|
Antibodies
|
| anti-human CD45 |
Biolegend |
Cat# 304032 |
| anti-human CD45 |
Biolegend |
Cat# 304028 |
| anti-human CD3 |
Biolegend |
Cat# 317322 |
| anti-human CD8 |
Biolegend |
Cat# 301066 |
| anti-human CD8 |
Biolegend |
Cat# 301016 |
| anti-human CD8 |
BD Pharmingen |
Cat# 560179 |
| anti-human CD4 |
Biolegend |
Cat# 317440 |
| anti-human CD4 |
Biolegend |
Cat# 317414 |
| anti-human CD28 |
Biolegend |
Cat# 302926 |
| anti-human CD38 |
eBioscience |
Cat# 25-0388-42 |
| anti-human CD39 |
Biolegend |
Cat# 328228 |
| anti-human PD-1 |
Biolegend |
Cat# 329928 |
| anti-human PD-1 |
Biolegend |
Cat# 329918 |
| anti-human TIM3 |
eBioscience |
Cat# 46-3109-42 |
| anti-human LAG3 |
eBioscience |
Cat# 11-2239-42 |
| anti-human CTLA-4 |
Invitrogen |
Cat# 12-159-42 |
| anti-human CD45RO |
Biolegend |
Cat# 304244 |
| anti-human CD45RO |
BD Pharmingen |
Cat# 555493 |
| anti-human CCR7 |
BD Pharmingen |
Cat# 130-126-090 |
| anti-human CD107a |
Biolegend |
Cat# 328618 |
| anti-human IL-2 |
Invitrogen |
Cat# 46-7029-42 |
| anti-human TNFa |
Biolegend |
Cat# 502928 |
| anti-human GM-CSF |
BD Horizon |
Cat# 562930 |
| anti-human IFNg |
Biolegend |
Cat# 506507 |
| anti-human Granzyme B |
BD Horizon |
Cat# 562462 |
| anti-human Ki67 |
Biolegend |
Cat# 350526 |
| anti-human CD80 |
Biolegend |
Cat# 305230 |
| anti-human CD86 |
Biolegend |
Cat# 305442 |
| anti-human ICOS |
Biolegend |
Cat# 313536 |
| anti-mouse CD45 |
Biolegend |
Cat# 103116 |
| anti-mouse FMC63 scFv MAb |
Bioswan |
Cat# 200106 |
| anti-mouse FMC63 scFv MAb |
Bioswan |
Cat# 200102 |
| BCMA CAR Detection |
Miltenyi Biotec |
Cat# 130-126-090 |
| BTK/ITK (Tyr551, Tyr511) Monoclonal Antibody (M4G3LN) |
Thermo Fisher |
Cat#12-9015-42 |
| Phospho-LCK (Tyr505) monoclonal antibody (SRRCHA) |
Thermo Fisher |
Cat#50-9076-42 |
| Phospho-ZAP70/Syk (Tyr319, Tyr352) Monoclonal Antibody (n3kobu5) |
Thermo Fisher |
Cat#12-9006-42 |
| mouse IgG2a, κ Isotype control Antibody |
Biolegend |
Cat# 400269 |
| mouse IgG1, κ Isotype control Antibody |
Biolegend |
Cat# 400126 |
| mouse IgG1, κ Isotype control Antibody |
Biolegend |
Cat# 400168 |
|
Bacterial and virus strains
|
|
|
| One Shot™ Stbl3™ Chemically Competent E. coli |
Invitrogen |
C7373-03 |
|
Biological samples
|
|
|
| T lymphocytes from human healthy donors |
UPenn Human Immunology Core |
N/A |
|
Chemicals, peptides, and recombinant proteins
|
|
|
| Live/Dead Aqua |
ThermoFisher |
Cat# L34957
|
| Zombie NIR (Biolegend) Fixable Viability Kits |
Biolegend |
Cat# 423106 |
| Apotracker™ Green |
Biolegend |
Cat# 427403 |
| Annexin V with 7AAD |
Biolegend |
Cat# 640930 |
| Alt-R® Cas9 Electroporation Enhancer, 10 nmol |
Integrated DNA Technologies |
Cat# 1075916 |
| SpyFi Cas9 |
Aldeveron |
Cat# 9214 |
| P3 Primary cell 4D-nucleofactor X Kit L |
Lonza |
Cat# V4XP-3024 |
| OpTmizer T Cell Expansion SFM |
Gibco |
Cat# A1048501 |
| Human AB Serum |
GeminiBio |
Cat#100-512 |
| Recombinant Human IL-7 |
Peprotech |
Cat#200-07 |
| Recombinant Human IL-15 |
Peprotech |
Cat#200-15 |
| DNAse I roche |
Sigma |
Cat#10104159001 |
| Lipofectamine 2000 |
Thermo Fisher Scientific |
Cat#1166500 |
| DNase I from bovine pancreas |
Sigma |
Cat# 11284932001 |
| EDTA (0.5 M), pH 8.0, RNase-free |
Thermo Fisher |
Cat# AM9261 |
| PE Streptavidin |
BD Pharmingen |
Cat# 554061 |
| APC Streptavidin |
Biolegend |
Cat# 405235 |
| Golgi Stop protein transport inhibitor (containing monensin |
Thermo Fisher |
Cat# BD554724 |
| Cell stimulation cocktail (PMA/Ionomycin) |
Thermo Fisher |
Cat#00497093 |
|
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|
|
Critical commercial assays
|
|
|
| RNA Clean & Concentrator™-5 |
ZYMO |
Cat#R1016 |
