title: Sample 16
organism: Homo sapiens
description: Protocols: Cells were harvested at 6, 12, 18 or 24 h as indicated.  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.  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.  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.
attributes.tag: ENA first public
attributes.value: 2026-04-18
attributes.tag: INSDC center name
attributes.value: University of Cambridge
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-16460:Sample 16
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: Caco-2
attributes.tag: cell type
attributes.value: NA
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: NA
attributes.tag: disease
attributes.value: NA
attributes.tag: genotype
attributes.value: NA
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: colon
attributes.tag: proteinase k treatment
attributes.value: No
attributes.tag: replicate
attributes.value: 2
attributes.tag: sample name
attributes.value: E-MTAB-16460:Sample 16
attributes.tag: scientific_name
attributes.value: Homo sapiens
attributes.tag: technical replicate
attributes.value: 2
attributes.tag: virus
attributes.value: HAstV1