| Antibodies |
| Mouse anti-human MLH1 |
Roche |
M1; Cat#6472966001 |
| Mouse anti-human MSH2 |
Roche |
G219-1129; Cat#5269270001 |
| Mouse anti-human MSH6 |
Abcam |
EP49; Cat#AC-0047 |
| Mouse anti-human PMS2 |
Agilent Technologies |
EP51; Cat# M3647 |
| Mouse anti-human CD28 |
eBioscience |
CD28.2; Cat#16-0289-81 |
| Mouse anti-human HLA-ABC (PE-conjugated) |
BD |
G46-2.6; Cat#555553 |
| Mouse anti-human CD274 (PD-L1) (APC-conjugated) |
eBioscience |
MIH1; Cat#17-5983-41 |
| Mouse IgG1 κ isotype control (PE-conjugated) |
BD |
MOPC-21; Cat#556650 |
| Mouse IgG1 κ isotype control (APC-conjugated) |
eBioscience |
P3.6.2.8.1; Cat#17-4714-41 |
| Mouse anti-human CD107a (PE-conjugated) |
BD |
H4A3; Cat#555801 |
| Mouse anti-human CD3 (PerCP-Cy5.5-conjugated) |
eBioscience |
SK7; Cat#332771 |
| Mouse anti-human CD4 (FITC-conjugated) |
BD |
RPA-T4; Cat#555346 |
| Mouse anti-human CD8 (BV421-conjugated) |
BD |
RPA-T8; Cat#562429 |
| Mouse anti-human IFNγ (APC-conjugated) |
BD |
B27; Cat#554702 |
| Mouse anti-human CD137 (APC-conjugated) |
BD |
4B4-1; Cat#550890 |
| Mouse anti-human CD3 |
eBioscience |
OKT-3; Cat#16-0037-85 |
| Mouse anti-human HLA-ABC |
The Netherlands Cancer Institute |
W6/32 |
| Mouse anti-human HLA-DR/DP/DQ (sodium azide free) |
BD |
Tü39; Cat#555556 |
| Mouse anti-human CD3 (Alexa Fluor 700-conjugated) |
Invitrogen |
UCHT1; Cat#CD0329 |
| Mouse anti-human CD326 (EpCAM) (PE/Cy7-conjugated) |
Biolegend |
9C4; Cat#324222 |
| Anti-human PD1 |
Merus |
N/A |
| Mouse anti-human HLA-ABC |
Nordic Mubio |
HCA2; Cat#MUB2036P |
| Mouse anti-human HLA-ABC |
Nordic Mubio |
HC10; Cat#MUB2037P |
| Mouse anti-human p53 |
Agilent Technologies |
DO-7 |
| Biological Samples |
| Patient tumor and normal colon or lung tissue |
The Netherlands Cancer Institute |
study NL48824.031.14 |
| Patient blood |
The Netherlands Cancer Institute |
study NL48824.031.14 |
| Healthy donor blood (buffy coat) |
Sanquin blood bank |
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
| B27 supplement without vitamin A |
Gibco |
Cat#C12587-010 |
| B27 supplement |
Gibco |
Cat#17504-044 |
| N-Acetylcysteine |
Sigma-Aldrich |
Cat#A9165-5G |
| Nicotinamide |
Sigma-Aldrich |
Cat#N0636 |
| Human recombinant EGF |
Peprotech |
Cat#AF-100-15 |
| A83-01 |
Tocris |
Cat#2939 |
| SB202190 |
Cayman Chemicals |
Cat#10010399 |
| Prostaglandin E2 |
Cayman Cehmicals |
Cat#14010-1 |
| Y-27632 |
Sigma-Aldrich |
Cat#Y-0503 |
| Human recombinant FGF-7 |
Peprotech |
Cat#100-19 |
| Human recombinant FGF-10 |
Peprotech |
Cat#100-26 |
| Geltrex LDEV-free reduced growth factor basement membrane |
Gibco |
Cat#A1413202 |
| Collagenase type II |
Sigma-Aldrich |