| DNeasy Blood & Tissue Kit |
Qiagen |
Cat#69504 |
| NovaSeq6000 S2-100 cycle kit |
Illumina |
Cat#20028316 |
| Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 |
10X Genomics |
Cat#1000121 |
| Chromium Next GEM Chip G Single Cell Kit |
10X Genomics |
Cat#1000120 |
| Chromium Next GEM Single Cell 3’ Library Construction Kit v3.1 |
10X Genomics |
Cat#1000157 |
| Single Index Kit T Set A |
10X Genomics |
Cat#1000213 |
| XT_HS_CART Panel_CSO |
Nanostring |
Cat# 115000343 |
| Master Kit-12 rxns |
Nanostring |
Cat# 100052 |
| DynaBeads CD3x28 (Human) |
ThermoFisher |
Cat# 11131D |
| NucleoSpin Gel and PCR Clean-up |
Macherey-Nagel |
Cat# 74609.50 |
| QIAGEN Plasmid Plus Maxi Kit |
QIAGEN |
Cat# 12963 |
| Fixation Medium (Medium A) |
Invitrogen |
Cat# GAS001S100 |
| Permeabilization Medium (Medium B) |
Invitrogen |
Cat# GAS002S100 |
| CountBright Absolute Counting Beads, (ThermoFisher) |
Thermo Fisher |
Cat# C36950
|
| LongAmp™ Taq 2X Master Mix |
New England Biolabs |
Cat# M0287S |
| Vacuum Filter/Storage Systems |
Corning |
Cat# 430770 |
| Dead cell removal kit |
Miltenyi Biotec |
Cat# 130-090-101 |
| CliniMACS CD4 GMP Microbeads |
Miltenyi Biotec |
Cat# 170-076-702 |
| CliniMACS CD4 GMP Microbeads |
Miltenyi Biotec |
Cat# 170-076-703 |
| LOVO Pouch Disposable Kit |
Fenwal |
Cat# X6R4907 |
| LOVO Processing kit w/ Acess |
Fenwal |
Cat# X6R4909 |
|
Deposited data
|
|
|
| Raw and analyzed data |
This paper |
dbGAP: phs001707.v3 |
|
|
|
|
Experimental models: Cell lines
|
|
|
| Human (female) HEK293T |
ATCC |
CRL-11268 |
| Human (female) NALM6 |
ATCC |
CRL-3273 |
| Human (female) MM.1S |
ATCC |
CRL-2974 |
|
Experimental models: Organisms/strains
|
|
|
| NOD/scid/IL2rγ−/− (NSG) |
Jackson Laboratory |
Cat# 5557 |
|
Oligonucleotides
|
|
|
| PD-1 sgRNA: 5’ GGCCAGGATGGTTCTTAGGT3’ |
Integrated DNA Technologies |
(Ren et al, 2017) |
| CTLA-4 sgRNA: 5’ TATGCCCAGGTAGTATGG3’ |
Integrated DNA Technologies |
N/A |
| PD-1.PCR.F (gDNA): 5’ AGTTTCCCTTCCGCTCACCTC3’ |
Genewiz |
N/A |
| PD-1.PCR.R (gDNA): 5’ ACTAACCTTGGCTTTACGACGT3’ |
Genewiz |
N/A |
| PD-1.Seq.R (PCR): 5’ TGGCAGCCCAGGGGTC3’ |
Genewiz |
N/A |
| CTLA-4.PCR.F (gDNA): 5’GGACATGGGGGAAGTGTGAC3’ |
Genewiz |
N/A |
| CTLA-4.PCR.R (gDNA): 5’AGGTTTACTTTTAGGACTGTGGACA3’ |
Genewiz |
N/A |
| CTLA-4.Seq.F (PCR): 5’ TGTTCTTCCTGCCACAACCA3’ |
Genewiz |
N/A |
| CTLA-4.Seq.R (PCR): 5’ GACACCTGTTGCATTGCAGTC3’ |
Genewiz |
N/A |
|
Recombinant DNA
|
|
|
| pTRPE CD19BBz |
This paper |
N/A |
| pTRPE BCMABBz |
This paper |
N/A |
|
Software and algorithms
|
|
|
| R version 4.1.0 |
CRAN |
https://cran.r-project.org/
|
| Seurat_4.1.0 |
(Butler et al., 2018; Stuart et al., 2019) |
https://satijalab.org/seurat/
|
| Cell Ranger v4.0 |
10X Genomics |
https://www.10xgenomics.com/
|
| sctransform_0.3.3 |
(Hafemeister and Satija, 2019) |
https://cran.r-project.org/web/packages/sctransform/index.html
|
| DESeq2 1.38.3 |
Love et al, 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| EdgeR 3.40.2 |
Robinson et al, 2010
|
https://bioconductor.org/packages/release/bioc/html/edgeR.html
|
| FlowJo™ v10.8 Software |
BD Life Sciences |
https://www.flowjo.com
|
| Ingenuity Pathway Analysis Software |
QIAGEN |
https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/
|
|
Other
|
|
|
| Benchling sgRNA designer tool (https://www.benchling.com, [2020]) |
Benchling |
https://benchling.com/
|
| BioRender illustration design tool |
BioRender |
https://biorender.com/
|
| TIDE: Tracking of Indels by DEcompositionTool |
TIDE |
http://shinyapps.datacurators.nl/tide/
|
| Gene Set enrichment Analysis Software |
GSEA |
https://www.gsea-msigdb.org/gsea/index.jsp
|
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