Recombinant:Article Title: Two Septin complexes mediate actin dynamics during cell wound repair.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins iTaq Universal SYBR Green Supermix Bio-Rad Cat# 1725120 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-Rad Cat# 1725034 Na2ATP Sigma-Aldrich Cat# A2383 Methyl Cellulose Sigma-Aldrich Cat# M0512 Protocatechuate Acid (PCA) Sigma-Aldrich Cat# 03930590 Protocatechuate 3,4-dioxygenase (PCD) Sigma-Aldrich Cat# P8279 Trolox Sigma-Aldrich Cat# 238813 Amyl Acetate Electron Microscopy Sciences Cat# 10815 Sterile Collodion (Parlodion) in 2% Amyl Acetate Electron Microscopy Sciences Cat# 12620-10 Rhodamine Muscle Actin Cytoskeleton, Inc. Cat# AR05 GDP Sigma-Aldrich Cat# G7252 GMP-PNP Sigma-Aldrich Cat# G0635 GST-Rho1 Rosales-Nieves et al.90 N/A GST-Rac1 Rosales-Nieves et al.90 N/A GST-Cdc42 Rosales-Nieves et al.90 N/A Experimental models: Organisms/strains sGMCA (GFP actin reporter) Kiehart et al.50 N/A sStMCA (mScarlet actin reporter) Bloomington Drosophila Stock Center BDSC_90928 UASp-Sep1-GFP Bloomington Drosophila Stock Center BDSC_51346 Sep2-GFP Bloomington Drosophila Stock Center BDSC_26257 UASp-mCh-Pnut Provided by T. Lecuit Guillot and Lecuit91 UASp-Sep4-GFP Bloomington Drosophila Stock Center BDSC_51345 UASp-Sep5-RFP Provided by A. Wilde N/A UASp-GFP-Anillin Bloomington Drosophila Stock Center BDSC_51348 Ubi-AniRBD-GFP Provided by T. Lecuit Munjal et al.71 TRiP.HMC03041 (Vermilion RNAi) Bloomington Drosophila Stock Center BDSC_50641 UASz-sep1-shRNA This study N/A Sep2[2] Provided by D Clark O’Neill and Clark54 TRiP.HMC05924 (Pnut RNAi) Bloomington Drosophila Stock Center BDSC_65157 TRiP.GL01287 (Sep4 RNAi) Bloomington Drosophila Stock Center BDSC_41859 Sep5[2] Provided by D Clark O’Neill and Clark54 TRiP.GL01269 (Ani RNAi) Bloomington Drosophila Stock Center BDSC_41841 matalpha4-GAL-VP16 Bloomington Drosophila Stock Center BDSC_7063 Oligonucleotides (5’ -> 30) qPCR-Sep1-F: CCAACCAGGTGCATCGAAAGT This study N/A qPCR-Sep1-R: CAGCTTTACGGTTTGCTTTTGTT This study N/A qPCR-Sep4-F: AGCGCATCGAGAAGACGAC This study N/A qPCR-Sep4-R: CTGTCCTCACAGTTGATGGCA This study N/A qPCR-Pnut-F: CATCTACAACGCGGAACAGTAT This study N/A qPCR-Pnut-R: ACCGTGAGTGTCAGATTGACG This study N/A qPCR-Ani-F: CTTTCCCAACGTAACGACCTT This study N/A qPCR-Ani-R: GAATCTCAACTTGCACCCCAA This study N/A qPCR-RpL32-F: ATGCTAAGCTGTCGCACAAATG Nakamura et al.92 N/A qPCR-RpL32-R: GTTCGATCCGTAACCGATGT Nakamura et al.92 N/A (Continued on next page) Cell Reports 43, 114215, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sep1-shRNA-top: ctagcagtGCATTATTCCGGA CGCCATAGtagttatattcaagcataCTATGGCGT CCGGAATAATGCgcg This study N/A Sep1-shRNA-bot: aattcgcGCATTATTCCGGAC GCCATAGtagttatattcaagcataCTATGGCGTCC GGAATAATGCactg This study N/A Recombinant DNA pCite4-Ani-RBD This study N/A pETDuet-Sep1-Sep2 This study N/A pETDuet-Sep4-Sep5 This study N/A pET28-dt-Pnut This study N/A pGEX-dt-Sep1 This study N/A pGEX-dt-Sep2 This study N/A pGEX-dt-Pnut This study N/A pGEX-dt-Sep4 This study N/A pGEX-dt-Sep5 This study N/A Software and algorithms Fiji Schindelin et al.93 http://fiji.sc/ R StatSoft https://www.r-project.org/ MATLAB Mathworks http://mathworks.com/ GraphPad Prism GraphPad https://www.graphpad.com/ Other Revolution WD spinning disk confocal microscope Andor N/A CSU-X1 spinning disk confocal microscope Yokogawa N/A LSM 780 Carl Zeiss N/A Micropoint Andor N/A CFX96TM Real-Time PCR Detection System Bio-Rad N/A Fred Hutchinson Cancer Center – Leica Center of Excellence Fred Hutchinson Cancer Center RRID:SCR_022720 Fred Hutchinson Cancer Center Cellular Imaging Core Facility Fred Hutchinson Cancer Center RRID:SCR_022609
Article Title: Endometrial Axin2 + Cells Drive Epithelial Homeostasis, Regeneration, and Cancer following Oncogenic Transformation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Pronase Sigma-Aldrich Cat#10165921001 DNase I Sigma-Aldrich Cat#10104159001 Fetal Bovine Serum Bovogen Cat#SFBS-F L-glutamine HyClone Cat#SH30034.01 Penicillin-streptomycin Thermo Fisher Scientific Cat#15070-063 Matrigel Trevigen Cat#3433-010-01 GlutaMAX (100X) Thermo Fisher Scientific (GIBCO) Cat#35050-061 B27 supplement Thermo Fisher Scientific (GIBCO) Cat#12587-010 N-2 supplement Thermo Fisher Scientific (GIBCO) Cat#17502-048 ITS liquid media supplement Sigma-Aldrich Cat#I3146 Nicotinamide Sigma-Aldrich Cat#N0636 Mouse EGF recombinant Sigma-Aldrich Cat#SRP3196 Human FGF-10 Peprotech Cat#100-26 A83-01 Tocris Cat#2939 TrypLE express Thermo Fisher Scientific (GIBCO) Cat#12604-021 Protein Block Serum Free (Lot#10096977) DAKO Cat#X0909 Ab Diluent with Background Reducing Compoents (Lot#10090973) DAKO Cat#S3022 Doxycycline hyclate (lot#086M4035V) Sigma-Aldrich Cat#D9891 Neutral Red Sigma-Aldrich N3020 Y-27632 dihydrochloride Tocris Cat#1254 DMEM/F12 HAM Sigma-Aldrich Cat#D8437 HBSS/Modified HyClone Cat#SH30031.02 Tamoxifen (Lot#SLBF8049V) Sigma-Aldrich Cat#T5648; CAS#10540-29-1 b-Estradiol (Lot#SLBH0091V) Sigma-Aldrich Cat#E8875; CAS#50-28-2 Progesterone (Lot#SLBG1644V) Sigma-Aldrich Cat#P 0130; CAS#57-83-0 DAPI dilactate Sigma-Aldrich Cat#D9564 Paraformaldehyde 16% solution EM Grade Electron Microscopy Sciences Cat#15710 Xgal (Lot#ES531-B061890) Bioline Cat#BIO-37035 5-Chloro-2‘-Deoxyuridine (Lot#QR10915) MP Biochemicals LLC. .. Cat#105478; CAS#50-90-8 5-Iodo-2‘-Deoxyuridine (Lot#BCBP3111V) Sigma-Aldrich Cat#17152 Diphtheria Toxin (Lot#MKCH2452) Sigma-Aldrich Cat#D0564 Recombinant Murine Wnt-3a Peprotech Cat#315-20 Recombinant Human R-Spondin 1 R&D Systems Cat#4645-RS Noggin Peprotech Cat#120-10C-100 IWR1 Sigma-Aldrich Cat#10161 N,N,N0,N0-Tetrakis(2-Hydroxypropyl) ethylenediamine Sigma-Aldrich Cat #122262 Critical Commercial Assays EnVisionTM+ Dual Link System-HRP (DAB+) (Lot#10095442) DAKO Cat#K4065 Trichrome Stain (Masson) Kit Sigma-Aldrich Cat#HT15 RNeasy Micro Kit QIAGEN Cat#74004 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-rad Cat#172-5034 iTaq Universal SYBR Green Supermix Bio-rad Cat#172-5121 RNAscope 2.5 HD Assay-RED kit Advanced cell Diagnostics Cat# 322350 RNAscope 2.5 HD Detection Reagents-RED Advanced cell Diagnostics Cat# 322360 (Continued on next page) Cell Stem Cell 26, 1–17.e1–e13, February 6, 2020 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER RNAscope H202 & Protease Plus Reagents Advanced cell Diagnostics Cat# 322330 TruSeq PE Cluster Kit v3 Illumina Cat#PE-401-3001 TruSeq SBS Kit v3 Illumina Cat#FC-401-3001 Deposited data RNA-seq data This paper