Cat#C6885 |
| Hyaluronidase type IV |
Sigma-Aldrich |
Cat#H3506 |
| Advanced DMEM-F12 |
Gibco |
Cat#12634-028 |
| Penicillin/streptomycin |
Gibco |
Cat#15070063 |
| Ultraglutamine type I |
Lonza |
Cat#BE17-605E |
| HEPES |
Gibco |
Cat#15630-056 |
| TrypLE Express |
Gibco |
Cat#12604-013 |
| Recovery Cell Culture Freezing Medium |
Gibco |
Cat#12648-010 |
| Nutlin-3a |
Cayman Chemicals |
Cat#10004372 |
| RPMI 1640 |
Gibco |
Cat#11875093 |
| Human serum, from human male AB plasma |
Sigma-Aldrich |
Cat#H3667 |
| Benzonase |
Merck |
Cat#70746-3 |
| Human recombinant interferon gamma |
Peprotech |
Cat#300-02 |
| GolgiSTOP (Monensin) |
BD |
Cat#554724 |
| GolgiPLUG (Brefeldin A) |
BD |
Cat#555029 |
| Phorbol 12-myristate 13-acetate (PMA) |
Sigma-Aldrich |
Cat#19-144 |
| Ionomycin |
Sigma-Aldrich |
Cat#I9657 |
| Dispase type II |
Sigma-Aldrich |
Cat#D4693 |
| Cell Recovery Solution |
Corning |
Cat#354253 |
| GMP DC medium |
CellGenix |
Cat#20801-0500 |
| Recombinant human GM-CSF |
CellGenix |
Cat#1012-050 |
| Recombinant human IL-1β |
CellGenix |
Cat#1011-050 |
| Recombinant human IL-4 |
CellGenix |
Cat#1003-050 |
| Recombinant human TNF-α |
CellGenix |
Cat#1006-050 |
| Recombinant human IL-6 |
CellGenix |
Cat#1004-060 |
| Interleukin-2 |
|
Proleukin |
| Prostaglandin E1 |
|
Alprostadil |
| Critical Commercial Assays |
| DNeasy blood and tissue kit |
Qiagen |
Cat#69504 |
| Fixation/Permeabilization solution kit |
BD |
Cat#554714 |
| Live/dead fixable near-IR dead cell stain kit |
Invitrogen |
Cat#L10119
|
| CD137 Microbead kit, human |
Miltenyi |
Cat#130-093-476 |
| CellTrace Yellow Cell Proliferation Kit |
Invitrogen |
Cat#C34567
|
| CellTrace Far Red Cell Proliferation Kit |
Invitrogen |
Cat#C34564
|
| AccuCount blank particles (7.0 – 7.9 μm) |
Spherotech |
Cat#ACBP-70-10 |
| NucView488 Caspase-3 assay kit |
Biotium |
Cat#30029 |
| Experimental Models: Cell Lines |
| L-Wnt3a cell line |
Laboratory of Hans Clevers, Hubrecht Institute |
L-Wnt3a |
| R-spondin producer cell line |
Laboratory of Calvin Kuo, Stanford |
293T-HA-RspoI-Fc |
| Noggin producer cell line |
Laboratory of Hans Clevers, Hubrecht Institute |
HEK293-mNoggin-Fc |
| Software and Algorithms |
| Optitype |
Szolek et al. 2014 |
https://github.com/F RED-2/OptiType |
| Somatic Sniper |
Larson et al. 2012 |
http://gmt.genome.wustl.edu/packages/somatic-sniper/ |
| Somatic Indel Detector (GATK) |
McKenna et al. 2010 |
https://software.broadinstitute.org/gatk/ |
| snpEff, version 4.3 |
Cingolani et al. 2012 |
http://snpeff.sourceforge.net |
| FlowJo version 10 |
|
https://www.flowjo.com/ |
| ImageJ version 1.50i |
Schneider et al. 2012 |
https://imagej.nih.gov/ij/ |
