| Antibodies |
| DDX39A |
Proteintech |
Cat#11723–1-AP |
| GAPDH |
Sigma |
Cat#CB1001 |
| Lamin B1 |
Abcam |
Cat#ab16048 |
| Tubulin |
Sigma |
Cat#T6199 |
| DDX39B |
Santa Cruz |
Cat#sc-271395 |
| Beta actin |
Santa Cruz |
Cat#sc-47778 |
| IFIT1 |
Cell Signaling Technology |
Cat#D2X9Z |
| CHIKV E1 |
Novus |
Cat# MAB97792 |
| CHIKV ascites |
ATCC |
Cat#V-548–701-562 |
| Histone H3 |
Abcam |
Cat#ab18521 |
| J2(dsRNA) |
Absolute |
Cat#Ab01299 |
| VEEV ascites |
ATCC |
Cat#V-532–711-562 |
| IAV NP |
BEI Resources |
Cat#NR-4282 |
| Rabbit IgG |
Bethyl |
Cat#P120–201 |
| VSV-M |
Absolute |
Cat#23H12 |
| DDX39A |
Abnova |
Cat# MAB6576 |
| DDX24 |
Proteintech |
Cat# 15769–1-AP |
| Streptavidin-HRP antibody |
Cell Signaling Technology |
Cat#3999 |
| ALY/REF |
Novus |
Cat#NB100670 |
| J2(dsRNA) |
Cherry Lab |
|
| DDX39B |
Proteintech |
Cat#14798–1-AP |
| RCK (p54) |
MBL |
Cat#PD009 |
| TIAR |
BD Biosciences |
Cat#610352 |
| Bacterial and virus strains |
| Coxsackie B Virus |
Carolyn B. Coyne (University of Pittsburgh) |
- |
| CHIKV, Ross strain |
Dr. D. Weiner (Wistar Institute) |
- |
| CHIKV 181/25 WT, δ5’CSE, δSL3 |
M. Heise (University of North Carolina) |
- |
| HCoV-OC43 |
ATCC |
Cat# VR-1558 |
| HCoV-229E |
ATCC |
Cat#VR-740 |
| O’nyong’ nyong (SG650) |
Dr. Thomas E. Morrison (University of Colorado) |
- |
| RVFV (MP12) |
Dr. Michael Diamond (Washington University in St. Louis) |
- |
| SeV |
Charles River |
Cat#10100774 |
| SINV-mKate |
M. Heise (University of North Carolina) |
- |
| VEEV (strain TC-83) |
M. Heise (University of North Carolina) |
- |
| VSV-EGFP |
Jack Rose (Yale University) |
- |
| NEB 5-alpha Competent E. coli
|
NEB |
Cat#C2988J |
| Chemicals, peptides, and recombinant proteins |
| Random Primers |
Invitrogen |
Cat#48190011 |
| IFNβ |
STEMCELL Technologies |
Cat#78113 |
| M MLV Reverse Transcriptase |
Invitrogen |
Cat#28025013 |
| SYBR green master mix |
Applied Biosystems |
Cat#4368708 |
| Hoechst 33342 |
Sigma Aldrich |
Cat#B2261–25MG |
| HiPerFect reagent |
Qiagen |
Cat#301709 |
| TRIzol |
Life Technologies |
Cat#15596018 |
| Cycloheximide |
Sigma Aldrich |
Cat#01810 |
| Ruxolitinib |
Invitrogen |
Cat#tlrl-rux |
| Poly(I:C)-LMW |
Invivogen |
Cat# tlrl-picw |
| Critical commercial assays |
| Dynabeads Streptavidin C1 |
Invitrogen |
Cat#65001) |
| Zymo RNA clean and concentrator 25 |
Zymo Research |
Cat#R1018 |
| T7 MEGAScript Kit |
Ambion |
Cat#AM1334 |
| Cell Fractionation Kit |
Cell Signaling Technology |
Cat#9038 |
| 3’ Biotinylation Kit |
ThermoScientific |
Cat#20160 |
| Experimental models: Cell lines |
|
Homo sapiens: U2OS |
ATCC |
HTB-96 |
|
Homo sapiens: A549 |
ATCC |
CCL-2 |
|
Homo sapiens: HeLa S3 |
ATCC |
CCL-185 |
|
Homo sapiens: HEK 293T |
ATCC |
CRL-3216 |
|
Mesocricetus auratus: BHK-21 |
Mesocricetus auratus: BHK-21 |
Mesocricetus auratus: BHK-21 |
|
Cercopithecus aethiops: Vero E6 |
ATCC |
CRL-1586 |
|
Cercopithecus aethiops: Vero CCL81 |
ATCC |
CCL81 |
| Oligonucleotides |
| Primers for qPCR analysis, see Table S5
|