GEO: GSM4156868 RNA-seq data This paper GEO: GSM4156869 RNA-seq data This paper GEO: GSM4156870 RNA-seq data This paper GEO: GSM4156871 RNA-seq data This paper GEO: GSM4156872 RNA-seq data This paper GEO: GSM4156873 Experimental Models: Cell Lines L-WRN cells ATCC Cat#CRL-3276; RRID: CVCL_DA06 Experimental Models: Organisms/Strains Mouse: Pax8rtTA: B6.Cg-Tg(Pax8rtTA2S*M2)1Koes/J The Jackson Laboratory JAX:007176; RRID:IMSR_JAX:007176 Mouse: Axin2rtTA: B6.Cg-Tg(Axin2rtTA2S*M2)7Cos/J The Jackson Laboratory JAX:016997; RRID:IMSR_JAX:016997 Mouse: tetOCre: STOCK Tg(tetO-cre) 1Jaw/J The Jackson Laboratory JAX:006224; RRID:IMSR_JAX:006224 Mouse: tetOH2BJGFP: STOCK Tg(tetOHIST1H2BJ/GFP)47Efu/J The Jackson Laboratory JAX:005104; RRID:IMSR_JAX:005104 Mouse: R26-lacZfl/fl: B6.129S4-Gt(ROSA) 26Sortm1Sor/J The Jackson Laboratory JAX:003474; RRID:IMSR_JAX:003474 Mouse: R26-EYFPfl/fl: B6.129X1-Gt(ROSA) 26Sortm1(EYFP)Cos/J The Jackson Laboratory JAX:006148; RRID:IMSR_JAX:006148 Mouse: Ctnnb1fl/fl: B6.129Ctnnb1tm2Kem/KnwJ The Jackson Laboratory JAX:004152; RRID:IMSR_JAX:004152 Mouse: Ctnnb1fl(ex3)/fl(ex3): C57BL/6NCatnblox(ex3) Harada et al., 1999 Prof Makoto M. Taketo; taketo@mol.f. u-tokyo.ac.jp Mouse: R26Pik3ca,EGFPfl/fl: C57BL/6Gt(ROSA)26Sortm7(Pik3ca*,EGFP)Rsky/J The Jackson Laboratory JAX:012343; RRID:IMSR_JAX:012343 Mouse: R26iDTR: C57BL/6-Gt(ROSA) 26Sortm1(HBEGF)Awai/J The Jackson Laboratory JAX:007900; RRID:IMSR_JAX:007900 Mouse: TCF/Lef:H2B/GFP: STOCK Tg(TCF/Lef1-HIST1H2BB/EGFP)61Hadj/J The Jackson Laboratory JAX:013752; RRID:IMSR_JAX:013752 Oligonucleotides Mouse Axin2 Forward# CGACCCAGTCAATCCTTATCAC (Boretto et al., 2017) N/A Mouse Axin2 Reverse# GGGACTCCATCTACGCTACTG (Boretto et al., 2017) N/A Mouse Gapdh Forward# TGGCAAAGTGGAGATTGTTGCC (Bonnans et al., 2012) N/A Mouse Gapdh Forward# AAGATGGTGATGGGCTTCCCG (Bonnans et al., 2012) N/A RNAscope Negative Control Probe - DapB Advanced cell Diagnostics Cat# 310043 RNAscope Positive Control Probe - Mm-Ppib Advanced cell Diagnostics Cat# 313911 RNAscope Probe-Mm-Axin2 Advanced cell Diagnostics Cat# 400331 RNAscope Probe- Hs-AXIN2 Advanced cell Diagnostics Cat# 400241 (Continued on next page) e3 Cell Stem Cell 26, 1–17.e1–e13, February 6, 2020
Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat1725035 iTaq SYBR green master mix BIO-RAD Cat#1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
SYBR Green Assay:Article Title: Two Septin complexes mediate actin dynamics during cell wound repair.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins iTaq Universal SYBR Green Supermix Bio-Rad Cat# 1725120 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-Rad Cat# 1725034 Na2ATP Sigma-Aldrich Cat# A2383 Methyl Cellulose Sigma-Aldrich Cat# M0512 Protocatechuate Acid (PCA) Sigma-Aldrich Cat# 03930590 Protocatechuate 3,4-dioxygenase (PCD) Sigma-Aldrich Cat# P8279 Trolox Sigma-Aldrich Cat# 238813 Amyl Acetate Electron Microscopy Sciences Cat# 10815 Sterile Collodion (Parlodion) in 2% Amyl Acetate Electron Microscopy Sciences Cat# 12620-10 Rhodamine Muscle Actin Cytoskeleton, Inc. Cat# AR05 GDP Sigma-Aldrich Cat# G7252 GMP-PNP Sigma-Aldrich Cat# G0635 GST-Rho1 Rosales-Nieves et al.90 N/A GST-Rac1 Rosales-Nieves et al.90 N/A GST-Cdc42 Rosales-Nieves et al.90 N/A Experimental models: Organisms/strains sGMCA (GFP actin reporter) Kiehart et al.50 N/A sStMCA (mScarlet actin reporter) Bloomington Drosophila Stock Center BDSC_90928 UASp-Sep1-GFP Bloomington Drosophila Stock Center BDSC_51346 Sep2-GFP Bloomington Drosophila Stock Center BDSC_26257 UASp-mCh-Pnut Provided by T. Lecuit Guillot and Lecuit91 UASp-Sep4-GFP Bloomington Drosophila Stock Center BDSC_51345 UASp-Sep5-RFP Provided by A. Wilde N/A UASp-GFP-Anillin Bloomington Drosophila Stock Center BDSC_51348 Ubi-AniRBD-GFP Provided by T. Lecuit Munjal et al.71 TRiP.HMC03041 (Vermilion RNAi) Bloomington Drosophila Stock Center BDSC_50641 UASz-sep1-shRNA This study N/A Sep2[2] Provided by D Clark O’Neill and Clark54 TRiP.HMC05924 (Pnut RNAi) Bloomington Drosophila Stock Center BDSC_65157 TRiP.GL01287 (Sep4 RNAi) Bloomington Drosophila Stock Center BDSC_41859 Sep5[2] Provided by D Clark O’Neill and Clark54 TRiP.GL01269 (Ani RNAi) Bloomington Drosophila Stock Center BDSC_41841 matalpha4-GAL-VP16 Bloomington Drosophila Stock Center BDSC_7063 Oligonucleotides (5’ -> 30) qPCR-Sep1-F: CCAACCAGGTGCATCGAAAGT This study N/A qPCR-Sep1-R: CAGCTTTACGGTTTGCTTTTGTT This study N/A qPCR-Sep4-F: AGCGCATCGAGAAGACGAC This study N/A qPCR-Sep4-R: CTGTCCTCACAGTTGATGGCA This study N/A qPCR-Pnut-F: CATCTACAACGCGGAACAGTAT This study N/A qPCR-Pnut-R: ACCGTGAGTGTCAGATTGACG This study N/A qPCR-Ani-F: CTTTCCCAACGTAACGACCTT This study N/A qPCR-Ani-R: GAATCTCAACTTGCACCCCAA This study N/A qPCR-RpL32-F: ATGCTAAGCTGTCGCACAAATG Nakamura et al.92 N/A qPCR-RpL32-R: GTTCGATCCGTAACCGATGT Nakamura et al.92 N/A (Continued on next page) Cell Reports 43, 114215, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sep1-shRNA-top: ctagcagtGCATTATTCCGGA CGCCATAGtagttatattcaagcataCTATGGCGT CCGGAATAATGCgcg This study N/A Sep1-shRNA-bot: aattcgcGCATTATTCCGGAC GCCATAGtagttatattcaagcataCTATGGCGTCC GGAATAATGCactg This study N/A Recombinant DNA pCite4-Ani-RBD This study N/A pETDuet-Sep1-Sep2 This study N/A pETDuet-Sep4-Sep5 This study N/A pET28-dt-Pnut This study N/A pGEX-dt-Sep1 This study N/A pGEX-dt-Sep2 This study N/A pGEX-dt-Pnut This study N/A pGEX-dt-Sep4 This study N/A pGEX-dt-Sep5 This study N/A Software and algorithms Fiji Schindelin et al.93 http://fiji.sc/ R StatSoft https://www.r-project.org/ MATLAB Mathworks http://mathworks.com/ GraphPad Prism GraphPad https://www.graphpad.com/ Other Revolution WD spinning disk confocal microscope Andor N/A CSU-X1 spinning disk confocal microscope Yokogawa N/A LSM 780 Carl Zeiss N/A Micropoint Andor N/A CFX96TM Real-Time PCR Detection System Bio-Rad N/A Fred Hutchinson Cancer Center – Leica Center of Excellence Fred Hutchinson Cancer Center RRID:SCR_022720 Fred Hutchinson Cancer Center Cellular Imaging Core Facility Fred Hutchinson Cancer Center RRID:SCR_022609
Article Title: Calcium influx rapidly establishes distinct spatial recruitments of Annexins to cell wounds
Article Snippet: .. iTaq Universal SYBR Green Supermix Bio-Rad Cat#1725120 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-Rad Cat1725034 5,5'-Dibromo BAPTA Invitrogen Cat#D1211 EGTA Sigma Cat#03777 phalloidin Invitrogen Cat#P3457 PIP Strips Membranes Invitrogen Cat#P23751 Rat anti-FLAG antibody BioLegend Cat#637303 ..
