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. Author manuscript; available in PMC: 2022 Aug 22.
Published in final edited form as: Cell Rep. 2022 Aug 2;40(5):111147. doi: 10.1016/j.celrep.2022.111147

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
c-Fos (9F6) Rabbit mAb Cell Signaling Technologies Cat# 2250, RRID: AB_2247211
Phospho-c-Fos (Ser32) (D82C12) XP® Rabbit mAb Cell Signaling Technologies Cat# 5348, RRID: AB_10557109
Recombinant Anti-FRA1 [EP4711] Rabbit mAb Abcam Cat# ab124722, RRID: AB_11001005
Phospho-FRA1 (Ser265) (D22B1) Rabbit mAb Cell Signaling Technologies Cat# 5841, RRID: AB_10835210
Fra2 (D2F1E) Rabbit mAb Cell Signaling Technologies Cat# 19967, RRID: AB_2722526
c-Jun (60A8) Rabbit mAb Cell Signaling Technologies Cat# 9165, RRID: AB_2130165
Phospho-c-Jun (Ser73) (D47G9) XP® Rabbit mAb Cell Signaling Technologies Cat# 3270, RRID: AB_2129575
JunD (D17G2) Rabbit mAb Cell Signaling Technologies Cat# 5000, RRID: AB_10949318
JunB (C37F9) Rabbit mAb Cell Signaling Technologies Cat# 3753, RRID: AB_2130002
Phospho Anti-ATF1 (S63) Rabbit mAb Abcam Cat# ab76085, RRID: AB_1523174
Recombinant Anti-ATF2 [E243] Abcam Cat# ab32160, RRID: AB_2243137
Recombinant Anti-ATF2 (phospho T71) [E268] Abcam Cat# ab32019, RRID: AB_725567
Anti-ATF3 Abcam Cat# ab87213, RRID: AB_1951498
Recombinant Anti-ATF4 antibody [EPR18111] Abcam Cat# ab184909, RRID: AB_2819059
Anti-ATF4 (phospho S245) Abcam Cat# ab28830, RRID: AB_725570
Recombinant Anti-ATF5 [EPR18286] Abcam Cat# ab184923, RRID: AB_2800462
Anti-ATF6 antibody [1–7] Abcam Cat# ab122897, RRID: AB_10899171
Phospho pErk1/2 (T202/Y204) Rabbit mAb Cell Signaling Technologies Cat# 4370, RRID: AB_2315112
Human MITF Antibody R&D Systems Cat# AF5769, RRID: AB_2235141
Anti-SOX10 antibody [SOX10/991] Abcam Cat# ab212843, RRID: AB_2889150
p75NTR Rabbit mAb Cell Signaling Technologies Cat# 8238, RRID: AB_10839265
Human Axl Antibody R&D Systems Cat# AF154, RRID: AB_354852
Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 647 Invitrogen Cat# A-21245, RRID: AB_141775
Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 568 Invitrogen Cat# A-11004, RRID: AB_2534072
Chemicals, peptides, and recombinant proteins
Vemurafenib Selleck Chemicals Cat# S1267
Trametinib Selleck Chemicals Cat# S2673
DharmaFECT 2 Horizon Discovery Cat# T-2002–01
MycoAlert™ PLUS Mycoplasma Detection Kit Lonza Cat# LT07–701
DMEM with 4.5 g/L glucose Corning Cat# 10–013-CV
Fetal bovine serum Gibco Cat# 26140079
EMEM Corning Cat# 10–009-CV
DMEM/F12 Gibco Cat# 11330–032
Sodium pyruvate Gibco Cat# 11360070
RPMI 1640 Corning Cat# 10–040-CV
Plasmocin Prophylactic Invivogen Cat# NC9886956
L-Glycine Sigma Cat# 50046
Urea Sigma Cat# U5128
Guanidinium chloride Sigma Cat# 3272
TCEP-HCl Sigma Cat# C4706
Intercept blocking buffer LiCor Cat# 927–70001
Maleimide Sigma Cat# 129585
N-Acetyl-Cysteine Sigma Cat# A7250
Hoechst 33342 Invitrogen Cat# H3570
CellMask Green ThermoFisher Cat# C37608
Deposited data
Single cell 4i protein measurements (Data S1, S4, and S5) This paper N/A
Bulk gene expression data for 53 melanoma cell lines (Tsoi et al., 2018) GEO Accession: GSE80829
Bulk gene expression data for 32 melanoma cell lines from the Cancer Cell Line Encyclopedia (CCLE). (Ghandi et al., 2019) https://sites.broadinstitute.org/ccle
SCENIC regulons of 10 melanoma cell lines (Wouters et al., 2020) http://scope.aertslab.org/#/Wouters_Human_Melanoma
Single cell gene expression data of patient-derived melanoma tumors (Jerby-Arnon et al., 2018; Tirosh et al., 2016) GEO Accession: GSE72056; GSE115978
Single cell signature enrichment and regulon activity data of melanoma cell lines and patient-derived tumors (Data S2 and S3) This paper N/A
AP-1 siRNA knockdown effects in melanoma cell lines measured by 4i (Data S6) This paper N/A
Experimental models: Cell lines
Human: COLO858, Melanoma Cell Line MGH Cancer Center, primary source ECACC Cat# 93052613, RRID: CVCL_2005
