ERC000011
ENA-CHECKLIST
2023-12-01T00:42:38Z
ENA-FIRST-PUBLIC
2023-12-01T00:42:38Z
ENA-LAST-UPDATE
SAMEA113537027
External Id
Division of Virology, Department of Pathology, University of Cambridge
INSDC center name
2023-12-01T00:42:38Z
INSDC first public
2023-12-01T00:42:38Z
INSDC last update
public
INSDC status
ERS15533452
SRA accession
E-MTAB-12970:Dak84_Ribo_Vero_REP2
Submitter Id
ArrayExpress
broker name
Vero
cell_line
fibroblast
cell_type
Protocols: Vero and U251 cells were grown on 100-mm dishes to 90% confluency and infected with ZIKV (PE243 or Dak84) at a multiplicity of infection (MOI) of 3. At 24 h p.i., cells were rinsed with 5 ml of ice-cold PBS, flash frozen in a dry ice/ethanol bath and lysed with 400 μl of lysis buffer [20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide and 25 U/ml TURBO DNase (Life Technologies)]. Cells were scraped extensively to ensure lysis, collected and triturated ten times with a 26-G needle. Cell lysates were clarified by centrifugation at 13,000 g for 20 min at 4°C. The supernatants were recovered and stored in liquid nitrogen. RNase I was added to the lysates for 45 minutes at room temperature, following which ribosomes and ribosome-protected fragments of RNA were purified by centrifugation through a sucrose cushion. RNA was extracted from the purified ribosomes by proteinase K digestion (enzyme from NEB, reaction at 42 degrees for 30 minutes) followed by hot acidic phenol: chloroform extraction and ethanol precipitation. The methodologies employed were based on the original protocols of Ingolia and colleagues (Ingolia et al., 2009; Ingolia et al., 2012), except library amplicons were constructed using a small RNA cloning strategy (Guo et al., 2010) adapted to Illumina smallRNA v2 to allow multiplexing. Ribosomal RNA was removed using Ribo-Zero Gold rRNA removal kit (Illumina), and remaining RNA was purified by 15% denaturing urea gel purification to select fragments of 25-35nt, and library amplicons were constructed.
description
adult
developmental stage
normal
disease
wild type genotype
genotype
ZIKV Dak84
infect
Chlorocebus sabaeus
organism
Chlorocebus sabaeus
organism
kidney
organism part
Chlorocebus sabaeus
scientific_name
Dak84_Ribo_Vero_REP2
title