other:Article Title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Table S6 This study N/A Recombinant DNA pLKO-Tet-On Novartis N/A Human ORFeome library collection 8.1 Broad Institute N/A pLX317 GFP Broad Institute BRDN0000559466 pLX317 ANPEP Broad Institute TRCN0000476147 pLX317 GRAMD1B Broad Institute TRCN0000481176 pLX317 HDAC6 Broad Institute TRCN0000471558 pLX317 HSP90AA1 Broad Institute TRCN0000491541 pLX317 MAP3K5 Broad Institute TRCN0000488584 pLX317 PIK3CB Broad Institute TRCN0000467602 pLX317 PRDM14 Broad Institute TRCN0000471194 pLX317 YAP1 Broad Institute TRCN0000477457 pLX317 WWTR1 Broad Institute TRCN0000472318 pLX317 CALM2 Broad Institute TRCN0000479230 pLX317 SLC2A1 Broad Institute TRCN0000476750 pLX317 TEAD2 Broad Institute TRCN0000478936 pLX304 GFP Broad Institute ccsbBroad304_99986 pLX304 PRDM14 Broad Institute ccsbBroad304_08822 pLX304 YAP1 Broad Institute ccsbBroad304_07601 pLX304 CALM2 Broad Institute ccsbBroad304_00207 pLX304 SLC2A1 Broad Institute ccsbBroad304_01540 pLKO.1 puro shGFP Previous Study (Kim et al., 2014) N/A pLKO.1 puro shYAP1-1 Broad Institute TRCN0000107265 pLKO.1 puro shYAP1-2 Broad Institute TRCN0000107266 pLKO.1 puro shPRDM14-1 Broad Institute TRCN0000018523 pLKO.1 puro shPRDM14-2 Broad Institute TRCN0000018525 pLKO.1 puro shPRDM14-3 Broad Institute TRCN0000018524 pLKO.1 puro shPRDM14-4 Broad Institute TRCN0000018527 pLKO.1 puro shPRDM14-5 Broad Institute TRCN0000018526 pLKO.1 puro shCALM2-1 Broad Institute TRCN0000195431 pLKO.1 puro shCALM2-2 Broad Institute TRCN0000196508 pLKO.1 puro shCALM2-3 Broad Institute TRCN0000052580 pLKO.1 puro shSLC2A1-1 Broad Institute TRCN0000043583 pLKO.1 puro shSLC2A1-2 Broad Institute TRCN0000043587 pLKO.1 puro shTEAD1/3/4-1 This study N/A pLKO.1 puro shTEAD1/3/4-2 This study N/A pLX307 P2A GFP Luciferase This study N/A pLX307 P2A GFP YAP1 This study N/A pLX307 P2A GFP PRDM14 This study N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Metascape Previous study (Tripathi et al., 2015) http://metascape.org ChiLin Previous study (Qin et al., 2016) http://cistrome.org/chilin/ deepTools Previous study (Ramı́rez et al., 2016) https://deeptools.readthedocs.io/ en/develop/ (Continued on next page) e3 Developmental Cell 57, 212–227.e1–e8, January 24, 2022
Article Title: Non-gonadal PIWIL1/Aubergine drives regenerative and tumorigenic stem cell proliferation and tumorigenesis in the intestine.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER B27 Invitrogen Cat# 12587-010 BME-2 phenol red Biotechne Cat# 3533-010-02P Bond Diluent Leica AR9352 Bond Wash prior to primary antibody application Leica AR9590 Bovine Serum Albumin Sigma-Aldrich Cat# A3294 CellTrics 30μm filters Sysmex Cat# 04-0042-2316 Countless Cell Counting Chamber Slides Life Technologies Cat# C10228 DAPI Sigma-Aldrich Cat# D9542 Dewax Solution Leica AR9222 Dimethyl Sulfoxide Thermo Fisher Scientific Cat# 10500151 DNAse Thermo Fisher Scientific Cat# 18068015 DPX CellPath SEA-1300-00A EGF Peprotech Cat# AF-100-15 Elastase from porcine pancreas Sigma-Aldrich Cat# E0258 Epitope Retrieval solution 2 (ER2) Leica AR9640 Gastrin Sigma-Aldrich Cat# G9145 1M HEPES Life Technologies Cat# 15630-056 Hexadimethrine bromide (Polybrene) Sigma-Aldrich Cat# H9268-5G High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Scientific Cat# 4368813 Intense R Kit Leica DS9263 IntestiCult Organoid Growth Medium (Human) Stem Cell Technologies Cat# 06010 Methanol Fisher Scientific Cat# 10675112 N-Acetyl-L-cysteine (NAC treatment for flies) Sigma-Aldrich Cat# A7250 N-Acetyl-L-cysteine (organoids culture) Sigma-Aldrich Cat# A9165 Neutral Buffered Formalin Solmedia FORM5000 Nicotinamide Sigma-Aldrich Car# N0636 Noggin conditioned media Labmade Myant’s lab N/A P38i (SB202190) Sigma-Aldrich Cat# S7067 Paraformaldehyde Polysciences Inc Cat#18814-20 PerfeCTa SYBR Green FastMix Low ROX 1250 Reactions (experiments in Drosophila) Quantabio Cat# 95074-012 PGE2 Tocris Cat# 2296 Primocin Invivogen Cat# ANT-PM1 Puromycin (organoids selection) Gibco Cat#A11138-03 Puromycin (Translation assay) Sigma-Aldrich Cat# P8833 qScript cDNA SuperMix VWR Cat# 95048-100 Resazurin Bio-Techne Cat# AR002 RNAscope 2.5 LS Reagent Kit-Brown ACD Cat# 322100 RNase-Free DNase set Qiagen Cat# 79254 RNaseZap RNase Decontamination Solution Invitrogen Cat# 9780 RNeasy Mini Kit Qiagen Cat# 74104/Cat# 74106 Schneider’s Insect Medium Sigma-Aldrich Cat# S0146 Sucrose Fisher Scientific Cat# 10634932 Sybr green (experiments in organoids) Life Technologies Cat#4472920 Triton X-100 Sigma-Aldrich Cat# X100 (Continued on next page) 22 Cell Reports 45, 117186, April 28, 2026
Next-Generation Sequencing:Article Title: Correction for Wijnakker et al., Integrin-activating Yersinia protein Invasin sustains long-term expansion of primary epithelial cells as 2D organoid sheets.
Article Snippet: .. Colon Ileum Airway Mouse lacrimal gland Snake venom gland Mouse intestine F12 advanced Gibco NA + + + + + HEPES Gibco 10 nM + + + + + Glutamax Gibco 1:100 + + + + + N-acetylcysteine (Nac) Sigma- Aldrich 1.25 mM + + + + + Nicotinamide (Nic) Sigma- Aldrich 10 mM + +(5 mM) + + B27 Sigma- Aldrich 1:50 + +(B27 + vitA) +(B27+ vitA) + + p38 inhibitor SB202190 Sigma- Aldrich 10 μM + +(1 μM) A83-01 inhibitor TGF- β type I receptor Tocris 0.5 μM + + + + PGE2 Tocris 1 μM + + + Gastrin Tocris 10 nM +(100 nM) TGFa Peprotech 20 ng/mL EGF Peprotech 50 ng/mL + + + FGF10 Peprotech 0.1 μg/mL + + + hHGF Peprotech 25 ng/mL FSK Peprotech 1 nM + FGF7/KGF Peprotech 100 ng/mL +(25 ng/mL) CHIR Sigma 3 μM NGS Wnt Surrogate-Fc #: N001 IpA 0.5 nM + + R-spondin 3-Fc #: R001 IpA 3% + +(1%) +(1%) + (2%) + Noggin-Fc #: N002 IpA 2% + +(1%) +(1%) + + Penicillin Streptomycin Gibco 100 U/mL + + + + + Primocin Invivogen 50 μg/mL + + + This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND). ..
Article Title: Integrin-activating Yersinia protein Invasin sustains long-term expansion of primary epithelial cells as 2D organoid sheets.
