|
| Antibodies |
|
| CD4 neg selection kit for IMag: human CD4 T cell |
BD Biosciences |
Cat#557939; RRID: AB_2802162 |
| Anti-human CD3 BB |
BD Biosciences |
Cat#564465; RRID: AB_2744386 |
| Anti-human CD8 PeCy7 |
BD Biosciences |
Cat#557746; RRID: AB_396852 |
| Anti-human CD45 PerCPCy5.5 |
BD Biosciences |
Cat#564105; RRID: AB_2744405 |
| Anti-human CD45 RO PE |
BD Biosciences |
Cat#555493; RRID: AB_395884 |
| Anti-human CD45 RO PerCPCy5.5 |
BD Biosciences |
Cat#560607; RRID: AB_1727500 |
| Anti-human CD45 RA APC |
BD Biosciences |
Cat#550855; RRID: AB_398468 |
| Anti-human CD27 APC |
BD Biosciences |
Cat#561400; RRID: AB_10645790 |
| Anti-human CD197 (CCR7) PE |
BD Biosciences |
Cat#560765; RRID: AB_2033949 |
| Anti-human CD34 GP 105–120 |
BD Biosciences |
Cat#560940; RRID: AB_10563908 |
| Lineage Cocktail 1 (lin1) |
BD Biosciences |
Cat#340546; RRID: AB_400053 |
| Anti-human CD206 |
BD Biosciences |
Cat#555954; RRID: AB_396250 |
| Viability stain 780 |
BD Biosciences |
Cat#565388 |
| FCR blocking reagent |
Milteyni Biotec |
Cat#130–059-901 |
|
| Chemicals, Peptides, and Recombinant Proteins |
|
| Leukosept tubes |
Fisher Scientific |
Cat#10349081 |
| Lymphoprep |
Elitech |
AXI-1114547 |
| RPMI |
Thermo Fisher |
Cat#21875034 |
| EDTA |
Thermo Fisher |
Cat#15575020 |
| PBS PH 7,2 |
Thermo Fisher |
Cat#20012019 |
| L-glutamine |
Thermo Fisher |
Cat#25030024 |
| Penicilin/Streptomycine |
Thermo Fisher |
Cat#15140122 |
| HBSS |
Thermo Fisher |
Cat#14175053 |
| DTT |
Thermo Fisher |
Cat#20290 |
| Costar 6 well plates |
Sigma Aldrich Costar |
SKU CLS3471–24EA |
| Lysis buffer (10mM TRisHCl, 0.5%NP-40, 0.5% Tween-20) |
Made in the lab following protocol |
N/A |
| Proteinase K 20mg/ml |
Ambion /Lifetechnologies |
Cat#AM2546 |
| PCR nucleotide mix 10mM 1ml |
Promega |
Cat#C1145 |
| 6M guanidinium thiocyanate BioUltr |
Sigma Aldrich |
SKU 50980–50ml; CAS 593–84-0 |
| Glycogen (from mussels) 20mg |
Roche |
SKU 10901393001 |
| Tris buffered saline (tablets) |
Sigma Aldrich |
T5030–100Tab |
| Isopropanol (2-propanolol) for molecular biology |
Sigma Aldrich |
I9516; CAS 67–63-0 |
| Ultracentrifuge tubes (optiseal, polypropylene 8,9, 16x60mm, (qty56) |
Beckman Coulter |
361623 |
| Ethanol 100%(ethyl alcohol, Pure 200 proof, for molecular biology) |
Sigma Aldrich |
E7023–1L; CAS 64–17-5 |
| Ultrapure 1MTrisHCL PH 8 |
Thermo Fisher Scientific |
Cat#15568–025 |
| Corning Cell strainers 40μm |
Sigma Aldrich |
CLS 431750–50AE |
| Corning Cell strainers 70μm |
Sigma Aldrich |
CLS 431751–50AE |
| Fetal Calf Serum (FCS) |
Hyclone RVM |
35888 |
|
| Critical Commercial Assays |
|
| Superscript III 1st strand |
Invitrogen |
Cat#18080051 |
