Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (H. sapiens) | Custom-defined gene set of NF-κB target genes |
see Supplementary file 2 of this paper |
N/A | |
| Gene (H. sapiens) | Custom-defined gene set of host restriction factors |
see Supplementary file 3 of this paper |
N/A | |
| Strain, strain background (E. coli) |
XL-2 blue | Stratagene | Cat#200150 | |
| Strain, strain background (E. coli) |
XL2-Blue MRF’ TM Ultracompetent cells |
Agilent Technologies | Cat#200151 | |
| Cell line (H. sapiens) |
HEK293T, female | ATCC | Cat#CRL-3216; RRID: CVCL_0063 |
|
| Cell line (H. sapiens) |
TZM-bl, female | NIH | Cat#8129; RRID: CVCL_B478 |
|
| Biological sample (H. sapiens) |
peripheral blood mononuclear cells (donors A and C: male; donors B and D: female) |
DRK-Blutspendedienst Baden-Württemberg-Hessen, Ulm, Germany |
N/A | derived from four healthy donors |
| Antibody | anti-HIV-1 p24 (capsid protein), FITC-conjugated (mouse monoclonal) |
Beckman Coulter | Cat#6604665; RRID: AB_1575987 |
FACS (1:25) |
| Antibody | anti-BST-2/tetherin, APC-conjugated (mouse monoclonal) |
Biolegend | Cat#348410; RRID:AB_2067121 |
FACS (1:20) |
| Antibody | anti-Human CD4, PerCP-conjugated (mouse monoclonal) |
BD Pharmingen | Cat#550631; RRID:AB_393791 |
FACS (1:12.5) |
| Antibody | anti-CD11c [3.9], FITC-conjugated (mouse monoclonal) |
Abcam | Cat#ab82445-100; RRID:AB_1859733 |
FACS (1:12.5) |
| Antibody | anti-CD11c [BU15], FITC-conjugated (mouse monoclonal) | Abcam | Cat#ab22540 | FACS (1:5) |
| Antibody | IgG1, κ, APC-conjugated (mouse) | Biolegend | Cat#400122; RRID:AB_326443 |
FACS (1:20) |
| Antibody | HIV-1 subtype C serum | NIH | Cat#11942 | WB (1:5000) |
| Antibody | HIV-1 NL4-3 Vpu antiserum | N/A | N/A | WB (1:500); kindly provided by S. Bolduan |
| Antibody | Anti-HIV1 p24 antibody [39/5.4A] | Abcam | Cat#ab9071; RRID:AB_306981 |
WB (1:5000) |
| Antibody | Purified anti-GAPDH antibody |
Biolegend | Cat#607902; RRID:AB_2734503 |
WB (1:1000) |
| Antibody | IRDye 800CW Goat anti-Mouse IgG (H + L) |
LI-COR | Cat#926–32210; RRID:AB_621842 |
WB (1:20000) |
| Antibody | IRDye 680RD Goat anti-Rabbit IgG (H + L) |
LI-COR | Cat#925–68071; RRID:AB_2721181 |
WB (1:20000) |
| Antibody | IRDye 800CW Goat anti-Rat IgG (H + L) |
LI-COR | Cat#925–32219; RRID:AB_2721932 |
WB (1:20000) |
| Antibody | anti-HIV-1 p24 (mouse monoclonal) | Abcam | Cat#ab9071; RRID:AB_306981 |
IF (1:500) |
| Antibody | anti-p65 (rabbit polyclonal IgG) |
Santa Cruz | Cat#sc-372; RRID:AB_632037 |
IF (1:150) |
| Antibody | Donkey anti-Mouse IgG (H + L), AF647- conjugated |
Thermo Scientific | Cat#A31571; RRID:AB_162542 |
IF (1:350) |
| Antibody | Goat anti-Rabbit IgG (H + L), AF568- conjugated |
Thermo Scientific | Cat#A11011; RRID:AB_143157 |
IF (1:350) |
| Recombinant DNA reagent |
pBR322_HIV-1 M subtype B STCO1 wt (plasmid) |
PMID: 23542380 | N/A | kindly provided by B. Hahn |
| Recombinant DNA reagent |
pBR322_HIV-1 M subtype B STCO1 vpu stop (plasmid) |