Article Snippet: .. Colon Ileum Airway Mouse lacrimal gland Snake Venom gland Mouse Intestine F12 advanced Gibco NA + + + + + HEPES Gibco 10 nM + + + + + GlutaMax Gibco 1:100 + + + + + N-acetylcysteine (Nac) Sigma-Aldrich 1,25 mM + + + + + Nicotinamide (Nic) Sigma-Aldrich 10 mM + + (5 mM) + + B27 Sigma-Aldrich 1:50 + + (B27 + vitA) + (B27+ vitA) + + p38 inhibitor SB202190 Sigma-Aldrich 10 μM + + (1 μM) A83-01 inhibitor TGF- β type I receptor Tocris 0,5 μM + + + + PGE2 Tocris 1 μM + + + Gastrin Tocris 10 nM + (100 nM) TGFa PeproTech 20 ng/mL EGF PeproTech 50 ng/mL + + + FGF10 PeproTech 0,1 μg/mL + + + hHGF PeproTech 25 ng/mL FSK PeproTech 1 nM + FGF7/KGF PeproTech 100 ng/mL + (25 ng/mL) CHIR Sigma 3 μM NGS Wnt Surrogate-Fc #: N001 IpA 0,5 nM + + R-spondin 3-Fc #: R001 IpA 3% + + (1%) + (1%) + (2%) + Noggin-Fc #: N002 IpA 2% + + (1%) + (1%) + + Penicillin Streptomycin Gibco 100 U/mL + + + + Primocin InvivoGen 50 μg/mL + + + Table 2. .. Antibody list for confocal imaging Antibody Conc. in PBS Villin (Santa Cruz, sc-58897) 1:1,000 Phalloidin 488 (Life Technologies, A12379) 1:1,000 Phalloidin 647 (Sigma, 65906) 1:1,000 EPCAM (BioLegend, 324210) 1:1,000 Acetylated tubulin (Santa Cruz, 6-11B-1, sc-23950) 1:200 Uteroglobin/CC10 (R&D, MAB4218) 1:250 Ki67 (Millipore, AB9260) 1:200 KRT5 (AF138, PRB 160P-100; 905501 1:2,000 AIIB2 (kind gift of A.Sonnenberg) (1 mg/mL) 1:1,000D ow nl oa de d fr om h ttp s: //w w w .p na s. or g by 1 03 .1 90 .4 1.
Article Title: Invasin-functionalized PIC hydrogels enable long-term 3D culture of epithelial organoids.
Article Snippet: Colon Ileum Airway Mouse intestine F12 advanced Gibco NA + + + Hepes Gibco 10 nM + + + Glutamax Gibco 1:100 + + + N-acetylcysteine (Nac) Sigma- Aldrich 1,25 mM + + + Nicotinamide (Nic) Sigma- Aldrich 10 mM + + (5 mM) B27 Sigma- Aldrich 1:50 + + (B27+vitA.) .. + p38 inhibitor SB202190 Sigma- Aldrich 10 μM + + (1 μM) A83-01 inhibitor TGF- β type I receptor Tocris 0,5 μM + + PGE2 Tocris 1 μM + EGF Peprotech 50 ng/mL + + FGF10 Peprotech 0,1 μg/mL + FGF7/KGF Peprotech 100 ng/mL + (25 ng/mL) NGS Wnt Surrogate-Fc #: N001 IpA 0,5 nM + + Rspondin3- Fc #: R001 IpA 3% + + (1%) + Noggin-Fc #: N002 IpA 2% + + (1%) + Penecillin/Streptomycin Gibco 100 U/mL + + + Primocin Invivogen 50 μg/mL + D ow nl oa de d fr om h ttp s: //w w w .p na s. or g by 2 02 .5 1. ..
Concentration Assay:Article Title: A single-chain derivative of an integrin-activating antibody potentiates organoid growth in Matrigel and collagen hydrogels.
Article Snippet: .. Reagent Source Concentration Intestinal Stomach Liver ductal Pancreas ductal F12 advanced Gibco Not applicable + + + + HEPES Gibco 10 nM + + + + Glutamax Gibco 1:100 + + + + N-acetylcysteine Sigma-Aldrich 1.25 mM + + + + Nicotinamide Sigma-Aldrich 10 μM + + + B27 Sigma-Aldrich 1:50 + + + p38-inhibitor SB202190 Sigma-Aldrich 10 μM + A83-01 inhibitor TGFβ type I receptor Tocris 0.5 μM + + + + PGE2 Tocris 1 μM + + Gastrin Tocris 10 nM + + + Forskolin Tocris 10 μM + EGF Peprotech 50 ng ml−1 + + + Nature Biotechnology Article https://doi.org/10.1038/s41587-025-02874-8 ..
Article Title: First-line treatment selection with organoids of an EGFR m + TP53 m stage IA1 patient with early metastatic recurrence after radical surgery and follow-up
Article Snippet: Data analyses were performed using GraphPad Prism 7.0 software, and the values of IC50 were calculated by applying nonlinear regression (curve fit). .. Table S1 Additive Supplier Catalogue # Concentration N-Acetylcysteine Sigma A9165 1.25 mM EGF PeproTech AF-100-15 50 ng/mL FGF-10 PeproTech 100-26 20 ng/mL FGF-basic PeproTech 100-10B 1 ng/mL Y-27632 Selleck S1049 10 μM A-83-01 Sigma SML0788 500 nM SB202190 Selleck S1077 10 μM Nicotinamide Sigma 72340 10 mM PGE2 Tocris 2296 1 ìM Noggin (conditional medium) In-house – 50 mL R-Spondin (conditional medium) In-house – 50 mL HEPES Sigma H6147 10 mM GlutaMAX Gibco 35050061 1× B27 Gibco 17504044 1× N2 Gibco 17502048 1× Open in a separate window R-Spondin 1 and Noggin conditioned media were prepared in house from the culture media of Rspo1 cell and the noggin cDNA transfected HEK-293 cell following the methods described before ( 36 , 37 ). ..
Clinical Proteomics:Article Title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EGF Life Technologies Cat# PMG8041 Y-27632 MilliporeSigma Cat# Y0503 SB431542 MilliporeSigma Cat# 616461 Collagenase XI MilliporeSigma Cat# C9407 DNase I StemCell Cat# 07900 Growth factor reduced Matrigel Corning Cat# 356231 B-27 supplement Thermo Fisher Scientific Cat# 17504044 Noggin Thermo Fisher Scientific Cat# PHC1506 N-acetylcysteine MilliporeSigma Cat# A9165 Nicotinamide MilliporeSigma Cat# N3376 SB202190 MilliporeSigma Cat# S7067 A 83-01 Tocris Cat# 2939 PGE2 Tocris Cat# 2296 Critical Commercial Assays DNA Blood Maxi Kit Qiagen Cat# 51194 Plasma Membrane Protein Extraction Kit Thermo Fisher Scientific Cat# NC1053482 RNeasy Plus Mini Kit Qiagen Cat# 74134 NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat# E7420 KAPA Complete Kit (ABI Prism) Kapa Biosystems Cat# KK4835 QIAquick PCR Purification Kit Qiagen Cat# 28104 Quant-iT PicoGreen dsDNA Thermo Fisher Scientific Cat# P7589 ThruPLEX DNA-seq Kit Rubicon Genomics Cat# R400427 DNeasy Blood & Tissue Mini Kit Qiagen Cat# 69504 CellTiter-Glo 3D Cell Viability Assay Promega Cat# G9683 Deposited Data ORF screen data This study Table S1 RNA-seq and ChIP-seq data This study NCBI GEO: GSE182432 Whole exome sequencing data This study NCBI SRA: PRJNA756046 Analysis of genetic alteration in cancer cBioPortal (Gao et al., 2013) https://www.cbioportal.org/ Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 HT-29 ATCC Cat# HTB-38, RRID:CVCL_0320 SK-CO-1 ATCC Cat# HTB-39, RRID:CVCL_0626 SW48 ATCC Cat# CCL-231, RRID:CVCL_1724 COLO 320 ATCC Cat# CCL-220, RRID:CVCL_0219 HA1E Previous study (Hahn et al., 1999) N/A Experimental Models: Organisms/Strains NCR-nude mouse (CrTac:NCr-Foxn1nu) Taconic Biosciences NCRNU-F Apc WT and KO mouse colon organoid models (Apcflox/flox; tdRFPLSL and Lgr5-eGFP-CreER; Apcflox/flox; tdRFPLSL) This study N/A Apc KO;Kras G12D mouse colon organoid model (Adeno-Cre treatment of Apcflox/flox; LSL-KrasG12D) Kevin Haigis lab at Dana-Farber Cancer Institute N/A Patient-derived colon organoid model (0544) This study N/A (Continued on next page) Developmental Cell 57, 212–227.e1–e8, January 24, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Table S6 This study N/A Recombinant DNA pLKO-Tet-On