| Antibodies |
| PLCG2 (Western blot) |
Cell Signaling Technology |
#3872 |
| Beta-catenin (Western blot) |
Cell Signaling Technology |
#8480 |
| pSMAD1/5 (Western blot) |
Cell Signaling Technology |
#9576 |
| SMAD1 (Western blot) |
Cell Signaling Technology |
#6944 |
| SMAD5 (Western blot) |
Cell Signaling Technology |
#12534 |
| N-cadherin (Western blot) |
Cell Signaling Technology |
#14215 |
| Vimentin (Western blot) |
Cell Signaling Technology |
#5741 |
| Twist (Western blot) |
Cell Signaling Technology |
#46702 |
| ZEB (Western blot) |
Cell Signaling Technology |
#70512 |
| NFIB (Western blot) |
Abcam |
#ab186738 |
| SOX2 (Western blot) |
Cell Signaling Technology |
#3579 |
| Nanog (Western blot) |
Cell Signaling Technology |
#4903 |
| Actin (Western blot) |
Cell Signaling Technology |
#3700 |
| donkey anti-rabbit IRDye 800CW |
LI-COR |
#926–32213 |
| donkey anti-mouse IRDye 680LT |
LI-COR |
#926–68022 |
| dsDNA (MIBI) |
Ionpath |
708901–100 |
| LAP2 (MIBI) |
BD Biosciences |
611000 |
| PLCG2 (MIBI) |
CST |
55512BF |
| CD163 (MIBI) |
Bio-Rad |
MCA1853 |
| CD4 (MIBI) |
Ionpath |
714301–100 |
| CD11c (MIBI) |
Ionpath |
714401–100 |
| FoxP3-AF488 (MIBI) |
BD Pharmingen |
561181 |
| Anti-Alexa Fluor 488 (MIBI) |
Invitrogen |
A11094 |
| CD81 (MIBI) |
Abcam |
ab233692 |
| PD-1 (MIBI) |
Ionpath |
714801–100 |
| PD-L1 (MIBI) |
Abcam |
ab226766 |
| CD56 (MIBI) |
Ionpath |
715101–100 |
| CD31 (MIBI) |
Ionpath |
715201–100 |
| ki-67 (MIBI) |
Ionpath |
715302–100 |
| CD68 (MIBI) |
Ionpath |
715601–100 |
| CD8 (MIBI) |
Ionpath |
715801–100 |
| CD3 (MIBI) |
Ionpath |
715901–100 |
| CD16 (MIBI) |
CST |
24326BF |
| TIM3 (MIBI) |
CST |
45208S |
| CD14 (MIBI) |
Abcam |
ab226121 |
| Keratin (MIBI) |
Ionpath |
716501–100 |
| S100A12 (MIBI) |
Lifespan Biosciences |
LS-C785701 |
| NULP1-TCF25 (MIBI) |
Invitrogen |
PA5–21418 |
| RRBP1 (MIBI) |
Millipore Sigma |
HPA009026 |
| VIMENTIN (MIBI) |
CST |
5741BF |
| ASCL1 (MIBI) |
Abcam |
ab240385 |
| ASCL1 (MIBI) |
Abcam |
ab251539 |
| HLA-DR (MIBI) |
Ionpath |
717201–100 |
| NeuroD1 (MIBI) |
Abcam |
ab226489 |
| CD45 (MIBI) |
Ionpath |
717501–100 |
| HLA I (176) (MIBI) |
Ionpath |
717602–100 |
| ASCL1 (IHC) |
BD |
#556604 |
| NEUROD1 (IHC) |
Abcam |
#ab205300 |
| POU2F3 (IHC) |
Santa Cruz |
#6D1 |
| PLCG2 (IHC) |
Sigma-Aldrich |
#HPA020100 |
| Bacterial and Virus Strains |
| Biological Samples |
| Chemicals, Peptides, and Recombinant Proteins |
| Critical Commercial Assays |
| Cultrex BME Cell invasion assay kit |
R&D Systems |
#3455–096-K |
| CellTiter-Glo 2.0 assay |
Promega |
#G9242 |
| Wnt signaling reporter assay |
BPS Biosciences |
#60500 |
| Firefly/Renilla luciferase assay kit |
Sigma Millipore |
#SCT152 |
| Deposited Data |
| scRNA-seq and MIBI data |
HTAN Data Portal |
https://data.humantumoratlas.org/
|
|
|
|
| Experimental Models: Cell Lines |
| H82 |
ATCC |
#HTB-175 |
| SHP-77 |
ATCC |
#CRL-2195 |
| H526 |
ATCC |
#CRL-5811 |
| H446 |
ATCC |
#HTB-171 |
| DMS-114 |
ATCC |
#CRL-2066 |
| Experimental Models: Organisms/Strains |
| Oligonucleotides |
| Recombinant DNA |
| PLCG2 overexpression lentiviral plasmid |
GeneCopoeia |
#EX-A8643-Lv201 |
|
PLCG2 CRISPR knock out lentiviral plasmid |
Sigma-Aldrich |
#HSPD0000031727 |
| Software and Algorithms |
| SEQC |
Azizi, et al., 2018
|
https://github.com/dpeerlab/seqc
|
| CB2 |
Ni, et al. 2020
|
https://github.com/zijianni/scCB2
|
| DoubletDetection |
Gayoso, et al. 2018 |
https://github.com/dpeerlab/doubletdetection
|
| scanpy (suite of single-cell algorithms, including UMAP, tSNE, score_genes, among others) |
Wolf, et al., 2018 |
https://scanpy.readthedocs.io/en/stable/#
|
| PhenoGraph (includes clustering and Markov absorption modeling) |
Levine, et al. 2015
|
https://github.com/dpeerlab/phenograph
|
| fastMNN (through the batchelor package) |
Haghverdi, et al. 2018 |
https://github.com/LTLA/batchelor/blob/master/R/fastMNN.R
|
| MAGIC and knnDREMI |
van Dijk, et al. 2018
|
https://github.com/dpeerlab/magic
|
| MAST |
Finak, et al. 2015
|
https://github.com/RGLab/MAST
|
| limma |
Ritchie, et al. 2015
|
https://bioconductor.org/packages/release/bioc/html/limma.html
|
| fGSEA |
Korotkevich, et al. 2019 |
https://bioconductor.org/packages/release/bioc/html/fgsea.html
|
| Ambient RNA detection |
Smillie, et al. 2019
|
https://github.com/cssmillie/ulcerative_colitis
|
| DirichletReg |
Maier, et al. 2014 |
https://cran.r-project.org/web/packages/DirichletReg/index.html
|
| cellphonedb |
Efremova, et al. 2020
|
https://github.com/Teichlab/cellphonedb
|
| survival |
Therneau, et al. 2020 |
https://cran.r-project.org/web/packages/survival/index.html
|
| Non-negative matrix factorization in Scikit-learn v. 20.0 |
Pedregosa, et al. 2011 |
https://scikit-learn.org/stable/
|
| Vectra Imaging Processing Pipeline |
|
https://github.com/dpeerlab/Vectra_Imaging_pipeline
|
| MaskRCNN_cell (segmentation for Vectra image) |
|
https://github.com/dpeerlab/MaskRCNN_cell
|
| ARK-analysis (MIBI analysis) |
|
https://github.com/angelolab/ark-analysis
|
| Mesmer |
Noah F. Greenwald et al. 2021
|
https://github.com/vanvalenlab/deepcell-tf
|
| squidpy |
Giovanni Palla, et al. 2021
|
https://github.com/theislab/squidpy/
|
|
|
|
| Other |