Article Title: Endometrial Axin2 + Cells Drive Epithelial Homeostasis, Regeneration, and Cancer following Oncogenic Transformation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Pronase Sigma-Aldrich Cat#10165921001 DNase I Sigma-Aldrich Cat#10104159001 Fetal Bovine Serum Bovogen Cat#SFBS-F L-glutamine HyClone Cat#SH30034.01 Penicillin-streptomycin Thermo Fisher Scientific Cat#15070-063 Matrigel Trevigen Cat#3433-010-01 GlutaMAX (100X) Thermo Fisher Scientific (GIBCO) Cat#35050-061 B27 supplement Thermo Fisher Scientific (GIBCO) Cat#12587-010 N-2 supplement Thermo Fisher Scientific (GIBCO) Cat#17502-048 ITS liquid media supplement Sigma-Aldrich Cat#I3146 Nicotinamide Sigma-Aldrich Cat#N0636 Mouse EGF recombinant Sigma-Aldrich Cat#SRP3196 Human FGF-10 Peprotech Cat#100-26 A83-01 Tocris Cat#2939 TrypLE express Thermo Fisher Scientific (GIBCO) Cat#12604-021 Protein Block Serum Free (Lot#10096977) DAKO Cat#X0909 Ab Diluent with Background Reducing Compoents (Lot#10090973) DAKO Cat#S3022 Doxycycline hyclate (lot#086M4035V) Sigma-Aldrich Cat#D9891 Neutral Red Sigma-Aldrich N3020 Y-27632 dihydrochloride Tocris Cat#1254 DMEM/F12 HAM Sigma-Aldrich Cat#D8437 HBSS/Modified HyClone Cat#SH30031.02 Tamoxifen (Lot#SLBF8049V) Sigma-Aldrich Cat#T5648; CAS#10540-29-1 b-Estradiol (Lot#SLBH0091V) Sigma-Aldrich Cat#E8875; CAS#50-28-2 Progesterone (Lot#SLBG1644V) Sigma-Aldrich Cat#P 0130; CAS#57-83-0 DAPI dilactate Sigma-Aldrich Cat#D9564 Paraformaldehyde 16% solution EM Grade Electron Microscopy Sciences Cat#15710 Xgal (Lot#ES531-B061890) Bioline Cat#BIO-37035 5-Chloro-2‘-Deoxyuridine (Lot#QR10915) MP Biochemicals LLC. .. Cat#105478; CAS#50-90-8 5-Iodo-2‘-Deoxyuridine (Lot#BCBP3111V) Sigma-Aldrich Cat#17152 Diphtheria Toxin (Lot#MKCH2452) Sigma-Aldrich Cat#D0564 Recombinant Murine Wnt-3a Peprotech Cat#315-20 Recombinant Human R-Spondin 1 R&D Systems Cat#4645-RS Noggin Peprotech Cat#120-10C-100 IWR1 Sigma-Aldrich Cat#10161 N,N,N0,N0-Tetrakis(2-Hydroxypropyl) ethylenediamine Sigma-Aldrich Cat #122262 Critical Commercial Assays EnVisionTM+ Dual Link System-HRP (DAB+) (Lot#10095442) DAKO Cat#K4065 Trichrome Stain (Masson) Kit Sigma-Aldrich Cat#HT15 RNeasy Micro Kit QIAGEN Cat#74004 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-rad Cat#172-5034 iTaq Universal SYBR Green Supermix Bio-rad Cat#172-5121 RNAscope 2.5 HD Assay-RED kit Advanced cell Diagnostics Cat# 322350 RNAscope 2.5 HD Detection Reagents-RED Advanced cell Diagnostics Cat# 322360 (Continued on next page) Cell Stem Cell 26, 1–17.e1–e13, February 6, 2020 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER RNAscope H202 & Protease Plus Reagents Advanced cell Diagnostics Cat# 322330 TruSeq PE Cluster Kit v3 Illumina Cat#PE-401-3001 TruSeq SBS Kit v3 Illumina Cat#FC-401-3001 Deposited data RNA-seq data This paper GEO: GSM4156868 RNA-seq data This paper GEO: GSM4156869 RNA-seq data This paper GEO: GSM4156870 RNA-seq data This paper GEO: GSM4156871 RNA-seq data This paper GEO: GSM4156872 RNA-seq data This paper GEO: GSM4156873 Experimental Models: Cell Lines L-WRN cells ATCC Cat#CRL-3276; RRID: CVCL_DA06 Experimental Models: Organisms/Strains Mouse: Pax8rtTA: B6.Cg-Tg(Pax8rtTA2S*M2)1Koes/J The Jackson Laboratory JAX:007176; RRID:IMSR_JAX:007176 Mouse: Axin2rtTA: B6.Cg-Tg(Axin2rtTA2S*M2)7Cos/J The Jackson Laboratory JAX:016997; RRID:IMSR_JAX:016997 Mouse: tetOCre: STOCK Tg(tetO-cre) 1Jaw/J The Jackson Laboratory JAX:006224; RRID:IMSR_JAX:006224 Mouse: tetOH2BJGFP: STOCK Tg(tetOHIST1H2BJ/GFP)47Efu/J The Jackson Laboratory JAX:005104; RRID:IMSR_JAX:005104 Mouse: R26-lacZfl/fl: B6.129S4-Gt(ROSA) 26Sortm1Sor/J The Jackson Laboratory JAX:003474; RRID:IMSR_JAX:003474 Mouse: R26-EYFPfl/fl: B6.129X1-Gt(ROSA) 26Sortm1(EYFP)Cos/J The Jackson Laboratory JAX:006148; RRID:IMSR_JAX:006148 Mouse: Ctnnb1fl/fl: B6.129Ctnnb1tm2Kem/KnwJ The Jackson Laboratory JAX:004152; RRID:IMSR_JAX:004152 Mouse: Ctnnb1fl(ex3)/fl(ex3): C57BL/6NCatnblox(ex3) Harada et al., 1999 Prof Makoto M. Taketo; taketo@mol.f. u-tokyo.ac.jp Mouse: R26Pik3ca,EGFPfl/fl: C57BL/6Gt(ROSA)26Sortm7(Pik3ca*,EGFP)Rsky/J The Jackson Laboratory JAX:012343; RRID:IMSR_JAX:012343 Mouse: R26iDTR: C57BL/6-Gt(ROSA) 26Sortm1(HBEGF)Awai/J The Jackson Laboratory JAX:007900; RRID:IMSR_JAX:007900 Mouse: TCF/Lef:H2B/GFP: STOCK Tg(TCF/Lef1-HIST1H2BB/EGFP)61Hadj/J The Jackson Laboratory JAX:013752; RRID:IMSR_JAX:013752 Oligonucleotides Mouse Axin2 Forward# CGACCCAGTCAATCCTTATCAC (Boretto et al., 2017) N/A Mouse Axin2 Reverse# GGGACTCCATCTACGCTACTG (Boretto et al., 2017) N/A Mouse Gapdh Forward# TGGCAAAGTGGAGATTGTTGCC (Bonnans et al., 2012) N/A Mouse Gapdh Forward# AAGATGGTGATGGGCTTCCCG (Bonnans et al., 2012) N/A RNAscope Negative Control Probe - DapB Advanced cell Diagnostics Cat# 310043 RNAscope Positive Control Probe - Mm-Ppib Advanced cell Diagnostics Cat# 313911 RNAscope Probe-Mm-Axin2 Advanced cell Diagnostics Cat# 400331 RNAscope Probe- Hs-AXIN2 Advanced cell Diagnostics Cat# 400241 (Continued on next page) e3 Cell Stem Cell 26, 1–17.e1–e13, February 6, 2020
Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat1725035 iTaq SYBR green master mix BIO-RAD Cat#1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
cDNA Synthesis:Article Title: Two Septin complexes mediate actin dynamics during cell wound repair.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins iTaq Universal SYBR Green Supermix Bio-Rad Cat# 1725120 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-Rad Cat# 1725034 Na2ATP Sigma-Aldrich Cat# A2383 Methyl Cellulose Sigma-Aldrich Cat# M0512 Protocatechuate Acid (PCA) Sigma-Aldrich Cat# 03930590 Protocatechuate 3,4-dioxygenase (PCD) Sigma-Aldrich Cat# P8279 Trolox Sigma-Aldrich Cat# 238813 Amyl Acetate Electron Microscopy Sciences Cat# 10815 Sterile Collodion (Parlodion) in 2% Amyl Acetate Electron Microscopy Sciences Cat# 12620-10 Rhodamine Muscle Actin Cytoskeleton, Inc. Cat# AR05 GDP Sigma-Aldrich Cat# G7252 GMP-PNP Sigma-Aldrich Cat# G0635 GST-Rho1 Rosales-Nieves et al.90 N/A GST-Rac1 Rosales-Nieves et al.90 N/A GST-Cdc42 Rosales-Nieves et al.90 N/A Experimental models: Organisms/strains sGMCA (GFP actin reporter) Kiehart et al.50 N/A sStMCA (mScarlet actin reporter) Bloomington Drosophila Stock Center BDSC_90928 UASp-Sep1-GFP Bloomington Drosophila Stock Center BDSC_51346 Sep2-GFP Bloomington Drosophila Stock Center BDSC_26257 UASp-mCh-Pnut Provided by T. Lecuit Guillot and Lecuit91 UASp-Sep4-GFP Bloomington Drosophila Stock Center BDSC_51345 UASp-Sep5-RFP Provided by A. Wilde N/A UASp-GFP-Anillin Bloomington Drosophila Stock Center BDSC_51348 Ubi-AniRBD-GFP Provided by T. Lecuit Munjal et al.71 TRiP.HMC03041 (Vermilion RNAi) Bloomington Drosophila Stock Center BDSC_50641 UASz-sep1-shRNA This study N/A Sep2[2] Provided by D Clark O’Neill and Clark54 TRiP.HMC05924 (Pnut RNAi) Bloomington Drosophila Stock Center BDSC_65157 TRiP.GL01287 (Sep4 RNAi) Bloomington Drosophila Stock Center BDSC_41859 Sep5[2] Provided by D Clark O’Neill and Clark54 TRiP.GL01269 (Ani RNAi) Bloomington Drosophila Stock Center BDSC_41841 matalpha4-GAL-VP16 Bloomington Drosophila Stock Center BDSC_7063 Oligonucleotides (5’ -> 30) qPCR-Sep1-F: CCAACCAGGTGCATCGAAAGT This study N/A qPCR-Sep1-R: CAGCTTTACGGTTTGCTTTTGTT This study N/A qPCR-Sep4-F: AGCGCATCGAGAAGACGAC This study N/A qPCR-Sep4-R: CTGTCCTCACAGTTGATGGCA This study N/A qPCR-Pnut-F: CATCTACAACGCGGAACAGTAT This study N/A qPCR-Pnut-R: ACCGTGAGTGTCAGATTGACG This study N/A qPCR-Ani-F: CTTTCCCAACGTAACGACCTT This study N/A qPCR-Ani-R: GAATCTCAACTTGCACCCCAA This study N/A qPCR-RpL32-F: ATGCTAAGCTGTCGCACAAATG Nakamura et al.92 N/A qPCR-RpL32-R: GTTCGATCCGTAACCGATGT Nakamura et al.92 N/A (Continued on next page) Cell Reports 43, 114215, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sep1-shRNA-top: ctagcagtGCATTATTCCGGA CGCCATAGtagttatattcaagcataCTATGGCGT CCGGAATAATGCgcg This study N/A Sep1-shRNA-bot: aattcgcGCATTATTCCGGAC GCCATAGtagttatattcaagcataCTATGGCGTCC GGAATAATGCactg This study N/A Recombinant DNA pCite4-Ani-RBD This study N/A pETDuet-Sep1-Sep2 This study N/A pETDuet-Sep4-Sep5 This study N/A pET28-dt-Pnut This study N/A pGEX-dt-Sep1 This study N/A pGEX-dt-Sep2 This study N/A pGEX-dt-Pnut This study N/A pGEX-dt-Sep4 This study N/A pGEX-dt-Sep5 This study N/A Software and algorithms Fiji Schindelin et al.93 http://fiji.sc/ R StatSoft https://www.r-project.org/ MATLAB Mathworks http://mathworks.com/ GraphPad Prism GraphPad https://www.graphpad.com/ Other Revolution WD spinning disk confocal microscope Andor N/A CSU-X1 spinning disk confocal microscope Yokogawa N/A LSM 780 Carl Zeiss N/A Micropoint Andor N/A CFX96TM Real-Time PCR Detection System Bio-Rad N/A Fred Hutchinson Cancer Center – Leica Center of Excellence Fred Hutchinson Cancer Center RRID:SCR_022720 Fred Hutchinson Cancer Center Cellular Imaging Core Facility Fred Hutchinson Cancer Center RRID:SCR_022609
Article Title: Calcium influx rapidly establishes distinct spatial recruitments of Annexins to cell wounds
Article Snippet: .. iTaq Universal SYBR Green Supermix Bio-Rad Cat#1725120 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-Rad Cat1725034 5,5'-Dibromo BAPTA Invitrogen Cat#D1211 EGTA Sigma Cat#03777 phalloidin Invitrogen Cat#P3457 PIP Strips Membranes Invitrogen Cat#P23751 Rat anti-FLAG antibody BioLegend Cat#637303 ..