Novartis N/A Human ORFeome library collection 8.1 Broad Institute N/A pLX317 GFP Broad Institute BRDN0000559466 pLX317 ANPEP Broad Institute TRCN0000476147 pLX317 GRAMD1B Broad Institute TRCN0000481176 pLX317 HDAC6 Broad Institute TRCN0000471558 pLX317 HSP90AA1 Broad Institute TRCN0000491541 pLX317 MAP3K5 Broad Institute TRCN0000488584 pLX317 PIK3CB Broad Institute TRCN0000467602 pLX317 PRDM14 Broad Institute TRCN0000471194 pLX317 YAP1 Broad Institute TRCN0000477457 pLX317 WWTR1 Broad Institute TRCN0000472318 pLX317 CALM2 Broad Institute TRCN0000479230 pLX317 SLC2A1 Broad Institute TRCN0000476750 pLX317 TEAD2 Broad Institute TRCN0000478936 pLX304 GFP Broad Institute ccsbBroad304_99986 pLX304 PRDM14 Broad Institute ccsbBroad304_08822 pLX304 YAP1 Broad Institute ccsbBroad304_07601 pLX304 CALM2 Broad Institute ccsbBroad304_00207 pLX304 SLC2A1 Broad Institute ccsbBroad304_01540 pLKO.1 puro shGFP Previous Study (Kim et al., 2014) N/A pLKO.1 puro shYAP1-1 Broad Institute TRCN0000107265 pLKO.1 puro shYAP1-2 Broad Institute TRCN0000107266 pLKO.1 puro shPRDM14-1 Broad Institute TRCN0000018523 pLKO.1 puro shPRDM14-2 Broad Institute TRCN0000018525 pLKO.1 puro shPRDM14-3 Broad Institute TRCN0000018524 pLKO.1 puro shPRDM14-4 Broad Institute TRCN0000018527 pLKO.1 puro shPRDM14-5 Broad Institute TRCN0000018526 pLKO.1 puro shCALM2-1 Broad Institute TRCN0000195431 pLKO.1 puro shCALM2-2 Broad Institute TRCN0000196508 pLKO.1 puro shCALM2-3 Broad Institute TRCN0000052580 pLKO.1 puro shSLC2A1-1 Broad Institute TRCN0000043583 pLKO.1 puro shSLC2A1-2 Broad Institute TRCN0000043587 pLKO.1 puro shTEAD1/3/4-1 This study N/A pLKO.1 puro shTEAD1/3/4-2 This study N/A pLX307 P2A GFP Luciferase This study N/A pLX307 P2A GFP YAP1 This study N/A pLX307 P2A GFP PRDM14 This study N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Metascape Previous study (Tripathi et al., 2015) http://metascape.org ChiLin Previous study (Qin et al., 2016) http://cistrome.org/chilin/ deepTools Previous study (Ramı́rez et al., 2016) https://deeptools.readthedocs.io/ en/develop/ (Continued on next page) e3 Developmental Cell 57, 212–227.e1–e8, January 24, 2022
Membrane:Article Title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EGF Life Technologies Cat# PMG8041 Y-27632 MilliporeSigma Cat# Y0503 SB431542 MilliporeSigma Cat# 616461 Collagenase XI MilliporeSigma Cat# C9407 DNase I StemCell Cat# 07900 Growth factor reduced Matrigel Corning Cat# 356231 B-27 supplement Thermo Fisher Scientific Cat# 17504044 Noggin Thermo Fisher Scientific Cat# PHC1506 N-acetylcysteine MilliporeSigma Cat# A9165 Nicotinamide MilliporeSigma Cat# N3376 SB202190 MilliporeSigma Cat# S7067 A 83-01 Tocris Cat# 2939 PGE2 Tocris Cat# 2296 Critical Commercial Assays DNA Blood Maxi Kit Qiagen Cat# 51194 Plasma Membrane Protein Extraction Kit Thermo Fisher Scientific Cat# NC1053482 RNeasy Plus Mini Kit Qiagen Cat# 74134 NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat# E7420 KAPA Complete Kit (ABI Prism) Kapa Biosystems Cat# KK4835 QIAquick PCR Purification Kit Qiagen Cat# 28104 Quant-iT PicoGreen dsDNA Thermo Fisher Scientific Cat# P7589 ThruPLEX DNA-seq Kit Rubicon Genomics Cat# R400427 DNeasy Blood & Tissue Mini Kit Qiagen Cat# 69504 CellTiter-Glo 3D Cell Viability Assay Promega Cat# G9683 Deposited Data ORF screen data This study Table S1 RNA-seq and ChIP-seq data This study NCBI GEO: GSE182432 Whole exome sequencing data This study NCBI SRA: PRJNA756046 Analysis of genetic alteration in cancer cBioPortal (Gao et al., 2013) https://www.cbioportal.org/ Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 HT-29 ATCC Cat# HTB-38, RRID:CVCL_0320 SK-CO-1 ATCC Cat# HTB-39, RRID:CVCL_0626 SW48 ATCC Cat# CCL-231, RRID:CVCL_1724 COLO 320 ATCC Cat# CCL-220, RRID:CVCL_0219 HA1E Previous study (Hahn et al., 1999) N/A Experimental Models: Organisms/Strains NCR-nude mouse (CrTac:NCr-Foxn1nu) Taconic Biosciences NCRNU-F Apc WT and KO mouse colon organoid models (Apcflox/flox; tdRFPLSL and Lgr5-eGFP-CreER; Apcflox/flox; tdRFPLSL) This study N/A Apc KO;Kras G12D mouse colon organoid model (Adeno-Cre treatment of Apcflox/flox; LSL-KrasG12D) Kevin Haigis lab at Dana-Farber Cancer Institute N/A Patient-derived colon organoid model (0544) This study N/A (Continued on next page) Developmental Cell 57, 212–227.e1–e8, January 24, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Table S6 This study N/A Recombinant DNA pLKO-Tet-On Novartis N/A Human ORFeome library collection 8.1 Broad Institute N/A pLX317 GFP Broad Institute BRDN0000559466 pLX317 ANPEP Broad Institute TRCN0000476147 pLX317 GRAMD1B Broad Institute TRCN0000481176 pLX317 HDAC6 Broad Institute TRCN0000471558 pLX317 HSP90AA1 Broad Institute TRCN0000491541 pLX317 MAP3K5 Broad Institute TRCN0000488584 pLX317 PIK3CB Broad Institute TRCN0000467602 pLX317 PRDM14 Broad Institute TRCN0000471194 pLX317 YAP1 Broad Institute TRCN0000477457 pLX317 WWTR1 Broad Institute TRCN0000472318 pLX317 CALM2 Broad Institute TRCN0000479230 pLX317 SLC2A1 Broad Institute TRCN0000476750 pLX317 TEAD2 Broad Institute TRCN0000478936 pLX304 GFP Broad Institute ccsbBroad304_99986 pLX304 PRDM14 Broad Institute ccsbBroad304_08822 pLX304 YAP1 Broad Institute ccsbBroad304_07601 pLX304 CALM2 Broad Institute ccsbBroad304_00207 pLX304 SLC2A1 Broad Institute ccsbBroad304_01540 pLKO.1 puro shGFP Previous Study (Kim et al., 2014) N/A pLKO.1 puro shYAP1-1 Broad Institute TRCN0000107265 pLKO.1 puro shYAP1-2 Broad Institute TRCN0000107266 pLKO.1 puro shPRDM14-1 Broad Institute TRCN0000018523 pLKO.1 puro shPRDM14-2 Broad Institute TRCN0000018525 pLKO.1 puro shPRDM14-3 Broad Institute TRCN0000018524 pLKO.1 puro shPRDM14-4 Broad Institute TRCN0000018527 pLKO.1 puro shPRDM14-5 Broad Institute TRCN0000018526 pLKO.1 puro shCALM2-1 Broad Institute TRCN0000195431 pLKO.1 puro shCALM2-2 Broad Institute TRCN0000196508 pLKO.1 puro shCALM2-3 Broad Institute TRCN0000052580 pLKO.1 puro shSLC2A1-1 Broad Institute TRCN0000043583 pLKO.1 puro shSLC2A1-2 Broad Institute TRCN0000043587 pLKO.1 puro shTEAD1/3/4-1 This study N/A pLKO.1 puro shTEAD1/3/4-2 This study N/A pLX307 P2A GFP Luciferase This study N/A pLX307 P2A GFP YAP1 This study N/A pLX307 P2A GFP PRDM14 This study N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Metascape Previous study (Tripathi et al., 2015) http://metascape.org ChiLin Previous study (Qin et al., 2016) http://cistrome.org/chilin/ deepTools Previous study (Ramı́rez et al., 2016) https://deeptools.readthedocs.io/ en/develop/ (Continued on next page) e3 Developmental Cell 57, 212–227.e1–e8, January 24, 2022