Human: RVH421, Melanoma Cell Line MGH Cancer Center, primary source DSMZ Cat# ACC 127, RRID: CVCL_1672
Human: A375, Melanoma Cell Line ATCC Cat# CRL-1619, RRID: CVCL_0132
Human: A375 NRAS(Q61K), Melanoma Cell Line ATCC Cat# CRL-1619IG-2, RRID: CVCL_JF22
Human: C32, Melanoma Cell Line MGH Cancer Center, primary source ATCC Cat# CRL-1585, RRID: CVCL_5246
Human: A2058, Melanoma Cell Line ATCC Cat# CRL-11147, RRID: CVCL_1059
Human: WM115, Melanoma Cell Line MGH Cancer Center, primary source ATCC Cat# CRL-1619, RRID: CVCL_0040
Human: SKMEL28, Melanoma Cell Line MGH Cancer Center, primary source ATCC Cat# HTB-72, RRID: CVCL_0526
Human: HS294T, Melanoma Cell Line ATCC Cat# HTB-140, RRID: CVCL_0331
Human: WM1552C, Melanoma Cell Line MGH Cancer Center, primary source ATCC Cat# CRL-2808, RRID: CVCL_6472
Human: SKMEL5, Melanoma Cell Line ATCC Cat# HTB-70, RRID: CVCL_0527
Human: A101D, Melanoma Cell Line ATCC Cat# CRL-7898, RRID: CVCL_1057
Human: IGR39, Melanoma Cell Line DSMZ Cat# ACC 239, RRID: CVCL_2076
Human: LOXIMVI, Melanoma Cell Line MGH Cancer Center, primary source Sigma Cat# SCC201, RRID: CVCL_1381
Human: MMACSF, Melanoma Cell Line MGH Cancer Center, primary source RIKEN BioResource Center Cat# RCB1200, RRID: CVCL_1420
Human: WM902B, Melanoma Cell Line Wistar Cat# WM902B-01–0001, RRID: CVCL_6807
Human: WM2664, Melanoma Cell Line Wistar Cat# WM266–4-01–0001, RRID: CVCL_2765
Human: UACC62, Melanoma Cell Line Broad Institute, primary source N/A RRID: CVCL_1780
Human: SKMEL19, Melanoma Cell Line Broad Institute, primary source N/A RRID: CVCL_6025
Oligonucleotides
See Table S1 for oligonucleotide sequences. This paper N/A
Software and algorithms
Source code for analyses This paper https://github.com/fallahi-sichani-lab/AP1-networkPlasticityMelanoma
CellProfiler (3.1.9) (McQuin et al., 2018) https://cellprofiler.org/
ImageJ (2.3.0) Public Domain Software https://imagej.nih.gov/ij/index.html
MATLAB (2020b) Mathworks https://matlab.mathworks.com/
R (4.0.4) The Comprehensive R Archive Network (CRAN) https://www.r-project.org/
stats R package (4.1.2) The R Project https://stat.ethz.ch/R-manual/R-devel/library/stats/html/00Index.html
AUCell R package (1.16.0) (Aibaretal., 2017) https://bioconductor.org/packages/release/bioc/vignettes/AUCell/inst/doc/AUCell.html
umap R package (0.2.7.0) CRAN https://cran.r-project.org/web/packages/umap/
SCopeLoomR R package (0.13.0) Aerts Lab https://github.com/aertslab/SCopeLoomR
Python (3.9.2) N/A https://www.python.org/downloads/
Scanpy (1.7.1) (Wolf et al., 2018) https://github. com/scverse/scanpy
pySCENIC (0.11.0) (Van de Sande et al., 2020) https://github.com/aertslab/SCENICprotocol
Nextflow (20.10.0) Seqera Labs https://www.nextflow.io/
Scikit-learn Library (0.24.1) (Pedregosa et al., 2018) https://scikit-learn.org/stable/
SHAP (Lundberg and Lee, 2017) https://github.com/slundberg/shap
Other
96-well plates Corning Cat# 3904
Differentiation signature gene sets (Tsoi et al., 2018) N/A
Proliferative and Invasive phenotype gene sets (Hoek et al., 2006) http://www.jurmo.ch/work_97.php
List of bZIP transcription factor genes (Vinson et al., 2002) https://github.com/fallahi-sichani-lab/AP1-networkPlasticityMelanoma
List of transcription factor genes (Van de Sande et al., 2020) https://raw.githubusercontent.com/aertslab/pySCENIC/master/resources/hs_hgnc_tfs.txt
Nextflow pipeline adapted for running SCENIC iteratively (Wouters et al., 2020) https://github.com/aertslab/singlecellRNA_melanoma_paper
R scripts adapted for extracting and filtering regulons from multiple SCENIC runs (Wouters et al., 2020) https://github.com/aertslab/singlecellRNA_melanoma_paper
Homo sapiens whole-genome motif ranking databases for SCENIC (motif collection v9) Aerts Lab https://resources.aertslab.org/cistarget/
Motif annotation file for SCENIC (motif collection v9) Aerts Lab https://resources.aertslab.org/cistarget/