PMID: 27531907 | N/A | |
| Recombinant DNA reagent |
pBR322_HIV-1 M subtype B STCO1 Vpu R45K (plasmid) |
PMID: 29324226 | N/A | |
| Recombinant DNA reagent |
pBR322_HIV-1 M subtype B STCO1 Vpu A15L/A19L (plasmid) |
PMID: 27531907 | N/A | |
| Recombinant DNA reagent |
pUC57rev_HIV-1 M subtype C CH293 w8 wt (plasmid) |
PMID: 23542380 | N/A | kindly provided by B. Hahn |
| Recombinant DNA reagent |
pUC57rev_HIV-1 M subtype C CH293 w8 vpu stop (plasmid) |
PMID: 2562070 | N/A | |
| Recombinant DNA reagent |
pUC57rev_HIV-1 M subtype C CH293 w8 Vpu R50K (plasmid) |
this paper | N/A | derived from pUC57rev_HIV-1 M subtype C CH293 w8 wt (plasmid) |
| Recombinant DNA reagent |
pUC57rev_HIV-1 M subtype C CH293 w8 Vpu A20L/A24L (plasmid) |
this paper | N/A | derived from pUC57rev_HIV-1 M subtype C CH293 w8 wt (plasmid) |
| Recombinant DNA reagent |
pCR-XL-TOPO_HIV-1 M subtype B CH077 wt (plasmid) |
PMID: 22190722 | N/A | kindly provided by B. Hahn |
| Recombinant DNA reagent |
pCR-XL-TOPO_HIV-1 M subtype B CH077 vpu stop (plasmid) |
PMID: 27531907 | N/A | |
| Recombinant DNA reagent |
pCR-XL-TOPO_HIV-1 M subtype B CH077 Vpu R45K (plasmid) |
this paper | N/A | derived from pCR-XL-TOPO_HIV-1 M subtype B CH077 wt (plasmid) |
| Recombinant DNA reagent |
pCR-XL-TOPO_HIV-1 M subtype B CH077 Vpu A15L/A19L (plasmid) |
PMID: 27531907 | N/A | |
| Recombinant DNA reagent |
p_human IKKβ, constitutively active mutant (S177E, S181E) (plasmid) |
PMID: 23552418 | N/A | kindly provided by B. Baumann |
| Recombinant DNA reagent |
p_NF-κB(3x)-Firefly Luciferase (plasmid) | PMID: 23552418 | N/A | kindly provided by B. Baumann |
| Recombinant DNA reagent |
pTAL_Gaussia Luciferase (plasmid) | PMID: 23552418 | N/A | |
| Recombinant DNA reagent |
pCG_human Tetherin IRES DsRed2 (plasmid) | PMID: 19917496 | N/A | |
| Recombinant DNA reagent |
pHIT-G_VSV-G (vesicular stomatitis virus glycoprotein) (plasmid) | PMID: 9303297 | N/A | |
| Sequence- based reagent |
Primers used for mutagenesis of vpu | see Supplementary file 4 of this paper |
N/A | |
| Sequence- based reagent |
TaqMan Gene Expression Assay for IFN-beta |
Thermo Fisher Scientific |
Cat#Hs01077958_s1 | |
| Sequence- based reagent |
Human GAPD (GAPDH) Endogenous Control (VIC/TAMRA probe, primer limited) | Thermo Fisher Scientific |
Cat#4310884E | |
| Peptide, recombinant protein |
IRDye 800CW streptavidin, 0.5 mg |
LI-COR | Cat#926–32230 | |
| Commercial assay or kit |
GalScreen | Applied Bioscience | Cat#T1027 | |
| Commercial assay or kit |
PrimeScript RT-PCR Kit |
TAKARA | Cat#RR014A | |
| Commercial assay or kit |
RNeasy Plus Mini kit |
QIAGEN | Cat#74136 | |
| Commercial assay or kit |
RosetteSep Human CD4 + T Cell Enrichment Cocktail |
Stem Cell Technologies |
Cat#15062 | |
| Commercial assay or kit |
Luciferase Assay System 10-pack |
Promega | Cat#E1501 | |
| Commercial assay or kit |
LEGENDplex Human Anti-Virus Response Panel |
BioLegend | Cat#740390 | |
| Commercial assay or kit |