Protein Extraction:Article Title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EGF Life Technologies Cat# PMG8041 Y-27632 MilliporeSigma Cat# Y0503 SB431542 MilliporeSigma Cat# 616461 Collagenase XI MilliporeSigma Cat# C9407 DNase I StemCell Cat# 07900 Growth factor reduced Matrigel Corning Cat# 356231 B-27 supplement Thermo Fisher Scientific Cat# 17504044 Noggin Thermo Fisher Scientific Cat# PHC1506 N-acetylcysteine MilliporeSigma Cat# A9165 Nicotinamide MilliporeSigma Cat# N3376 SB202190 MilliporeSigma Cat# S7067 A 83-01 Tocris Cat# 2939 PGE2 Tocris Cat# 2296 Critical Commercial Assays DNA Blood Maxi Kit Qiagen Cat# 51194 Plasma Membrane Protein Extraction Kit Thermo Fisher Scientific Cat# NC1053482 RNeasy Plus Mini Kit Qiagen Cat# 74134 NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat# E7420 KAPA Complete Kit (ABI Prism) Kapa Biosystems Cat# KK4835 QIAquick PCR Purification Kit Qiagen Cat# 28104 Quant-iT PicoGreen dsDNA Thermo Fisher Scientific Cat# P7589 ThruPLEX DNA-seq Kit Rubicon Genomics Cat# R400427 DNeasy Blood & Tissue Mini Kit Qiagen Cat# 69504 CellTiter-Glo 3D Cell Viability Assay Promega Cat# G9683 Deposited Data ORF screen data This study Table S1 RNA-seq and ChIP-seq data This study NCBI GEO: GSE182432 Whole exome sequencing data This study NCBI SRA: PRJNA756046 Analysis of genetic alteration in cancer cBioPortal (Gao et al., 2013) https://www.cbioportal.org/ Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 HT-29 ATCC Cat# HTB-38, RRID:CVCL_0320 SK-CO-1 ATCC Cat# HTB-39, RRID:CVCL_0626 SW48 ATCC Cat# CCL-231, RRID:CVCL_1724 COLO 320 ATCC Cat# CCL-220, RRID:CVCL_0219 HA1E Previous study (Hahn et al., 1999) N/A Experimental Models: Organisms/Strains NCR-nude mouse (CrTac:NCr-Foxn1nu) Taconic Biosciences NCRNU-F Apc WT and KO mouse colon organoid models (Apcflox/flox; tdRFPLSL and Lgr5-eGFP-CreER; Apcflox/flox; tdRFPLSL) This study N/A Apc KO;Kras G12D mouse colon organoid model (Adeno-Cre treatment of Apcflox/flox; LSL-KrasG12D) Kevin Haigis lab at Dana-Farber Cancer Institute N/A Patient-derived colon organoid model (0544) This study N/A (Continued on next page) Developmental Cell 57, 212–227.e1–e8, January 24, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Table S6 This study N/A Recombinant DNA pLKO-Tet-On Novartis N/A Human ORFeome library collection 8.1 Broad Institute N/A pLX317 GFP Broad Institute BRDN0000559466 pLX317 ANPEP Broad Institute TRCN0000476147 pLX317 GRAMD1B Broad Institute TRCN0000481176 pLX317 HDAC6 Broad Institute TRCN0000471558 pLX317 HSP90AA1 Broad Institute TRCN0000491541 pLX317 MAP3K5 Broad Institute TRCN0000488584 pLX317 PIK3CB Broad Institute TRCN0000467602 pLX317 PRDM14 Broad Institute TRCN0000471194 pLX317 YAP1 Broad Institute TRCN0000477457 pLX317 WWTR1 Broad Institute TRCN0000472318 pLX317 CALM2 Broad Institute TRCN0000479230 pLX317 SLC2A1 Broad Institute TRCN0000476750 pLX317 TEAD2 Broad Institute TRCN0000478936 pLX304 GFP Broad Institute ccsbBroad304_99986 pLX304 PRDM14 Broad Institute ccsbBroad304_08822 pLX304 YAP1 Broad Institute ccsbBroad304_07601 pLX304 CALM2 Broad Institute ccsbBroad304_00207 pLX304 SLC2A1 Broad Institute ccsbBroad304_01540 pLKO.1 puro shGFP Previous Study (Kim et al., 2014) N/A pLKO.1 puro shYAP1-1 Broad Institute TRCN0000107265 pLKO.1 puro shYAP1-2 Broad Institute TRCN0000107266 pLKO.1 puro shPRDM14-1 Broad Institute TRCN0000018523 pLKO.1 puro shPRDM14-2 Broad Institute TRCN0000018525 pLKO.1 puro shPRDM14-3 Broad Institute TRCN0000018524 pLKO.1 puro shPRDM14-4 Broad Institute TRCN0000018527 pLKO.1 puro shPRDM14-5 Broad Institute TRCN0000018526 pLKO.1 puro shCALM2-1 Broad Institute TRCN0000195431 pLKO.1 puro shCALM2-2 Broad Institute TRCN0000196508 pLKO.1 puro shCALM2-3 Broad Institute TRCN0000052580 pLKO.1 puro shSLC2A1-1 Broad Institute TRCN0000043583 pLKO.1 puro shSLC2A1-2 Broad Institute TRCN0000043587 pLKO.1 puro shTEAD1/3/4-1 This study N/A pLKO.1 puro shTEAD1/3/4-2 This study N/A pLX307 P2A GFP Luciferase This study N/A pLX307 P2A GFP YAP1 This study N/A pLX307 P2A GFP PRDM14 This study N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Metascape Previous study (Tripathi et al., 2015) http://metascape.org ChiLin Previous study (Qin et al., 2016) http://cistrome.org/chilin/ deepTools Previous study (Ramı́rez et al., 2016) https://deeptools.readthedocs.io/ en/develop/ (Continued on next page) e3 Developmental Cell 57, 212–227.e1–e8, January 24, 2022
Polymerase Chain Reaction:Article Title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EGF Life Technologies Cat# PMG8041 Y-27632 MilliporeSigma Cat# Y0503 SB431542 MilliporeSigma Cat# 616461 Collagenase XI MilliporeSigma Cat# C9407 DNase I StemCell Cat# 07900 Growth factor reduced Matrigel Corning Cat# 356231 B-27 supplement Thermo Fisher Scientific Cat# 17504044 Noggin Thermo Fisher Scientific Cat# PHC1506 N-acetylcysteine MilliporeSigma Cat# A9165 Nicotinamide MilliporeSigma Cat# N3376 SB202190 MilliporeSigma Cat# S7067 A 83-01 Tocris Cat# 2939 PGE2 Tocris Cat# 2296 Critical Commercial Assays DNA Blood Maxi Kit Qiagen Cat# 51194 Plasma Membrane Protein Extraction Kit Thermo Fisher Scientific Cat# NC1053482 RNeasy Plus Mini Kit Qiagen Cat# 74134 NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat# E7420 KAPA Complete Kit (ABI Prism) Kapa Biosystems Cat# KK4835 QIAquick PCR Purification Kit Qiagen Cat# 28104 Quant-iT PicoGreen dsDNA Thermo Fisher Scientific Cat# P7589 ThruPLEX DNA-seq Kit Rubicon Genomics Cat# R400427 DNeasy Blood & Tissue Mini Kit Qiagen Cat# 69504 CellTiter-Glo 3D Cell Viability Assay Promega Cat# G9683 Deposited Data ORF screen data This study Table S1 RNA-seq and ChIP-seq data This study NCBI GEO: GSE182432 Whole exome sequencing data This study NCBI SRA: PRJNA756046 Analysis of genetic alteration in cancer cBioPortal (Gao et al., 2013) https://www.cbioportal.org/ Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 HT-29 ATCC Cat# HTB-38, RRID:CVCL_0320 SK-CO-1 ATCC Cat# HTB-39, RRID:CVCL_0626 SW48 ATCC Cat# CCL-231, RRID:CVCL_1724 COLO 320 ATCC Cat# CCL-220, RRID:CVCL_0219 HA1E Previous study (Hahn et al., 1999) N/A Experimental Models: Organisms/Strains NCR-nude mouse (CrTac:NCr-Foxn1nu) Taconic Biosciences NCRNU-F Apc WT and KO mouse colon organoid models (Apcflox/flox; tdRFPLSL and Lgr5-eGFP-CreER; Apcflox/flox; tdRFPLSL) This study N/A Apc