Article Title: Differentiation of stem cell-derived pancreatic progenitors into insulin-secreting islet clusters in a multiwell-based static 3D culture system.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Alexa Fluor 647 mouse IgG1k, isotype control BD Biosciences Cat# 557714; RRID: AB_396823 Biological samples Human islets ADI Islet Core https://www.epicore.ualberta.ca/IsletCore/ Chemicals, peptides, and recombinant proteins Matrigel, hESC-qualified Corning Cat# 08-774-552 TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604021 Accutase STEMCELL Technologies Cat# 07920 Gentle Cell Dissociation Reagent STEMCELL Technologies Cat# 07174 Y-27632 STEMCELL Technologies Cat# 72304 STEMdiffTM Pancreatic Progenitor Kit STEMCELL Technologies Cat# 05120 mTeSR1 Complete Kit STEMCELL Technologies Cat# 85850 DPBS, without Ca2+ and Mg2+ Sigma-Aldrich Cat# D8537 DMEM/F-12, HEPES Thermo Fisher Scientific Cat# 11330-032 MCDB131 medium Life technologies Cat# 10372019 CMRL 1066, Supplemented, CIT modification Corning Cat# 98-304-CV Glutamax Thermo Fisher Scientific Cat# 35050061 ITS-X Thermo Fisher Scientific Cat# 51500056 NaHCO3 Sigma-Aldrich Cat# S6297 D-glucose Sigma-Aldrich Cat# G8769 Fatty acid-free BSA Proliant Cat# 68700 GDF-8 PeproTech Cat# 120-00 MCX-928 Janssen Internal compound N/A CHIR99021 Sigma-Aldrich Cat# SML1046 L-ascorbic acid Sigma-Aldrich Cat# A4544 FGF-7 R&D Systems Cat# 251-KG SANT-1 Sigma-Aldrich Cat# S4572 Retinoid acid, all-trans Sigma-Aldrich Cat# R2625 LDN193189 STEMCELL Technologies Cat# 72147 TPPB Tocris Cat# 5343/1 Triiodothyronine (T3) Sigma-Aldrich Cat# T6397 ALK5 inhibitor II Cayman Chemicals Cat# 14794 Zinc sulfate Sigma-Aldrich Cat# Z0251 Heparin Sigma-Aldrich Cat# H3149 Gamma secretase inhibitor XX (GSi XX) Sigma-Aldrich Cat# 565789 N-acetyl cysteine (NAC) Sigma-Aldrich Cat# A9165 Trolox Sigma-Aldrich Cat# 648471 R428 Cayman Chemicals Cat# 21523 ZM447439 (ZM) SelleckChem Cat# S1103 WNT4 Biorbyt Cat# orb358133 Forskolin (FSK) STEMCELL Technologies Cat# 72114 Critical commercial assays MycoSEQ Mycoplasma Detection Kit Life technologies Cat# 4399363 Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Live/Dead Viability/Cytotoxicity Kit Life technologies Cat# L3224 Human Insulin ELISA Kit ALPCO Cat# 80-INSHU-E01.1 Glucagon ELISA Kit Thermo Fisher Scientific Cat# EHGCG Ultralow Attachment Flat Bottom 96-well plate Corning Costar (VWR) Cat# CLS3474 AggrewellTM 400, 24-well plate STEMCELL Technologies Cat# 34415 (Continued on next page) Cell Reports Methods 3, 100466, May 22, 2023 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER AggrewellTM 800, 24-well plate STEMCELL Technologies Cat# 34815 Anti-Adherence Rinsing Solution STEMCELL Technologies Cat# 07010 QIAzol lysis reagent Qiagen Cat# 79306 RNeasy Mini Kit Qiagen Cat# 74106 iScriptTM gDNA Clear cDNA Synthesis kit Bio-Rad Cat# 1725035 SsoFastTM EvaGreen Supermix Bio-Rad Cat# 1725202 UltraPure DNase/RNase-Free Distilled Water Life technologies Cat# 10977-015 Dithizone Sigma-Aldrich Cat# 43820-50G 4% Paraformaldehyde (PFA) solution in PBS Santa Cruz Biotechnology Cat# sc-281692 100% Triton X-100 Thermo Fisher Scientific Cat# BP151-100 Bovine serum albumin (BSA) Thermo Fisher Scientific Cat# BP1600-100 DAPI Sigma-Aldrich Cat# D9542 RIPA Lysis Buffer, 10X Sigma-Aldrich Cat# 20-188 Cell-Tak Cell and Tissue Adhesive Corning Cat# 354240 Experimental models: Cell lines Human: H1 hESC line WiCell Research Institute James A. Thomson et al., 1998 Human:Mel1 INSGFP/W hESC line Kindly provided by Dr. Edouard G. Stanley Suzanne J Micallef et al., 2011 Human:HUES4 PDXeG hESC line Kindly provided by Dr. Henrik Semb Jacqueline Ameri et al., 2017 Human: GCaMP_CRISPRi hiPSC line Kindly provided by Dr. Bruce Conklin and Dr. Knut Woltjen Mohammad A. Mandegar et al., 2016 Oligonucleotides See Table S2 Integrated DNA Technologies https://www.idtdna.com/pages/ Software and algorithms GraphPad Prism 9.0 GraphPad https://www.graphpad.com/ Fiji/ImageJ Schneider et al.47 https://imagej.nih.gov/ij/ Zen Microscopy Software Zeiss https://www.zeiss.com/microscopy/int/ products/microscope-software/zen.html/ FlowJo v10 FlowJo, LLC http://www.flowjo.com/ BioRender BioRender https://app.biorender.com VisualParadigm Online VisualParadigm https://online.visual-paradigm.com ..
Article Title: Endometrial Axin2 + Cells Drive Epithelial Homeostasis, Regeneration, and Cancer following Oncogenic Transformation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Pronase Sigma-Aldrich Cat#10165921001 DNase I Sigma-Aldrich Cat#10104159001 Fetal Bovine Serum Bovogen Cat#SFBS-F L-glutamine HyClone Cat#SH30034.01 Penicillin-streptomycin Thermo Fisher Scientific Cat#15070-063 Matrigel Trevigen Cat#3433-010-01 GlutaMAX (100X) Thermo Fisher Scientific (GIBCO) Cat#35050-061 B27 supplement Thermo Fisher Scientific (GIBCO) Cat#12587-010 N-2 supplement Thermo Fisher Scientific (GIBCO) Cat#17502-048 ITS liquid media supplement Sigma-Aldrich Cat#I3146 Nicotinamide Sigma-Aldrich Cat#N0636 Mouse EGF recombinant Sigma-Aldrich Cat#SRP3196 Human FGF-10 Peprotech Cat#100-26 A83-01 Tocris Cat#2939 TrypLE express Thermo Fisher Scientific (GIBCO) Cat#12604-021 Protein Block Serum Free (Lot#10096977) DAKO Cat#X0909 Ab Diluent with Background Reducing Compoents (Lot#10090973) DAKO Cat#S3022 Doxycycline hyclate (lot#086M4035V) Sigma-Aldrich Cat#D9891 Neutral Red Sigma-Aldrich N3020 Y-27632 dihydrochloride Tocris Cat#1254 DMEM/F12 HAM Sigma-Aldrich Cat#D8437 HBSS/Modified HyClone Cat#SH30031.02 Tamoxifen (Lot#SLBF8049V) Sigma-Aldrich Cat#T5648; CAS#10540-29-1 b-Estradiol (Lot#SLBH0091V) Sigma-Aldrich Cat#E8875; CAS#50-28-2 Progesterone (Lot#SLBG1644V) Sigma-Aldrich Cat#P 0130; CAS#57-83-0 DAPI dilactate Sigma-Aldrich Cat#D9564 Paraformaldehyde 16% solution EM Grade Electron Microscopy Sciences Cat#15710 Xgal (Lot#ES531-B061890) Bioline Cat#BIO-37035 5-Chloro-2‘-Deoxyuridine (Lot#QR10915) MP Biochemicals LLC. .. Cat#105478; CAS#50-90-8 5-Iodo-2‘-Deoxyuridine (Lot#BCBP3111V) Sigma-Aldrich Cat#17152 Diphtheria Toxin (Lot#MKCH2452) Sigma-Aldrich Cat#D0564 Recombinant Murine Wnt-3a Peprotech Cat#315-20 Recombinant Human R-Spondin 1 R&D Systems Cat#4645-RS Noggin Peprotech Cat#120-10C-100 IWR1 Sigma-Aldrich Cat#10161 N,N,N0,N0-Tetrakis(2-Hydroxypropyl) ethylenediamine Sigma-Aldrich Cat #122262 Critical Commercial Assays EnVisionTM+ Dual Link System-HRP (DAB+) (Lot#10095442) DAKO Cat#K4065 Trichrome Stain (Masson) Kit Sigma-Aldrich Cat#HT15 RNeasy Micro Kit QIAGEN Cat#74004 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-rad Cat#172-5034 iTaq Universal SYBR Green Supermix Bio-rad Cat#172-5121 RNAscope 2.5 HD Assay-RED kit Advanced cell Diagnostics Cat# 322350 RNAscope 2.5 HD Detection Reagents-RED Advanced cell Diagnostics Cat# 322360 (Continued on next page) Cell Stem Cell 26, 1–17.e1–e13, February 6, 2020 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER RNAscope H202 & Protease Plus Reagents Advanced cell Diagnostics Cat# 322330 TruSeq PE Cluster Kit v3 Illumina Cat#PE-401-3001 TruSeq SBS Kit v3 Illumina Cat#FC-401-3001 Deposited data RNA-seq data This paper GEO: GSM4156868 RNA-seq data This paper GEO: GSM4156869 RNA-seq data This paper GEO: GSM4156870 RNA-seq data This paper GEO: GSM4156871 RNA-seq data This paper GEO: GSM4156872 RNA-seq data This paper GEO: GSM4156873 Experimental Models: Cell Lines L-WRN cells ATCC Cat#CRL-3276; RRID: CVCL_DA06 Experimental Models: Organisms/Strains Mouse: Pax8rtTA: B6.Cg-Tg(Pax8rtTA2S*M2)1Koes/J The Jackson Laboratory JAX:007176; RRID:IMSR_JAX:007176 Mouse: Axin2rtTA: B6.Cg-Tg(Axin2rtTA2S*M2)7Cos/J The Jackson Laboratory JAX:016997; RRID:IMSR_JAX:016997 Mouse: tetOCre: STOCK Tg(tetO-cre) 1Jaw/J The Jackson Laboratory JAX:006224; RRID:IMSR_JAX:006224 Mouse: tetOH2BJGFP: STOCK Tg(tetOHIST1H2BJ/GFP)47Efu/J The Jackson Laboratory JAX:005104; RRID:IMSR_JAX:005104 Mouse: R26-lacZfl/fl: B6.129S4-Gt(ROSA) 26Sortm1Sor/J The Jackson Laboratory JAX:003474; RRID:IMSR_JAX:003474 Mouse: R26-EYFPfl/fl: B6.129X1-Gt(ROSA) 26Sortm1(EYFP)Cos/J The Jackson Laboratory JAX:006148; RRID:IMSR_JAX:006148 Mouse: Ctnnb1fl/fl: B6.129Ctnnb1tm2Kem/KnwJ The Jackson Laboratory JAX:004152; RRID:IMSR_JAX:004152 Mouse: Ctnnb1fl(ex3)/fl(ex3): C57BL/6NCatnblox(ex3) Harada et al., 1999 Prof Makoto M. Taketo; taketo@mol.f. u-tokyo.ac.jp Mouse: R26Pik3ca,EGFPfl/fl: C57BL/6Gt(ROSA)26Sortm7(Pik3ca*,EGFP)Rsky/J The Jackson Laboratory JAX:012343; RRID:IMSR_JAX:012343 Mouse: R26iDTR: C57BL/6-Gt(ROSA) 26Sortm1(HBEGF)Awai/J The Jackson Laboratory JAX:007900; RRID:IMSR_JAX:007900 Mouse: TCF/Lef:H2B/GFP: STOCK Tg(TCF/Lef1-HIST1H2BB/EGFP)61Hadj/J The Jackson Laboratory JAX:013752; RRID:IMSR_JAX:013752 Oligonucleotides Mouse Axin2 Forward# CGACCCAGTCAATCCTTATCAC (Boretto et al., 2017) N/A Mouse Axin2 Reverse# GGGACTCCATCTACGCTACTG (Boretto et al., 2017) N/A Mouse Gapdh Forward# TGGCAAAGTGGAGATTGTTGCC (Bonnans et al., 2012) N/A Mouse Gapdh Forward# AAGATGGTGATGGGCTTCCCG (Bonnans et al., 2012) N/A RNAscope Negative Control Probe - DapB Advanced cell Diagnostics Cat# 310043 RNAscope Positive Control Probe - Mm-Ppib Advanced cell Diagnostics Cat# 313911 RNAscope Probe-Mm-Axin2 Advanced cell Diagnostics Cat# 400331 RNAscope Probe- Hs-AXIN2 Advanced cell Diagnostics Cat# 400241 (Continued on next page) e3 Cell Stem Cell 26, 1–17.e1–e13, February 6, 2020
Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat1725035 iTaq SYBR green master mix BIO-RAD Cat#1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
Electron Microscopy:Article Title: Two Septin complexes mediate actin dynamics during cell wound repair.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins iTaq Universal SYBR Green Supermix Bio-Rad Cat# 1725120 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-Rad Cat# 1725034 Na2ATP Sigma-Aldrich Cat# A2383 Methyl Cellulose Sigma-Aldrich Cat# M0512 Protocatechuate Acid (PCA) Sigma-Aldrich Cat# 03930590 Protocatechuate 3,4-dioxygenase (PCD) Sigma-Aldrich Cat# P8279 Trolox Sigma-Aldrich Cat# 238813 Amyl Acetate Electron Microscopy Sciences Cat# 10815 Sterile Collodion (Parlodion) in 2% Amyl Acetate Electron Microscopy Sciences Cat# 12620-10 Rhodamine Muscle Actin Cytoskeleton, Inc. Cat# AR05 GDP Sigma-Aldrich Cat# G7252 GMP-PNP Sigma-Aldrich Cat# G0635 GST-Rho1 Rosales-Nieves et al.90 N/A GST-Rac1 Rosales-Nieves et al.90 N/A GST-Cdc42 Rosales-Nieves et al.90 N/A Experimental models: Organisms/strains sGMCA (GFP actin reporter) Kiehart et al.50 N/A sStMCA (mScarlet actin reporter) Bloomington Drosophila Stock Center BDSC_90928 UASp-Sep1-GFP Bloomington Drosophila Stock Center BDSC_51346 Sep2-GFP Bloomington Drosophila Stock Center BDSC_26257 UASp-mCh-Pnut Provided by T. Lecuit Guillot and Lecuit91 UASp-Sep4-GFP Bloomington Drosophila Stock Center BDSC_51345 UASp-Sep5-RFP Provided by A. Wilde N/A UASp-GFP-Anillin Bloomington Drosophila Stock Center BDSC_51348 Ubi-AniRBD-GFP Provided by T. Lecuit Munjal et al.71 TRiP.HMC03041 (Vermilion RNAi) Bloomington Drosophila Stock Center BDSC_50641 UASz-sep1-shRNA This study N/A Sep2[2] Provided by D Clark O’Neill and Clark54 TRiP.HMC05924 (Pnut RNAi) Bloomington Drosophila Stock Center BDSC_65157 TRiP.GL01287 (Sep4 RNAi) Bloomington Drosophila Stock Center BDSC_41859 Sep5[2] Provided by D Clark O’Neill and Clark54 TRiP.GL01269 (Ani RNAi) Bloomington Drosophila Stock Center BDSC_41841 matalpha4-GAL-VP16 Bloomington Drosophila Stock Center BDSC_7063 Oligonucleotides (5’ -> 30) qPCR-Sep1-F: CCAACCAGGTGCATCGAAAGT This study N/A qPCR-Sep1-R: CAGCTTTACGGTTTGCTTTTGTT This study N/A qPCR-Sep4-F: AGCGCATCGAGAAGACGAC This study N/A qPCR-Sep4-R: CTGTCCTCACAGTTGATGGCA This study N/A qPCR-Pnut-F: CATCTACAACGCGGAACAGTAT This study N/A qPCR-Pnut-R: ACCGTGAGTGTCAGATTGACG This study N/A qPCR-Ani-F: CTTTCCCAACGTAACGACCTT This study N/A qPCR-Ani-R: GAATCTCAACTTGCACCCCAA This study N/A qPCR-RpL32-F: ATGCTAAGCTGTCGCACAAATG Nakamura et al.92 N/A qPCR-RpL32-R: GTTCGATCCGTAACCGATGT Nakamura et al.92 N/A (Continued on next page) Cell