RayBio C-Series Human Cytokine Antibody Array C5 |
RayBiotech | Cat#AAH-CYT-5–8 | |
| Commercial assay or kit |
FIX and PERM Kit (CE-IVD) (1000 Tests) |
Nordic-MUbio | Cat#GAS-002–1 | |
| Commercial assay or kit |
DNA-free DNA Removal Kit |
ThermoFisher Scientific |
Cat#AM1906 | |
| Commercial assay or kit |
QuikChange II XL Site-Directed Mutagenesis Kit |
Agilent | Cat#200522 | |
| Commercial assay or kit |
TruSeq Stranded mRNA Sample Prep Kit |
illumina | Cat#RS-122–2101 | |
| Commercial assay or kit |
Thermo Script RT-PCR system |
Invitrogen | Cat#11146–016 | |
| Commercial assay or kit |
Signal Enhancer HIKARI kit for Western Blotting and ELISA |
Nacalai Tesque | Cat#02267–41 | |
| Chemical compound, drug |
Human IL-2 IS, premium grade |
MACS Miltenyi Biotec |
Cat#130-097-745 | |
| Chemical compound, drug |
Remel PHA purified | ThermoFisher Scientific |
Cat#R30852801 | |
| Chemical compound, drug |
Recombinant human TNFα |
Sigma Aldrich | Cat#H8916-10UG | |
| Chemical compound, drug |
DAPI | Sigma Aldrich | Cat#D9542-1MG | |
| Software, algorithm |
BD FACSDiva Version 8.0 |
BD Biosciences | https://www.bdbiosciences.com; RRID: SCR_001456 | |
| Software, algorithm |
Corel DRAW 2017 | Corel Corporation | https://www.coreldraw.com/ | |
| Software, algorithm |
GraphPad Prism Version 5.03 |
GraphPad Software, Inc. | https://www.graphpad.com; RRID: SCR_002798 | |
| Software, algorithm |
ImageJ | Open source | http://imagej.nih.gov/ij/ | |
| Software, algorithm |
LI-COR Image Studio Lite Version 3.1 | LI-COR | www.licor.com/; RRID: SCR_013715 | |
| Software, algorithm |
FlowJo_V10 | Tree Star, Inc. | https://www.flowjo.com | |
| Software, algorithm |
ZEN | Zeiss | https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html; RRID:SCR_013672 | |
| Software, algorithm |
Fiji | Open source (Max Planck Institute of Molecular Cell Biology and genetics, Dresden, Germany) |
https://imagej.net/Fiji; RRID:SCR_002285 | |
| Software, algorithm |
GeneMANIA | Open source | http://genemania.org/ | |
| Software, algorithm |
Heatmapper | Open source | http://www2.heatmapper.ca/expression/ | |
| Software, algorithm |
R | Open source | https://www.r-project.org/ | |
| Software, algorithm |
Kallisto | PMID: 27043002 | https://pachterlab.github.io/kallisto/ | |
| Software, algorithm |
DESeq2 | PMID: 25516281 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | |
| Software, algorithm |
GAGE | PMID: 19473525 | https://bioconductor.org/packages/release/bioc/html/gage.html | |
| Software, algorithm |
StepOne and StepOnePlus Software v2.3 |
Thermo Fisher Scientific |
https://www.thermofisher.com/de/de/home/technical-resources/software-downloads/StepOne-and-StepOnePlus-Real-Time-PCR-System.html | |
| Other | Rel/NF-κB target gene database |
Open source | http://bioinfo.lifl.fr/NF-KB/ | |
| Other | RNAseq Data | this paper | GEO accession GSE117655 | |
| Other | Interferome database |
PMID: 23203888 | http://www.interferome.org/interferome/home.jspx |