KO;Kras G12D mouse colon organoid model (Adeno-Cre treatment of Apcflox/flox; LSL-KrasG12D) Kevin Haigis lab at Dana-Farber Cancer Institute N/A Patient-derived colon organoid model (0544) This study N/A (Continued on next page) Developmental Cell 57, 212–227.e1–e8, January 24, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Table S6 This study N/A Recombinant DNA pLKO-Tet-On Novartis N/A Human ORFeome library collection 8.1 Broad Institute N/A pLX317 GFP Broad Institute BRDN0000559466 pLX317 ANPEP Broad Institute TRCN0000476147 pLX317 GRAMD1B Broad Institute TRCN0000481176 pLX317 HDAC6 Broad Institute TRCN0000471558 pLX317 HSP90AA1 Broad Institute TRCN0000491541 pLX317 MAP3K5 Broad Institute TRCN0000488584 pLX317 PIK3CB Broad Institute TRCN0000467602 pLX317 PRDM14 Broad Institute TRCN0000471194 pLX317 YAP1 Broad Institute TRCN0000477457 pLX317 WWTR1 Broad Institute TRCN0000472318 pLX317 CALM2 Broad Institute TRCN0000479230 pLX317 SLC2A1 Broad Institute TRCN0000476750 pLX317 TEAD2 Broad Institute TRCN0000478936 pLX304 GFP Broad Institute ccsbBroad304_99986 pLX304 PRDM14 Broad Institute ccsbBroad304_08822 pLX304 YAP1 Broad Institute ccsbBroad304_07601 pLX304 CALM2 Broad Institute ccsbBroad304_00207 pLX304 SLC2A1 Broad Institute ccsbBroad304_01540 pLKO.1 puro shGFP Previous Study (Kim et al., 2014) N/A pLKO.1 puro shYAP1-1 Broad Institute TRCN0000107265 pLKO.1 puro shYAP1-2 Broad Institute TRCN0000107266 pLKO.1 puro shPRDM14-1 Broad Institute TRCN0000018523 pLKO.1 puro shPRDM14-2 Broad Institute TRCN0000018525 pLKO.1 puro shPRDM14-3 Broad Institute TRCN0000018524 pLKO.1 puro shPRDM14-4 Broad Institute TRCN0000018527 pLKO.1 puro shPRDM14-5 Broad Institute TRCN0000018526 pLKO.1 puro shCALM2-1 Broad Institute TRCN0000195431 pLKO.1 puro shCALM2-2 Broad Institute TRCN0000196508 pLKO.1 puro shCALM2-3 Broad Institute TRCN0000052580 pLKO.1 puro shSLC2A1-1 Broad Institute TRCN0000043583 pLKO.1 puro shSLC2A1-2 Broad Institute TRCN0000043587 pLKO.1 puro shTEAD1/3/4-1 This study N/A pLKO.1 puro shTEAD1/3/4-2 This study N/A pLX307 P2A GFP Luciferase This study N/A pLX307 P2A GFP YAP1 This study N/A pLX307 P2A GFP PRDM14 This study N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Metascape Previous study (Tripathi et al., 2015) http://metascape.org ChiLin Previous study (Qin et al., 2016) http://cistrome.org/chilin/ deepTools Previous study (Ramı́rez et al., 2016) https://deeptools.readthedocs.io/ en/develop/ (Continued on next page) e3 Developmental Cell 57, 212–227.e1–e8, January 24, 2022
Purification:Article Title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EGF Life Technologies Cat# PMG8041 Y-27632 MilliporeSigma Cat# Y0503 SB431542 MilliporeSigma Cat# 616461 Collagenase XI MilliporeSigma Cat# C9407 DNase I StemCell Cat# 07900 Growth factor reduced Matrigel Corning Cat# 356231 B-27 supplement Thermo Fisher Scientific Cat# 17504044 Noggin Thermo Fisher Scientific Cat# PHC1506 N-acetylcysteine MilliporeSigma Cat# A9165 Nicotinamide MilliporeSigma Cat# N3376 SB202190 MilliporeSigma Cat# S7067 A 83-01 Tocris Cat# 2939 PGE2 Tocris Cat# 2296 Critical Commercial Assays DNA Blood Maxi Kit Qiagen Cat# 51194 Plasma Membrane Protein Extraction Kit Thermo Fisher Scientific Cat# NC1053482 RNeasy Plus Mini Kit Qiagen Cat# 74134 NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat# E7420 KAPA Complete Kit (ABI Prism) Kapa Biosystems Cat# KK4835 QIAquick PCR Purification Kit Qiagen Cat# 28104 Quant-iT PicoGreen dsDNA Thermo Fisher Scientific Cat# P7589 ThruPLEX DNA-seq Kit Rubicon Genomics Cat# R400427 DNeasy Blood & Tissue Mini Kit Qiagen Cat# 69504 CellTiter-Glo 3D Cell Viability Assay Promega Cat# G9683 Deposited Data ORF screen data This study Table S1 RNA-seq and ChIP-seq data This study NCBI GEO: GSE182432 Whole exome sequencing data This study NCBI SRA: PRJNA756046 Analysis of genetic alteration in cancer cBioPortal (Gao et al., 2013) https://www.cbioportal.org/ Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 HT-29 ATCC Cat# HTB-38, RRID:CVCL_0320 SK-CO-1 ATCC Cat# HTB-39, RRID:CVCL_0626 SW48 ATCC Cat# CCL-231, RRID:CVCL_1724 COLO 320 ATCC Cat# CCL-220, RRID:CVCL_0219 HA1E Previous study (Hahn et al., 1999) N/A Experimental Models: Organisms/Strains NCR-nude mouse (CrTac:NCr-Foxn1nu) Taconic Biosciences NCRNU-F Apc WT and KO mouse colon organoid models (Apcflox/flox; tdRFPLSL and Lgr5-eGFP-CreER; Apcflox/flox; tdRFPLSL) This study N/A Apc KO;Kras G12D mouse colon organoid model (Adeno-Cre treatment of Apcflox/flox; LSL-KrasG12D) Kevin Haigis lab at Dana-Farber Cancer Institute N/A Patient-derived colon organoid model (0544) This study N/A (Continued on next page) Developmental Cell 57, 212–227.e1–e8, January 24, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Table S6 This study N/A Recombinant DNA pLKO-Tet-On Novartis N/A Human ORFeome library collection 8.1 Broad Institute N/A pLX317 GFP Broad Institute BRDN0000559466 pLX317 ANPEP Broad Institute TRCN0000476147 pLX317 GRAMD1B Broad Institute TRCN0000481176 pLX317 HDAC6 Broad Institute TRCN0000471558 pLX317 HSP90AA1 Broad Institute TRCN0000491541 pLX317 MAP3K5 Broad Institute TRCN0000488584 pLX317 PIK3CB Broad Institute TRCN0000467602 pLX317 PRDM14 Broad Institute TRCN0000471194 pLX317 YAP1 Broad Institute TRCN0000477457 pLX317 WWTR1 Broad Institute TRCN0000472318 pLX317 CALM2 Broad Institute TRCN0000479230 pLX317 SLC2A1 Broad Institute TRCN0000476750 pLX317 TEAD2 Broad Institute TRCN0000478936 pLX304 GFP Broad Institute ccsbBroad304_99986 pLX304 PRDM14 Broad Institute ccsbBroad304_08822 pLX304 YAP1 Broad Institute ccsbBroad304_07601 pLX304 CALM2 Broad Institute ccsbBroad304_00207 pLX304 SLC2A1 Broad Institute ccsbBroad304_01540 pLKO.1 puro shGFP Previous Study (Kim et al., 2014) N/A pLKO.1 puro shYAP1-1 Broad Institute TRCN0000107265 pLKO.1 puro shYAP1-2 Broad Institute TRCN0000107266 pLKO.1 puro shPRDM14-1 Broad Institute TRCN0000018523 pLKO.1 puro shPRDM14-2 Broad Institute TRCN0000018525 pLKO.1 puro shPRDM14-3 Broad Institute TRCN0000018524 pLKO.1 puro shPRDM14-4 Broad Institute TRCN0000018527 pLKO.1 puro shPRDM14-5 Broad Institute TRCN0000018526 pLKO.1 puro shCALM2-1 Broad Institute TRCN0000195431 pLKO.1 puro shCALM2-2 Broad Institute TRCN0000196508 pLKO.1 puro shCALM2-3 Broad Institute TRCN0000052580 pLKO.1 puro shSLC2A1-1 Broad Institute TRCN0000043583 pLKO.1 puro shSLC2A1-2 Broad Institute TRCN0000043587 pLKO.1 puro shTEAD1/3/4-1 This study N/A pLKO.1 puro shTEAD1/3/4-2 This study N/A pLX307 P2A GFP Luciferase This study N/A pLX307 P2A GFP YAP1 This study N/A pLX307 P2A GFP PRDM14 This study N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Metascape Previous study (Tripathi et al., 2015) http://metascape.org ChiLin Previous study (Qin et al., 2016) http://cistrome.org/chilin/ deepTools Previous study (Ramı́rez et al., 2016) https://deeptools.readthedocs.io/ en/develop/ (Continued on next page) e3 Developmental Cell 57, 212–227.e1–e8, January 24, 2022
