| Strain, strain background (chikungunya virus) |
CHIKV |
Dr. P. Roques (CEA, Fontenay-aux-Roses, France) |
KT449801.1 |
Isolate LR2006-OPY1 |
| Chemical compound, drug |
TRIzol |
Sigma-Aldrich |
Cat# 15596026 |
|
| Chemical compound, drug |
MitoTEMPO |
Sigma-Aldrich |
Cat#1334850-99-5 |
|
| Commercial assay, kit |
TruSeq RNA Sample Prep Kit (v2) |
Illumina |
SCR_010233 |
|
| Commercial assay, kit |
TruSeq Stranded mRNA library preparation kit |
Illumina |
SCR_010233 |
|
| Commercial assay, kit |
QIAamp DNA Micro Kit |
QIAGEN |
Cat# 56304 |
|
| Commercial assay, kit |
iScript cDNA Synthesis Kit |
Bio-Rad |
Cat# 1708890 |
|
| Commercial assay, kit |
Q5 Hot Start High-Fidelity DNA Polymerase |
NEB |
Cat# M0493S |
Enzyme |
| Other |
Illumina HiSeq 2000 Sequencer |
Illumina |
RRID:SCR_010233
|
Sequencing platform |
| Other |
NextSeq 550 |
Illumina |
RRID:SCR_016381
|
Sequencing platform |
| Other |
NovaSeq 6000 |
Illumina |
RRID:SCR_016387
|
Sequencing platform |
| Software, algorithm |
k-mer_mining_SRA |
GitHub |
|
https://github.com/CameronBishop/k-mer_mining_SRA
|
| Cell line (Cercopithecus aethiops) |
Vero cells |
ATCC |
RRID:CVCL_0059
|
|
| Cell line (Aedes albopictus) |
C6/36 cells |
ATCC |
RRID:CVCL_Z230
|
|
| Strain, strain background (Mus musculus) |
C57BL/6J |
Animal Resources Centre (Canning Vale, WA, Australia) |
IMSR_JAX:000664 |
|
| Strain, strain background (M. musculus) |
C57BL/6N |
The Jackson Laboratory |
Stock no. 005304 |
|
| Strain, strain background (M. musculus) |
C57BL/6-Gzma-/-
|
Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia |
Knockout mouse |
|
| Strain, strain background (M. musculus) |
C57BL/6J-Gzmb-/-
|
Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia |
Knockout mouse |
|
| Strain, strain background (M. musculus) |
C57BL/6J-GzmaS211A
|
The Australian Phenomics Network, Monash University, Melbourne, Australia (this paper) |
Mutant mouse |
|
| Strain, strain background (M. musculus) |
C57BL/6N∆Nnt8-12
|
The Australian Phenomics Network, Monash University, Melbourne, Australia (this paper) |
Knockout mouse |
|
| Strain, strain background (M. musculus) |
C57BL/6J-Ifnar-/-
|
Dr P. Hertzog (Monash University, Melbourne, Australia) |
Knockout mouse |
|
| Strain, strain background (M. musculus) |
C57BL/6-Il28ra-/-
|
Bristol-Myers Squibb (PMID:25901316) |
Knockout mouse |
|
| Sequence-based reagent |
Nnt_RTPCR_F1 |
This paper |
PCR primers |
AACAGTGCAAGGAGGTGGAC |
| Sequence-based reagent |
Nnt_RTPCR_R1 |
This paper |
PCR primers |
GTGCCAAGGTAAGCCACAAT |
| Software, algorithm |
FastQC |
Babraham Institute |
RRID:SCR_014583
|
|
| Software, algorithm |
MultiQC |
PMID:27312411
|
RRID:SCR_014982
|
|
| Software, algorithm |
Cutadapt |
DOI: https://doi.org/10.14806/ej.17.1.200
|
RRID:SCR_011841
|
|
| Software, algorithm |
STAR |
PMID:23104886
|
RRID:SCR_004463
|
|
| Software, algorithm |
RSEM |
PMID:21816040
|
RRID:SCR_013027
|
|
| Software, algorithm |
EdgeR |
PMID:27280887
|
RRID:SCR_012802
|
|
| Software, algorithm |
‘Ingenuity Pathway Analysis’ (IPA) |
QIAGEN |
RRID:SCR_008653
|
|
| Software, algorithm |
Cytoscape |
PMID:14597658
|
RRID:SCR_003032
|
|
| Software, algorithm |
STRING |
PMID:30476243
|
RRID:SCR_005223
|
|
| Software, algorithm |
‘Gene Set Enrichment Analysis’ (GSEA) |
PMID:16199517
|
RRID:SCR_003199
|
|
| Software, algorithm |
‘Integrative Genomics Viewer‘ (IGV) |
PMID:21221095
|
RRID:SCR_011793
|
|
| Software, algorithm |
minimap2 |
PMID:29750242
|
RRID:SCR_018550
|
|
| Software, algorithm |
BigQuery |
Google Cloud Platform |
RRID:SCR_001011
|
|
| Software, algorithm |
fasterq-dump |
SRA tool kit |
sra-tools v 2.9.1 |
|
