| Anti-human CD45RO APC |
BD Biosciences |
Cat#559865; AB_398673 |
| Anti-human CD45RA PcrCP5.5 |
BD Biosciences |
Cat#563429; AB_2738199 |
| Anti-human HLA-DR APC-Cy7 |
BD Biosciences |
Cat#641393; AB_1645739 |
| Anti-human CD39 FITC |
BD Biosciences |
Cat#561444; AB_10896292 |
| Anti-human CD39 FITC |
Biolegend |
Cat#328206; AB_940425 |
| Anti-human CD103 PE |
Biolegend |
Cat#350206; AB_10641843 |
| Anti-human CD4 PE-Cy7 |
BD Biosciences |
Cat#348789; AB_400379 |
| Anti-human CD8 PE-Cy7 |
BD Biosciences |
Cat#335787; AB_399966 |
| Anti-mTCRp PE |
BD Biosciences |
Cat#553172; AB_394684 |
| Anti-human CD3 APC-Cy7 |
BD Biosciences |
Cat#341090; AB_400214 |
| Anti-human CD137 (4–1BB) APC |
BD Biosciences |
Cat#550890; AB_398477 |
| TotalSeqC Anti-human LGALS3 |
Biolegend |
Cat#125423; AB_2819851 |
| TotalSeqC Anti-human KLRG1 |
Biolegend |
Cat#138433; AB_2800649 |
| TotalSeqC Anti-human CD28 |
Biolegend |
Cat#302963; AB_2800751 |
| TotalSeqC Anti-human CD29 |
Biolegend |
Cat#303029; AB_10752594 |
| TotalSeqC Anti-human CD45RA |
Biolegend |
Cat#304163; AB_2800764 |
| TotalSeqC Anti-human CD45RO |
Biolegend |
Cat#304259; AB_2800766 |
| TotalSeqC Anti-human CD62L |
Biolegend |
Cat#304851; AB_2800770 |
| TotalSeqC Anti-human CD94 |
Biolegend |
Cat#305523; AB_2814143 |
| TotalSeqC Anti-human HLA-DR |
Biolegend |
Cat#307663; AB_2800795 |
| TotalSeqC Anti-human CD39 |
Biolegend |
Cat#328237; AB_2800853 |
| TotalSeqC Anti-human CD274 (PD-L1) |
Biolegend |
Cat#329751; AB_2800860 |
| TotalSeqC Anti-human CD279 (PD-1) |
Biolegend |
Cat#329963; AB_2800862 |
| TotalSeqC Anti-human TIM-3 |
Biolegend |
Cat#345049; AB_2800925 |
| TotalSeqC Anti-human CD103 |
Biolegend |
Cat#350233; AB_2800933 |
| TotalSeqC Anti-human CD127 (IL7R) |
Biolegend |
Cat#351356; AB_2800937 |
| TotalSeqC Anti-human CD197 (CCR7) |
Biolegend |
Cat#353251; AB_2800943 |
| TotalSeqC Anti-human CD183 (CXCR3) |
Biolegend |
Cat#353747; AB_2800949 |
| TotalSeqC Anti-human CD357 (GITR) |
Biolegend |
Cat#371227; AB_2810583 |
| TotalSeqC Anti-human TIGIT |
Biolegend |
Cat#372729; AB_2801021 |
| TotalSeqC Anti-human LAG-3 |
Biolegend |
Cat#369335; AB_2814327 |
| TotalSeqC PE Strepavidin (EBV LMP2A tetramer) |
Biolegend |
Cat#405265 |
| TotalSeqC PE Strepavidin (Influenza M1 tetramer) |
Biolegend |
Cat#405263 |
|
|
Biological samples
|
|
| Patient peripheral blood samples |
This Paper |
n/a |
|
|
Chemicals, peptides, and recombinant proteins
|
|
| Tandem mini genes |
Genscript |
custom made |
| HPLC peptides |
Genscript |
custom made |
| Crude peptides |
Genscript and inhouse |
custom made |
| Custom-made photo-cleavable HLA monomers |
Gift from Pia Kvistborg |
custom made |
|
|
Critical commercial assays
|
|
| Chromium Next GEM Single Cell 5’ Kit v2 |
10xGenomics |
Cat#1000263 |
| Chromium Single Cell Human TCR Amplification Kit |
10xGenomics |
Cat#1000252 |
| Chromium Next GEM Chip K Single Cell kit |
10xGenomics |
Cat#1000287 |
| Library Construction Kit |
10xGenomics |
Cat#1000190 |
| 10x Chromium controller system |
10xGenomics |
Cat#120223 |
| NextSeq 2000 |
Illumina |
Cat#20038897 |
|
|
Deposited data
|
|
| Human GI cancer patient 4246 PBL scRNAseq dataset |
This paper |
dbGaP: phs003064.v1.p1 |
| Human breast cancer patient 4180 PBL scRNAseq dataset |
This paper |
dbGaP: phs003064.v1.p1 |
| Human GI cancer patient 4287 PBL scRNAseq dataset |
This paper |
dbGaP: phs003064.v1.p1 |
| Human GI cancer patient 4324 PBL scRNAseq dataset |
This paper |
dbGaP: phs003064.v1.p1 |
| Human GI cancer patient 4422 PBL scRNAseq dataset |
This paper |
dbGaP: phs003064.v1.p1 |
| Human GI cancer patient 4317 PBL scRNAseq dataset |
This paper |
dbGaP: phs003064.v1.p1 |
| Human GI cancer patient 4382 PBL scRNAseq dataset |
This paper |
dbGaP: phs003064.v1.p1 |
| Human melanoma cancer patient 3791 PBL scRNAseq dataset |
This paper |
dbGaP: phs003064.v1.p1 |
| Human GI cancer patient 4359 PBL scRNAseq dataset |
This paper |
dbGaP: phs003064.v1.p1 |
|
|
Software and algorithms
|
|
| CellRanger |
10xGenomics |
https://support.10xgenomics.com/single-cell-gene-expression/software
|
| Seurat (4.0.2) |
Satija Laboratory |
https://github.com/satijalab/seurat
|
| R (4.0.4) |
R project |
https://www.r-project.org/
|
|
| FlowJo v10.08 |
Tree Star |
https://www.flowjo.com/
|
| GraphPad Prism 9.0 |
GraphPad |
https://www.graphpad.com/scientific-software/prism/
|