Viability Assay:Article Title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EGF Life Technologies Cat# PMG8041 Y-27632 MilliporeSigma Cat# Y0503 SB431542 MilliporeSigma Cat# 616461 Collagenase XI MilliporeSigma Cat# C9407 DNase I StemCell Cat# 07900 Growth factor reduced Matrigel Corning Cat# 356231 B-27 supplement Thermo Fisher Scientific Cat# 17504044 Noggin Thermo Fisher Scientific Cat# PHC1506 N-acetylcysteine MilliporeSigma Cat# A9165 Nicotinamide MilliporeSigma Cat# N3376 SB202190 MilliporeSigma Cat# S7067 A 83-01 Tocris Cat# 2939 PGE2 Tocris Cat# 2296 Critical Commercial Assays DNA Blood Maxi Kit Qiagen Cat# 51194 Plasma Membrane Protein Extraction Kit Thermo Fisher Scientific Cat# NC1053482 RNeasy Plus Mini Kit Qiagen Cat# 74134 NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat# E7420 KAPA Complete Kit (ABI Prism) Kapa Biosystems Cat# KK4835 QIAquick PCR Purification Kit Qiagen Cat# 28104 Quant-iT PicoGreen dsDNA Thermo Fisher Scientific Cat# P7589 ThruPLEX DNA-seq Kit Rubicon Genomics Cat# R400427 DNeasy Blood & Tissue Mini Kit Qiagen Cat# 69504 CellTiter-Glo 3D Cell Viability Assay Promega Cat# G9683 Deposited Data ORF screen data This study Table S1 RNA-seq and ChIP-seq data This study NCBI GEO: GSE182432 Whole exome sequencing data This study NCBI SRA: PRJNA756046 Analysis of genetic alteration in cancer cBioPortal (Gao et al., 2013) https://www.cbioportal.org/ Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 HT-29 ATCC Cat# HTB-38, RRID:CVCL_0320 SK-CO-1 ATCC Cat# HTB-39, RRID:CVCL_0626 SW48 ATCC Cat# CCL-231, RRID:CVCL_1724 COLO 320 ATCC Cat# CCL-220, RRID:CVCL_0219 HA1E Previous study (Hahn et al., 1999) N/A Experimental Models: Organisms/Strains NCR-nude mouse (CrTac:NCr-Foxn1nu) Taconic Biosciences NCRNU-F Apc WT and KO mouse colon organoid models (Apcflox/flox; tdRFPLSL and Lgr5-eGFP-CreER; Apcflox/flox; tdRFPLSL) This study N/A Apc KO;Kras G12D mouse colon organoid model (Adeno-Cre treatment of Apcflox/flox; LSL-KrasG12D) Kevin Haigis lab at Dana-Farber Cancer Institute N/A Patient-derived colon organoid model (0544) This study N/A (Continued on next page) Developmental Cell 57, 212–227.e1–e8, January 24, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Table S6 This study N/A Recombinant DNA pLKO-Tet-On Novartis N/A Human ORFeome library collection 8.1 Broad Institute N/A pLX317 GFP Broad Institute BRDN0000559466 pLX317 ANPEP Broad Institute TRCN0000476147 pLX317 GRAMD1B Broad Institute TRCN0000481176 pLX317 HDAC6 Broad Institute TRCN0000471558 pLX317 HSP90AA1 Broad Institute TRCN0000491541 pLX317 MAP3K5 Broad Institute TRCN0000488584 pLX317 PIK3CB Broad Institute TRCN0000467602 pLX317 PRDM14 Broad Institute TRCN0000471194 pLX317 YAP1 Broad Institute TRCN0000477457 pLX317 WWTR1 Broad Institute TRCN0000472318 pLX317 CALM2 Broad Institute TRCN0000479230 pLX317 SLC2A1 Broad Institute TRCN0000476750 pLX317 TEAD2 Broad Institute TRCN0000478936 pLX304 GFP Broad Institute ccsbBroad304_99986 pLX304 PRDM14 Broad Institute ccsbBroad304_08822 pLX304 YAP1 Broad Institute ccsbBroad304_07601 pLX304 CALM2 Broad Institute ccsbBroad304_00207 pLX304 SLC2A1 Broad Institute ccsbBroad304_01540 pLKO.1 puro shGFP Previous Study (Kim et al., 2014) N/A pLKO.1 puro shYAP1-1 Broad Institute TRCN0000107265 pLKO.1 puro shYAP1-2 Broad Institute TRCN0000107266 pLKO.1 puro shPRDM14-1 Broad Institute TRCN0000018523 pLKO.1 puro shPRDM14-2 Broad Institute TRCN0000018525 pLKO.1 puro shPRDM14-3 Broad Institute TRCN0000018524 pLKO.1 puro shPRDM14-4 Broad Institute TRCN0000018527 pLKO.1 puro shPRDM14-5 Broad Institute TRCN0000018526 pLKO.1 puro shCALM2-1 Broad Institute TRCN0000195431 pLKO.1 puro shCALM2-2 Broad Institute TRCN0000196508 pLKO.1 puro shCALM2-3 Broad Institute TRCN0000052580 pLKO.1 puro shSLC2A1-1 Broad Institute TRCN0000043583 pLKO.1 puro shSLC2A1-2 Broad Institute TRCN0000043587 pLKO.1 puro shTEAD1/3/4-1 This study N/A pLKO.1 puro shTEAD1/3/4-2 This study N/A pLX307 P2A GFP Luciferase This study N/A pLX307 P2A GFP YAP1 This study N/A pLX307 P2A GFP PRDM14 This study N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Metascape Previous study (Tripathi et al., 2015) http://metascape.org ChiLin Previous study (Qin et al., 2016) http://cistrome.org/chilin/ deepTools Previous study (Ramı́rez et al., 2016) https://deeptools.readthedocs.io/ en/develop/ (Continued on next page) e3 Developmental Cell 57, 212–227.e1–e8, January 24, 2022
RNA Sequencing:Article Title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EGF Life Technologies Cat# PMG8041 Y-27632 MilliporeSigma Cat# Y0503 SB431542 MilliporeSigma Cat# 616461 Collagenase XI MilliporeSigma Cat# C9407 DNase I StemCell Cat# 07900 Growth factor reduced Matrigel Corning Cat# 356231 B-27 supplement Thermo Fisher Scientific Cat# 17504044 Noggin Thermo Fisher Scientific Cat# PHC1506 N-acetylcysteine MilliporeSigma Cat# A9165 Nicotinamide MilliporeSigma Cat# N3376 SB202190 MilliporeSigma Cat# S7067 A 83-01 Tocris Cat# 2939 PGE2 Tocris Cat# 2296 Critical Commercial Assays DNA Blood Maxi Kit Qiagen Cat# 51194 Plasma Membrane Protein Extraction Kit Thermo Fisher Scientific Cat# NC1053482 RNeasy Plus Mini Kit Qiagen Cat# 74134 NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat# E7420 KAPA Complete Kit (ABI Prism) Kapa Biosystems Cat# KK4835 QIAquick PCR Purification Kit Qiagen Cat# 28104 Quant-iT PicoGreen dsDNA Thermo Fisher Scientific Cat# P7589 ThruPLEX DNA-seq Kit Rubicon Genomics Cat# R400427 DNeasy Blood & Tissue Mini Kit Qiagen Cat# 69504 CellTiter-Glo 3D Cell Viability Assay Promega Cat# G9683 Deposited Data ORF screen data This study Table S1 RNA-seq and ChIP-seq data This study NCBI GEO: GSE182432 Whole exome sequencing data This study NCBI SRA: PRJNA756046 Analysis of genetic alteration in cancer cBioPortal (Gao et al., 2013) https://www.cbioportal.org/ Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 HT-29 ATCC Cat# HTB-38, RRID:CVCL_0320 SK-CO-1 ATCC Cat# HTB-39, RRID:CVCL_0626 