{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Andrew Firth"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of total RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16460"],"description":["The 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Valeria Lulla","Andrew Firth"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq analysis of HAstV1, HAstV4, MLB1, MLB2 and VA1 astrovirus infection in cell culture","description":"The 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.","dates":{"release":"2026-04-17T00:00:00Z","modification":"2026-04-17T07:37:24.284Z","creation":"2025-12-22T10:59:07.711Z"},"accession":"E-MTAB-16460","cross_references":{"ENA":["ERP186902"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0004184"]}}