| Platinum Taq PCR polymerase |
Invitrogen |
Cat#10966083 |
| E-Gel 96 well 1% agarose |
Thermo Fisher Scientific |
Cat#G700801 |
|
| Oligonucleotides |
|
| E20 F 5'GGGCCACACATGCCTGTGTACCCACAG 3' |
Josefsson et al., 2012; von Stockenstrom et al., 2015
|
N/A |
| E115 5' GAAAAATTCCCCTCCACAATTAA 3' |
Josefsson et al., 2012; von Stockenstrom et al., 2015
|
N/A |
| E30 F 5'GTGTACCCACAGACCCCAGCCCACAAG3' |
Josefsson et al., 2012; von Stockenstrom et al., 2015
|
N/A |
| E125 R 5'CAATTTCTGGGTCCCCTCCTGAGG 3' |
Josefsson et al., 2012; von Stockenstrom et al., 2015
|
N/A |
|
| Deposited Data |
|
| RNA and DNA sequencing |
Genbank |
MH642355 |
| RNA and DNA sequencing |
Genbank |
MH642607 |
| RNA and DNA sequencing |
Genbank |
MH642608 |
| RNA and DNA sequencing |
Genbank |
MH643062 |
| RNA and DNA sequencing |
Genbank |
MH643063 |
| RNA and DNA sequencing |
Genbank |
MH643573 |
|
| Software and Algorithms |
|
| Subtype analyses |
Smartgene, Lausanne, Switzerland |
https://www.smartgene.com/
|
| Viral Tropism |
Web PSSM, Mullins lab, University of Washington |
https://indra.mullins.microbiol.washington.edu/webpssm/
|
| Flow Jo software |
BD Biosciences |
https://www.flowjo.com/
|
| Perl script language |
Perl |
https://www.perl.org/
|
| MUSCLE |
Edgar, 2004
|
http://www.megasoftware.net/
|
| MAFFT |
Katoh and Standley, 2013
|
https://mafft.cbrc.jp/alignment/software/
|
| Aliview |
Larsson, 2014
|
www.ormbunkar.se/aliview/downloads
|
| RDP4 |
Martin et al., 2015
|
http://web.cbio.uct.ac.za/~darren/rdp.html
|
| Translator X |
Abascal et al., 2010
|
http://www.translatorx.co.uk/
|
| PhyML v3.0 |
Guindon and Gascuel, 2003
|
https://github.com/stephaneguindon/phyml/
|
| BaTS |
Parker et al., 2008
|
http://evolve.zoo.ox.ac.uk/Evolve/BaTS.html
|
| Mr Bayes v3.6.2 |
Ronquist et al., 2012
|
http://nbisweden.github.io/MrBayes/download.html
|
| Tracer |
BEAST |
https://github.com/beast-dev/tracer/releases/tag/v1.7.1
|
| Biopython |
Cock et al., 2009
|
https://biopython.org/wiki/Download
|
| Elim Dupes |
Los Alamos HIV Database |
http://www.hiv.lanl.gov
|
| R: A language and environment for statistical computing. |
R script |
https://www.R-project.org/
|
| General Liner hypothesis function (glht) |
R package multcomp |
https://cran.r-project.org/web/packages/multcomp/index.html
|
| FigTree |
BEAST |
http://beast.community/figtree
|
| iTol v3 |
Letunic and Bork, 2016
|
https://itol.embl.de/
|
| NETWORK v5.0.0.3 |
Fluxus |
http://www.fluxus-engineering.com
|
| SPADS 1.0 |
Dellicour and Mardulyn, 2014
|
http://ebe.ulb.ac.be/ebe/SPADS.html
|
|
| Others |
|
| Sanger sequencing |
AGRF Australian Genome Research Facility, Sydney, Australia |
N/A |