Reports 43, 114215, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sep1-shRNA-top: ctagcagtGCATTATTCCGGA CGCCATAGtagttatattcaagcataCTATGGCGT CCGGAATAATGCgcg This study N/A Sep1-shRNA-bot: aattcgcGCATTATTCCGGAC GCCATAGtagttatattcaagcataCTATGGCGTCC GGAATAATGCactg This study N/A Recombinant DNA pCite4-Ani-RBD This study N/A pETDuet-Sep1-Sep2 This study N/A pETDuet-Sep4-Sep5 This study N/A pET28-dt-Pnut This study N/A pGEX-dt-Sep1 This study N/A pGEX-dt-Sep2 This study N/A pGEX-dt-Pnut This study N/A pGEX-dt-Sep4 This study N/A pGEX-dt-Sep5 This study N/A Software and algorithms Fiji Schindelin et al.93 http://fiji.sc/ R StatSoft https://www.r-project.org/ MATLAB Mathworks http://mathworks.com/ GraphPad Prism GraphPad https://www.graphpad.com/ Other Revolution WD spinning disk confocal microscope Andor N/A CSU-X1 spinning disk confocal microscope Yokogawa N/A LSM 780 Carl Zeiss N/A Micropoint Andor N/A CFX96TM Real-Time PCR Detection System Bio-Rad N/A Fred Hutchinson Cancer Center – Leica Center of Excellence Fred Hutchinson Cancer Center RRID:SCR_022720 Fred Hutchinson Cancer Center Cellular Imaging Core Facility Fred Hutchinson Cancer Center RRID:SCR_022609
Sterility:Article Title: Two Septin complexes mediate actin dynamics during cell wound repair.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins iTaq Universal SYBR Green Supermix Bio-Rad Cat# 1725120 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-Rad Cat# 1725034 Na2ATP Sigma-Aldrich Cat# A2383 Methyl Cellulose Sigma-Aldrich Cat# M0512 Protocatechuate Acid (PCA) Sigma-Aldrich Cat# 03930590 Protocatechuate 3,4-dioxygenase (PCD) Sigma-Aldrich Cat# P8279 Trolox Sigma-Aldrich Cat# 238813 Amyl Acetate Electron Microscopy Sciences Cat# 10815 Sterile Collodion (Parlodion) in 2% Amyl Acetate Electron Microscopy Sciences Cat# 12620-10 Rhodamine Muscle Actin Cytoskeleton, Inc. Cat# AR05 GDP Sigma-Aldrich Cat# G7252 GMP-PNP Sigma-Aldrich Cat# G0635 GST-Rho1 Rosales-Nieves et al.90 N/A GST-Rac1 Rosales-Nieves et al.90 N/A GST-Cdc42 Rosales-Nieves et al.90 N/A Experimental models: Organisms/strains sGMCA (GFP actin reporter) Kiehart et al.50 N/A sStMCA (mScarlet actin reporter) Bloomington Drosophila Stock Center BDSC_90928 UASp-Sep1-GFP Bloomington Drosophila Stock Center BDSC_51346 Sep2-GFP Bloomington Drosophila Stock Center BDSC_26257 UASp-mCh-Pnut Provided by T. Lecuit Guillot and Lecuit91 UASp-Sep4-GFP Bloomington Drosophila Stock Center BDSC_51345 UASp-Sep5-RFP Provided by A. Wilde N/A UASp-GFP-Anillin Bloomington Drosophila Stock Center BDSC_51348 Ubi-AniRBD-GFP Provided by T. Lecuit Munjal et al.71 TRiP.HMC03041 (Vermilion RNAi) Bloomington Drosophila Stock Center BDSC_50641 UASz-sep1-shRNA This study N/A Sep2[2] Provided by D Clark O’Neill and Clark54 TRiP.HMC05924 (Pnut RNAi) Bloomington Drosophila Stock Center BDSC_65157 TRiP.GL01287 (Sep4 RNAi) Bloomington Drosophila Stock Center BDSC_41859 Sep5[2] Provided by D Clark O’Neill and Clark54 TRiP.GL01269 (Ani RNAi) Bloomington Drosophila Stock Center BDSC_41841 matalpha4-GAL-VP16 Bloomington Drosophila Stock Center BDSC_7063 Oligonucleotides (5’ -> 30) qPCR-Sep1-F: CCAACCAGGTGCATCGAAAGT This study N/A qPCR-Sep1-R: CAGCTTTACGGTTTGCTTTTGTT This study N/A qPCR-Sep4-F: AGCGCATCGAGAAGACGAC This study N/A qPCR-Sep4-R: CTGTCCTCACAGTTGATGGCA This study N/A qPCR-Pnut-F: CATCTACAACGCGGAACAGTAT This study N/A qPCR-Pnut-R: ACCGTGAGTGTCAGATTGACG This study N/A qPCR-Ani-F: CTTTCCCAACGTAACGACCTT This study N/A qPCR-Ani-R: GAATCTCAACTTGCACCCCAA This study N/A qPCR-RpL32-F: ATGCTAAGCTGTCGCACAAATG Nakamura et al.92 N/A qPCR-RpL32-R: GTTCGATCCGTAACCGATGT Nakamura et al.92 N/A (Continued on next page) Cell Reports 43, 114215, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sep1-shRNA-top: ctagcagtGCATTATTCCGGA CGCCATAGtagttatattcaagcataCTATGGCGT CCGGAATAATGCgcg This study N/A Sep1-shRNA-bot: aattcgcGCATTATTCCGGAC GCCATAGtagttatattcaagcataCTATGGCGTCC GGAATAATGCactg This study N/A Recombinant DNA pCite4-Ani-RBD This study N/A pETDuet-Sep1-Sep2 This study N/A pETDuet-Sep4-Sep5 This study N/A pET28-dt-Pnut This study N/A pGEX-dt-Sep1 This study N/A pGEX-dt-Sep2 This study N/A pGEX-dt-Pnut This study N/A pGEX-dt-Sep4 This study N/A pGEX-dt-Sep5 This study N/A Software and algorithms Fiji Schindelin et al.93 http://fiji.sc/ R StatSoft https://www.r-project.org/ MATLAB Mathworks http://mathworks.com/ GraphPad Prism GraphPad https://www.graphpad.com/ Other Revolution WD spinning disk confocal microscope Andor N/A CSU-X1 spinning disk confocal microscope Yokogawa N/A LSM 780 Carl Zeiss N/A Micropoint Andor N/A CFX96TM Real-Time PCR Detection System Bio-Rad N/A Fred Hutchinson Cancer Center – Leica Center of Excellence Fred Hutchinson Cancer Center RRID:SCR_022720 Fred Hutchinson Cancer Center Cellular Imaging Core Facility Fred Hutchinson Cancer Center RRID:SCR_022609
Real-time Polymerase Chain Reaction:Article Title: Two Septin complexes mediate actin dynamics during cell wound repair.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins iTaq Universal SYBR Green Supermix Bio-Rad Cat# 1725120 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-Rad Cat# 1725034 Na2ATP Sigma-Aldrich Cat# A2383 Methyl Cellulose Sigma-Aldrich Cat# M0512 Protocatechuate Acid (PCA) Sigma-Aldrich Cat# 03930590 Protocatechuate 3,4-dioxygenase (PCD) Sigma-Aldrich Cat# P8279 Trolox Sigma-Aldrich Cat# 238813 Amyl Acetate Electron Microscopy Sciences Cat# 10815 Sterile Collodion (Parlodion) in 2% Amyl Acetate Electron Microscopy Sciences Cat# 12620-10 Rhodamine Muscle Actin Cytoskeleton, Inc. Cat# AR05 GDP Sigma-Aldrich Cat# G7252 GMP-PNP Sigma-Aldrich Cat# G0635 GST-Rho1 Rosales-Nieves et al.90 N/A GST-Rac1 Rosales-Nieves et al.90 N/A GST-Cdc42 Rosales-Nieves et al.90 N/A Experimental models: Organisms/strains sGMCA (GFP actin reporter) Kiehart et al.50 N/A sStMCA (mScarlet actin reporter) Bloomington Drosophila Stock Center BDSC_90928 UASp-Sep1-GFP Bloomington Drosophila Stock Center BDSC_51346 Sep2-GFP