1 or MLB2.Library Construction - Total RNA was extracted by Direct-zol RNA Prep kit (Zymo research). RNA was fragmented, and 50-150 nt fragments were used for RNA-seq library preparation using an Illumina library protocol as described in Lulla et al (2019, PMID 30478287) and Irigoyen et al (2016, PMID 26919232), except that the Ribo-Zero rRNA removal kit (Illumina) was used to deplete ribosomal RNA. For the indicated experiments, proteinase K (NEB) treatment was performed using 10 µg of total RNA extracted from infected cells, 1% SDS (final concentration) at 42°C for 45 minutes.Sequencing - Amplicon libraries were sequenced using an Illumina NextSeq platform with 76 cycles single-end (samples 1-6), 76 fwd 76 rev cycles paired-end (samples 7-22), or 37 fwd 38 rev cycles (samples 23-32).Nucleic Acid Extraction - Total RNA was extracted by Direct-zol RNA Prep kit (Zymo research). RNA was fragmented, and 50-150 nt fragments were used for RNA-seq library preparation using an Illumina library protocol as described in Lulla et al (2019, PMID 30478287) and Irigoyen et al (2016, PMID 26919232), except that the Ribo-Zero rRNA removal kit (Illumina) was used to deplete ribosomal RNA. For the indicated experiments, proteinase K (NEB) treatment was performed using 10 µg of total RNA extracted from infected cells, 1% SDS (final concentration) at 42°C for 45 minutes.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesValeria LullaAndrew FirthfalseRNA-seq analysis of HAstV1, HAstV4, MLB1, MLB2 and VA1 astrovirus infection in cell cultureThe purpose of the study was to investigate the dynamics of viral RNA production during astrovirus infection. Caco-2 cells were infected at MOI 5 with HAstV1, HAstV4 or VA1; Huh7.5.1 cells were infected at MOI 5 with MLB1 or MLB2. Cells were harvested at 6, 12, 18, 24 (HAstV1) or 24 (HAstV4, MLB1, MLB2, VA1) hours post-infection, and total RNA was extracted, fragmented, depleted for rRNA and sequenced.2026-04-17T00:00:00Z2026-04-17T07:37:24.284Z2025-12-22T10:59:07.711ZE-MTAB-16460ERP186902EFO_0002944EFO_0004170EFO_0009653EFO_0003789EFO_0005518EFO_0004184