SW48 ATCC Cat# CCL-231, RRID:CVCL_1724 COLO 320 ATCC Cat# CCL-220, RRID:CVCL_0219 HA1E Previous study (Hahn et al., 1999) N/A Experimental Models: Organisms/Strains NCR-nude mouse (CrTac:NCr-Foxn1nu) Taconic Biosciences NCRNU-F Apc WT and KO mouse colon organoid models (Apcflox/flox; tdRFPLSL and Lgr5-eGFP-CreER; Apcflox/flox; tdRFPLSL) This study N/A Apc KO;Kras G12D mouse colon organoid model (Adeno-Cre treatment of Apcflox/flox; LSL-KrasG12D) Kevin Haigis lab at Dana-Farber Cancer Institute N/A Patient-derived colon organoid model (0544) This study N/A (Continued on next page) Developmental Cell 57, 212–227.e1–e8, January 24, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Table S6 This study N/A Recombinant DNA pLKO-Tet-On Novartis N/A Human ORFeome library collection 8.1 Broad Institute N/A pLX317 GFP Broad Institute BRDN0000559466 pLX317 ANPEP Broad Institute TRCN0000476147 pLX317 GRAMD1B Broad Institute TRCN0000481176 pLX317 HDAC6 Broad Institute TRCN0000471558 pLX317 HSP90AA1 Broad Institute TRCN0000491541 pLX317 MAP3K5 Broad Institute TRCN0000488584 pLX317 PIK3CB Broad Institute TRCN0000467602 pLX317 PRDM14 Broad Institute TRCN0000471194 pLX317 YAP1 Broad Institute TRCN0000477457 pLX317 WWTR1 Broad Institute TRCN0000472318 pLX317 CALM2 Broad Institute TRCN0000479230 pLX317 SLC2A1 Broad Institute TRCN0000476750 pLX317 TEAD2 Broad Institute TRCN0000478936 pLX304 GFP Broad Institute ccsbBroad304_99986 pLX304 PRDM14 Broad Institute ccsbBroad304_08822 pLX304 YAP1 Broad Institute ccsbBroad304_07601 pLX304 CALM2 Broad Institute ccsbBroad304_00207 pLX304 SLC2A1 Broad Institute ccsbBroad304_01540 pLKO.1 puro shGFP Previous Study (Kim et al., 2014) N/A pLKO.1 puro shYAP1-1 Broad Institute TRCN0000107265 pLKO.1 puro shYAP1-2 Broad Institute TRCN0000107266 pLKO.1 puro shPRDM14-1 Broad Institute TRCN0000018523 pLKO.1 puro shPRDM14-2 Broad Institute TRCN0000018525 pLKO.1 puro shPRDM14-3 Broad Institute TRCN0000018524 pLKO.1 puro shPRDM14-4 Broad Institute TRCN0000018527 pLKO.1 puro shPRDM14-5 Broad Institute TRCN0000018526 pLKO.1 puro shCALM2-1 Broad Institute TRCN0000195431 pLKO.1 puro shCALM2-2 Broad Institute TRCN0000196508 pLKO.1 puro shCALM2-3 Broad Institute TRCN0000052580 pLKO.1 puro shSLC2A1-1 Broad Institute TRCN0000043583 pLKO.1 puro shSLC2A1-2 Broad Institute TRCN0000043587 pLKO.1 puro shTEAD1/3/4-1 This study N/A pLKO.1 puro shTEAD1/3/4-2 This study N/A pLX307 P2A GFP Luciferase This study N/A pLX307 P2A GFP YAP1 This study N/A pLX307 P2A GFP PRDM14 This study N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Metascape Previous study (Tripathi et al., 2015) http://metascape.org ChiLin Previous study (Qin et al., 2016) http://cistrome.org/chilin/ deepTools Previous study (Ramı́rez et al., 2016) https://deeptools.readthedocs.io/ en/develop/ (Continued on next page) e3 Developmental Cell 57, 212–227.e1–e8, January 24, 2022
Chromatin Immunoprecipitation:Article Title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EGF Life Technologies Cat# PMG8041 Y-27632 MilliporeSigma Cat# Y0503 SB431542 MilliporeSigma Cat# 616461 Collagenase XI MilliporeSigma Cat# C9407 DNase I StemCell Cat# 07900 Growth factor reduced Matrigel Corning Cat# 356231 B-27 supplement Thermo Fisher Scientific Cat# 17504044 Noggin Thermo Fisher Scientific Cat# PHC1506 N-acetylcysteine MilliporeSigma Cat# A9165 Nicotinamide MilliporeSigma Cat# N3376 SB202190 MilliporeSigma Cat# S7067 A 83-01 Tocris Cat# 2939 PGE2 Tocris Cat# 2296 Critical Commercial Assays DNA Blood Maxi Kit Qiagen Cat# 51194 Plasma Membrane Protein Extraction Kit Thermo Fisher Scientific Cat# NC1053482 RNeasy Plus Mini Kit Qiagen Cat# 74134 NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat# E7420 KAPA Complete Kit (ABI Prism) Kapa Biosystems Cat# KK4835 QIAquick PCR Purification Kit Qiagen Cat# 28104 Quant-iT PicoGreen dsDNA Thermo Fisher Scientific Cat# P7589 ThruPLEX DNA-seq Kit Rubicon Genomics Cat# R400427 DNeasy Blood & Tissue Mini Kit Qiagen Cat# 69504 CellTiter-Glo 3D Cell Viability Assay Promega Cat# G9683 Deposited Data ORF screen data This study Table S1 RNA-seq and ChIP-seq data This study NCBI GEO: GSE182432 Whole exome sequencing data This study NCBI SRA: PRJNA756046 Analysis of genetic alteration in cancer cBioPortal (Gao et al., 2013) https://www.cbioportal.org/ Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 HT-29 ATCC Cat# HTB-38, RRID:CVCL_0320 SK-CO-1 ATCC Cat# HTB-39, RRID:CVCL_0626 SW48 ATCC Cat# CCL-231, RRID:CVCL_1724 COLO 320 ATCC Cat# CCL-220, RRID:CVCL_0219 HA1E Previous study (Hahn et al., 1999) N/A Experimental Models: Organisms/Strains NCR-nude mouse (CrTac:NCr-Foxn1nu) Taconic Biosciences NCRNU-F Apc WT and KO mouse colon organoid models (Apcflox/flox; tdRFPLSL and Lgr5-eGFP-CreER; Apcflox/flox; tdRFPLSL) This study N/A Apc KO;Kras G12D mouse colon organoid model (Adeno-Cre treatment of Apcflox/flox; LSL-KrasG12D) Kevin Haigis lab at Dana-Farber Cancer Institute N/A Patient-derived colon organoid model (0544) This study N/A (Continued on next page) Developmental Cell 57, 212–227.e1–e8, January 24, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Table S6 This study N/A Recombinant DNA pLKO-Tet-On Novartis N/A Human ORFeome library collection 8.1 Broad Institute N/A pLX317 GFP Broad Institute BRDN0000559466 pLX317 ANPEP Broad Institute TRCN0000476147 pLX317 GRAMD1B Broad Institute TRCN0000481176 pLX317 HDAC6 Broad Institute TRCN0000471558 pLX317 HSP90AA1 Broad Institute TRCN0000491541 pLX317 MAP3K5 Broad Institute TRCN0000488584 pLX317 PIK3CB Broad Institute TRCN0000467602 pLX317 PRDM14 Broad Institute TRCN0000471194 pLX317 YAP1 Broad Institute TRCN0000477457 pLX317 WWTR1 Broad Institute TRCN0000472318 pLX317 CALM2 Broad Institute TRCN0000479230 pLX317 SLC2A1 Broad Institute TRCN0000476750 pLX317 TEAD2 Broad Institute TRCN0000478936 pLX304 GFP Broad Institute ccsbBroad304_99986 pLX304 PRDM14 Broad Institute ccsbBroad304_08822 pLX304 YAP1 Broad Institute ccsbBroad304_07601 pLX304 CALM2 Broad Institute ccsbBroad304_00207 pLX304 SLC2A1 Broad Institute ccsbBroad304_01540 pLKO.1 puro shGFP Previous Study (Kim et al., 2014) N/A pLKO.1 puro shYAP1-1 Broad Institute TRCN0000107265 pLKO.1 puro shYAP1-2 Broad Institute TRCN0000107266 pLKO.1 puro shPRDM14-1 Broad Institute TRCN0000018523 pLKO.1 puro shPRDM14-2 Broad Institute TRCN0000018525 pLKO.1 puro shPRDM14-3 Broad Institute TRCN0000018524 pLKO.1 puro shPRDM14-4 Broad Institute TRCN0000018527 pLKO.1 puro shPRDM14-5 Broad Institute TRCN0000018526 pLKO.1 puro shCALM2-1 Broad Institute TRCN0000195431 pLKO.1 puro shCALM2-2 Broad Institute TRCN0000196508 pLKO.1 puro shCALM2-3 Broad Institute TRCN0000052580 pLKO.1 puro shSLC2A1-1 Broad Institute TRCN0000043583 pLKO.1 puro shSLC2A1-2 Broad Institute TRCN0000043587 pLKO.1 puro shTEAD1/3/4-1 This study N/A pLKO.1 puro shTEAD1/3/4-2 This study N/A pLX307 P2A GFP Luciferase This study N/A pLX307 P2A GFP YAP1 This study N/A pLX307 P2A GFP PRDM14 This study N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Metascape Previous study (Tripathi et al., 2015) http://metascape.org ChiLin Previous study (Qin et al., 2016) http://cistrome.org/chilin/ deepTools Previous study (Ramı́rez et al., 2016) https://deeptools.readthedocs.io/ en/develop/ (Continued on next page) e3 Developmental Cell 57, 212–227.e1–e8, January 24, 2022
