Antibodies |
|
Goat-anti human IgG-Fc |
Bethyl Laboratories |
A80-104A |
MSD SULFO-TAG Labeled Anti-Human Antibody (Goat) |
MSD |
R32AJ-1 |
Anti-human CD45 PerCP/Cy5.5 |
BioLegend |
304028 |
Anti-mouse CD45 Dazzle594 |
BioLegend |
103146 |
Anti-human CD3 BV650 |
BioLegend |
317324 |
Anti-human CD4 AF700 |
BioLegend |
357418 |
Anti-human CD8 BV785 |
BioLegend |
344740 |
Anti-human CD19 BV421 |
BioLegend |
302234 |
Anti-human CD27 BV711 |
BioLegend |
356430 |
Anti-human CD62L BV510 |
BioLegend |
304844 |
Anti-human PD1 PE |
BD |
557946 |
Anti-human TIM-3 APC/Cyanine7 |
BioLegend |
345026 |
Anti-human CD45RA PerCP/Cyanine5.5 |
BioLegend |
304122 |
Anti-human CD45RO PE/Cyanine7 |
BioLegend |
304230 |
|
Bacterial and virus strains |
|
pHAGE-Ef1a-IRES-WPRE |
This paper |
N/A |
|
Biological samples |
|
Leukopak |
StemCell |
70500 |
Apheresis leukoreduction collars |
obtained from the blood bank of the Brigham and Women's Hospital under DFCI approved IRB protocol #14-343 |
N/A |
|
Chemicals, peptides, and recombinant proteins |
|
Polyethylenimine, PEI |
|
|
Lenti-X™ Concentrator |
Clontech |
631231 |
Ficoll-Paque-PLUS |
GE Healthcare |
45001750 |
Gentamicin |
Gibco |
15750060 |
IL-21 |
Miltenyi Biotec |
130-095-784 |
IL-7 |
Miltenyi Biotec |
130-095-363 |
IL-15 |
Miltenyi Biotec |
130-095-765 |
D-luciferin potassium salt |
Promega |
E1605 |
|
Critical commercial assays |
|
Zombie Yellow™ Fixable Viability Kit |
BioLegend |
423104 |
Tumor Dissociation Kit |
Miltenyi Biotec |
130-095-929 |
CD34 microbead kit |
Miltenyi Biotec |
130-100-453 |
CD4 microbeads |
Miltenyi Biotec |
130-097-048 |
CD8 microbeads |
Miltenyi Biotec |
130-097-057 |
TransAct kit |
Miltenyi Biotec |
130-111-160 |
|
Deposited data |
|
scRNAseq data |
This paper |
GSE210664 |
Kevin Bi et al. |
Single Cell Portal |
Single Cell Portal: https://singlecell.broadinstitute.org/single_cell/study/SCP1288/tumor-and-immune-reprogramming-during-immunotherapy-in-advanced-renal-cell-carcinoma#study-summary
|
Codes |
This paper |
https://doi.org/10.5281/zenodo.7274663 |
Supplementary tables |
This paper; Zenodo Data |
Table S2∼10; https://doi.org/10.5281/zenodo.10456704
|
|
Software and algorithms |
|
Cellranger |
10x genomics |
https://www.10xgenomics.com/support/software/cell-ranger |
Seurat |
Hao et al.99
|
https://satijalab.org/seurat/ |
harmony |
Korsunsky et al.100
|
https://portals.broadinstitute.org/harmony/index.html |
CellChat |
Jin et al.64
|
https://github.com/sqjin/CellChat |
Velocyto |
La Manno et al.50
|
https://velocyto.org/ |