This paper |
- |
| siRNA sequences, see Table S5
|
This paper |
- |
| Primers for RNA affinity experiments, see S5
|
This paper |
- |
| Deposited data |
| Microscope images and blots |
Mendeley |
Mendeley Data, V1, doi: 10.17632/fvzkrcb5n2.1
|
| Recombinant DNA |
| PLX304-DDX39A plasmid |
DNASU |
http://dnasu.org/DNASU/GetCloneDetail.do?cloneid=440517
|
| lentiCRISPR v2 |
lentiCRISPR v2 was a gift from Feng Zhang |
(Addgene plasmid # 52961; http://n2t.net/addgene:52961; RRID:Addgene_52961) |
| pCMV-VSV-G |
pCMV-VSV-G was a gift from Bob Weinberg |
Addgene plasmid # 8454; http://n2t.net/addgene:8454; RRID:Addgene_8454 |
| psPAX-2 |
psPAX2 was a gift from Didier Trono |
Addgene plasmid # 12260; http://n2t.net/addgene:12260; RRID:Addgene_12260) |
| Software and algorithms |
| Trimmomatic |
(Bolger et al., 2014) |
version 0.32 https://github.com/usadellab/Trimmomatic
|
| Cutadapt |
(Martin, 2011) |
version 1.5 https://cutadapt.readthedocs.io/en/stable/index.html
|
| STAR |
(Dobin et al., 2013) |
version 2.5.2a https://github.com/alexdobin/STAR
|
| Samtools |
(Li et al., 2009) |
version 1.1 http://samtools.sourceforge.net/
|
| Picard |
http://broadinstitute.github.io/picard
|
version 1.141 https://broadinstitute.github.io/picard/
|
| HOMER |
(Heinz et al., 2010) |
Version 4.11 http://homer.ucsd.edu/homer/
|
| CLIP-seq Analysis of Multi-mapped reads (CLAM) |
(Zhang and Xing, 2017) |
version 1.2.1 https://github.com/Xinglab/CLAM
|
| Bedtools |
(Quinlan and Hall, 2010) |
version 2.30.0 https://bedtools.readthedocs.io/en/latest/
|
| RStudio |
Team RS. 2016. RStudio: Integrated Development for R, RStudio, Inc., Boston, MA. |
1.4.1106 http://www.rstudio.com/. |
| MetaXpress |
Molecular Devices Corporation |
|
| Deeptools2 |
(Ramırez et al., 2016) |
version 2.0 https://deeptools.readthedocs.io/en/develop/content/installation.html
|
| QuantStudio 6 1.3 |
Applied Biosystems |
N/A |
| PRISM 8.4.3 |
GraphPad Software |
N/A |
| Spotfire |
PerkinElmer |
N/A |
| Other |
| VECTASHIELD Antifade Mounting Medium containing DAPI |
Vector Laboratories |
H-1200 |
| 4 NUPAGE 4–12% Bis-Tris Gels |
Invitrogen |
Cat# NP0323 |
| Complete EDTA-free protease inhibitor cocktail |
Sigma-Aldrich |
Cat# 4693159001 |
| Dynabeads protein A |
Invitrogen |
Cat# 10002D |
| Nitrocellulose membrane |
GE Healthcare Life Sciences |
Cat#10600002 |
| SuperSignal™ West Femto Maximum Sensitivity |
Thermo Fisher Scientific |
Cat# 34095 |
| Lipofectamine 2000 |
Thermo Fisher Scientific |
Cat# L3000008 |
| RNase T1 |
Thermo Fisher Scientific |
Cat#AM2294 |
| RQ1 DNase |
Promega |
Cat# M6101 |
| SuperScript III Reverse Transcriptase Superscript RT buffer |
Invitrogen |
Cat#214351 |
| Accuprime Pfx supermix |
Invitrogen |
Cat# 12344040 |
| TURBO DNase |
Thermo Fisher Scientific |
Cat#AM2238 |
| ProteinaseK |
Sigma-Aldrich |
Cat# 3115828001 |
| T4 Polynucleotide Kinase |
Thermo Fisher Scientific |
Cat#EK003 |
| T4 RNA ligase |
ThermoScientific |
Cat#00864622 |
| T4 Polynucleotide kinase |
Biolabs |
Cat#M0201S |