Sequencing:Article Title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EGF Life Technologies Cat# PMG8041 Y-27632 MilliporeSigma Cat# Y0503 SB431542 MilliporeSigma Cat# 616461 Collagenase XI MilliporeSigma Cat# C9407 DNase I StemCell Cat# 07900 Growth factor reduced Matrigel Corning Cat# 356231 B-27 supplement Thermo Fisher Scientific Cat# 17504044 Noggin Thermo Fisher Scientific Cat# PHC1506 N-acetylcysteine MilliporeSigma Cat# A9165 Nicotinamide MilliporeSigma Cat# N3376 SB202190 MilliporeSigma Cat# S7067 A 83-01 Tocris Cat# 2939 PGE2 Tocris Cat# 2296 Critical Commercial Assays DNA Blood Maxi Kit Qiagen Cat# 51194 Plasma Membrane Protein Extraction Kit Thermo Fisher Scientific Cat# NC1053482 RNeasy Plus Mini Kit Qiagen Cat# 74134 NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat# E7420 KAPA Complete Kit (ABI Prism) Kapa Biosystems Cat# KK4835 QIAquick PCR Purification Kit Qiagen Cat# 28104 Quant-iT PicoGreen dsDNA Thermo Fisher Scientific Cat# P7589 ThruPLEX DNA-seq Kit Rubicon Genomics Cat# R400427 DNeasy Blood & Tissue Mini Kit Qiagen Cat# 69504 CellTiter-Glo 3D Cell Viability Assay Promega Cat# G9683 Deposited Data ORF screen data This study Table S1 RNA-seq and ChIP-seq data This study NCBI GEO: GSE182432 Whole exome sequencing data This study NCBI SRA: PRJNA756046 Analysis of genetic alteration in cancer cBioPortal (Gao et al., 2013) https://www.cbioportal.org/ Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 HT-29 ATCC Cat# HTB-38, RRID:CVCL_0320 SK-CO-1 ATCC Cat# HTB-39, RRID:CVCL_0626 SW48 ATCC Cat# CCL-231, RRID:CVCL_1724 COLO 320 ATCC Cat# CCL-220, RRID:CVCL_0219 HA1E Previous study (Hahn et al., 1999) N/A Experimental Models: Organisms/Strains NCR-nude mouse (CrTac:NCr-Foxn1nu) Taconic Biosciences NCRNU-F Apc WT and KO mouse colon organoid models (Apcflox/flox; tdRFPLSL and Lgr5-eGFP-CreER; Apcflox/flox; tdRFPLSL) This study N/A Apc KO;Kras G12D mouse colon organoid model (Adeno-Cre treatment of Apcflox/flox; LSL-KrasG12D) Kevin Haigis lab at Dana-Farber Cancer Institute N/A Patient-derived colon organoid model (0544) This study N/A (Continued on next page) Developmental Cell 57, 212–227.e1–e8, January 24, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Table S6 This study N/A Recombinant DNA pLKO-Tet-On Novartis N/A Human ORFeome library collection 8.1 Broad Institute N/A pLX317 GFP Broad Institute BRDN0000559466 pLX317 ANPEP Broad Institute TRCN0000476147 pLX317 GRAMD1B Broad Institute TRCN0000481176 pLX317 HDAC6 Broad Institute TRCN0000471558 pLX317 HSP90AA1 Broad Institute TRCN0000491541 pLX317 MAP3K5 Broad Institute TRCN0000488584 pLX317 PIK3CB Broad Institute TRCN0000467602 pLX317 PRDM14 Broad Institute TRCN0000471194 pLX317 YAP1 Broad Institute TRCN0000477457 pLX317 WWTR1 Broad Institute TRCN0000472318 pLX317 CALM2 Broad Institute TRCN0000479230 pLX317 SLC2A1 Broad Institute TRCN0000476750 pLX317 TEAD2 Broad Institute TRCN0000478936 pLX304 GFP Broad Institute ccsbBroad304_99986 pLX304 PRDM14 Broad Institute ccsbBroad304_08822 pLX304 YAP1 Broad Institute ccsbBroad304_07601 pLX304 CALM2 Broad Institute ccsbBroad304_00207 pLX304 SLC2A1 Broad Institute ccsbBroad304_01540 pLKO.1 puro shGFP Previous Study (Kim et al., 2014) N/A pLKO.1 puro shYAP1-1 Broad Institute TRCN0000107265 pLKO.1 puro shYAP1-2 Broad Institute TRCN0000107266 pLKO.1 puro shPRDM14-1 Broad Institute TRCN0000018523 pLKO.1 puro shPRDM14-2 Broad Institute TRCN0000018525 pLKO.1 puro shPRDM14-3 Broad Institute TRCN0000018524 pLKO.1 puro shPRDM14-4 Broad Institute TRCN0000018527 pLKO.1 puro shPRDM14-5 Broad Institute TRCN0000018526 pLKO.1 puro shCALM2-1 Broad Institute TRCN0000195431 pLKO.1 puro shCALM2-2 Broad Institute TRCN0000196508 pLKO.1 puro shCALM2-3 Broad Institute TRCN0000052580 pLKO.1 puro shSLC2A1-1 Broad Institute TRCN0000043583 pLKO.1 puro shSLC2A1-2 Broad Institute TRCN0000043587 pLKO.1 puro shTEAD1/3/4-1 This study N/A pLKO.1 puro shTEAD1/3/4-2 This study N/A pLX307 P2A GFP Luciferase This study N/A pLX307 P2A GFP YAP1 This study N/A pLX307 P2A GFP PRDM14 This study N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Metascape Previous study (Tripathi et al., 2015) http://metascape.org ChiLin Previous study (Qin et al., 2016) http://cistrome.org/chilin/ deepTools Previous study (Ramı́rez et al., 2016) https://deeptools.readthedocs.io/ en/develop/ (Continued on next page) e3 Developmental Cell 57, 212–227.e1–e8, January 24, 2022
Transfection:Article Title: First-line treatment selection with organoids of an EGFR m + TP53 m stage IA1 patient with early metastatic recurrence after radical surgery and follow-up
Article Snippet: Data analyses were performed using GraphPad Prism 7.0 software, and the values of IC50 were calculated by applying nonlinear regression (curve fit). .. Table S1 Additive Supplier Catalogue # Concentration N-Acetylcysteine Sigma A9165 1.25 mM EGF PeproTech AF-100-15 50 ng/mL FGF-10 PeproTech 100-26 20 ng/mL FGF-basic PeproTech 100-10B 1 ng/mL Y-27632 Selleck S1049 10 μM A-83-01 Sigma SML0788 500 nM SB202190 Selleck S1077 10 μM Nicotinamide Sigma 72340 10 mM PGE2 Tocris 2296 1 ìM Noggin (conditional medium) In-house – 50 mL R-Spondin (conditional medium) In-house – 50 mL HEPES Sigma H6147 10 mM GlutaMAX Gibco 35050061 1× B27 Gibco 17504044 1× N2 Gibco 17502048 1× Open in a separate window R-Spondin 1 and Noggin conditioned media were prepared in house from the culture media of Rspo1 cell and the noggin cDNA transfected HEK-293 cell following the methods described before ( 36 , 37 ). ..
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