Bloomington Drosophila Stock Center BDSC_26257 UASp-mCh-Pnut Provided by T. Lecuit Guillot and Lecuit91 UASp-Sep4-GFP Bloomington Drosophila Stock Center BDSC_51345 UASp-Sep5-RFP Provided by A. Wilde N/A UASp-GFP-Anillin Bloomington Drosophila Stock Center BDSC_51348 Ubi-AniRBD-GFP Provided by T. Lecuit Munjal et al.71 TRiP.HMC03041 (Vermilion RNAi) Bloomington Drosophila Stock Center BDSC_50641 UASz-sep1-shRNA This study N/A Sep2[2] Provided by D Clark O’Neill and Clark54 TRiP.HMC05924 (Pnut RNAi) Bloomington Drosophila Stock Center BDSC_65157 TRiP.GL01287 (Sep4 RNAi) Bloomington Drosophila Stock Center BDSC_41859 Sep5[2] Provided by D Clark O’Neill and Clark54 TRiP.GL01269 (Ani RNAi) Bloomington Drosophila Stock Center BDSC_41841 matalpha4-GAL-VP16 Bloomington Drosophila Stock Center BDSC_7063 Oligonucleotides (5’ -> 30) qPCR-Sep1-F: CCAACCAGGTGCATCGAAAGT This study N/A qPCR-Sep1-R: CAGCTTTACGGTTTGCTTTTGTT This study N/A qPCR-Sep4-F: AGCGCATCGAGAAGACGAC This study N/A qPCR-Sep4-R: CTGTCCTCACAGTTGATGGCA This study N/A qPCR-Pnut-F: CATCTACAACGCGGAACAGTAT This study N/A qPCR-Pnut-R: ACCGTGAGTGTCAGATTGACG This study N/A qPCR-Ani-F: CTTTCCCAACGTAACGACCTT This study N/A qPCR-Ani-R: GAATCTCAACTTGCACCCCAA This study N/A qPCR-RpL32-F: ATGCTAAGCTGTCGCACAAATG Nakamura et al.92 N/A qPCR-RpL32-R: GTTCGATCCGTAACCGATGT Nakamura et al.92 N/A (Continued on next page) Cell Reports 43, 114215, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sep1-shRNA-top: ctagcagtGCATTATTCCGGA CGCCATAGtagttatattcaagcataCTATGGCGT CCGGAATAATGCgcg This study N/A Sep1-shRNA-bot: aattcgcGCATTATTCCGGAC GCCATAGtagttatattcaagcataCTATGGCGTCC GGAATAATGCactg This study N/A Recombinant DNA pCite4-Ani-RBD This study N/A pETDuet-Sep1-Sep2 This study N/A pETDuet-Sep4-Sep5 This study N/A pET28-dt-Pnut This study N/A pGEX-dt-Sep1 This study N/A pGEX-dt-Sep2 This study N/A pGEX-dt-Pnut This study N/A pGEX-dt-Sep4 This study N/A pGEX-dt-Sep5 This study N/A Software and algorithms Fiji Schindelin et al.93 http://fiji.sc/ R StatSoft https://www.r-project.org/ MATLAB Mathworks http://mathworks.com/ GraphPad Prism GraphPad https://www.graphpad.com/ Other Revolution WD spinning disk confocal microscope Andor N/A CSU-X1 spinning disk confocal microscope Yokogawa N/A LSM 780 Carl Zeiss N/A Micropoint Andor N/A CFX96TM Real-Time PCR Detection System Bio-Rad N/A Fred Hutchinson Cancer Center – Leica Center of Excellence Fred Hutchinson Cancer Center RRID:SCR_022720 Fred Hutchinson Cancer Center Cellular Imaging Core Facility Fred Hutchinson Cancer Center RRID:SCR_022609
cDNA synthesis:Article Title: Differentiation of stem cell-derived pancreatic progenitors into insulin-secreting islet clusters in a multiwell-based static 3D culture system
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Alexa Fluor 647 mouse IgG1k, isotype control BD Biosciences Cat# 557714; RRID: AB_396823 Biological samples Human islets ADI Islet Core https://www.epicore.ualberta.ca/IsletCore/ Chemicals, peptides, and recombinant proteins Matrigel, hESC-qualified Corning Cat# 08-774-552 TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604021 Accutase STEMCELL Technologies Cat# 07920 Gentle Cell Dissociation Reagent STEMCELL Technologies Cat# 07174 Y-27632 STEMCELL Technologies Cat# 72304 STEMdiffTM Pancreatic Progenitor Kit STEMCELL Technologies Cat# 05120 mTeSR1 Complete Kit STEMCELL Technologies Cat# 85850 DPBS, without Ca2+ and Mg2+ Sigma-Aldrich Cat# D8537 DMEM/F-12, HEPES Thermo Fisher Scientific Cat# 11330-032 MCDB131 medium Life technologies Cat# 10372019 CMRL 1066, Supplemented, CIT modification Corning Cat# 98-304-CV Glutamax Thermo Fisher Scientific Cat# 35050061 ITS-X Thermo Fisher Scientific Cat# 51500056 NaHCO3 Sigma-Aldrich Cat# S6297 D-glucose Sigma-Aldrich Cat# G8769 Fatty acid-free BSA Proliant Cat# 68700 GDF-8 PeproTech Cat# 120-00 MCX-928 Janssen Internal compound N/A CHIR99021 Sigma-Aldrich Cat# SML1046 L-ascorbic acid Sigma-Aldrich Cat# A4544 FGF-7 R&D Systems Cat# 251-KG SANT-1 Sigma-Aldrich Cat# S4572 Retinoid acid, all-trans Sigma-Aldrich Cat# R2625 LDN193189 STEMCELL Technologies Cat# 72147 TPPB Tocris Cat# 5343/1 Triiodothyronine (T3) Sigma-Aldrich Cat# T6397 ALK5 inhibitor II Cayman Chemicals Cat# 14794 Zinc sulfate Sigma-Aldrich Cat# Z0251 Heparin Sigma-Aldrich Cat# H3149 Gamma secretase inhibitor XX (GSi XX) Sigma-Aldrich Cat# 565789 N-acetyl cysteine (NAC) Sigma-Aldrich Cat# A9165 Trolox Sigma-Aldrich Cat# 648471 R428 Cayman Chemicals Cat# 21523 ZM447439 (ZM) SelleckChem Cat# S1103 WNT4 Biorbyt Cat# orb358133 Forskolin (FSK) STEMCELL Technologies Cat# 72114 Critical commercial assays MycoSEQ Mycoplasma Detection Kit Life technologies Cat# 4399363 Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Live/Dead Viability/Cytotoxicity Kit Life technologies Cat# L3224 Human Insulin ELISA Kit ALPCO Cat# 80-INSHU-E01.1 Glucagon ELISA Kit Thermo Fisher Scientific Cat# EHGCG Ultralow Attachment Flat Bottom 96-well plate Corning Costar (VWR) Cat# CLS3474 AggrewellTM 400, 24-well plate STEMCELL Technologies Cat# 34415 (Continued on next page) Cell Reports Methods 3, 100466, May 22, 2023 e2 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER AggrewellTM 800, 24-well plate STEMCELL Technologies Cat# 34815 Anti-Adherence Rinsing Solution STEMCELL Technologies Cat# 07010 QIAzol lysis reagent Qiagen Cat# 79306 RNeasy Mini Kit Qiagen Cat# 74106 iScriptTM gDNA Clear cDNA Synthesis kit Bio-Rad Cat# 1725035 SsoFastTM EvaGreen Supermix Bio-Rad Cat# 1725202 UltraPure DNase/RNase-Free Distilled Water Life technologies Cat# 10977-015 Dithizone Sigma-Aldrich Cat# 43820-50G 4% Paraformaldehyde (PFA) solution in PBS Santa Cruz Biotechnology Cat# sc-281692 100% Triton X-100 Thermo Fisher Scientific Cat# BP151-100 Bovine serum albumin (BSA) Thermo Fisher Scientific Cat# BP1600-100 DAPI Sigma-Aldrich Cat# D9542 RIPA Lysis Buffer, 10X Sigma-Aldrich Cat# 20-188 Cell-Tak Cell and Tissue Adhesive Corning Cat# 354240 Experimental models: Cell lines Human: H1 hESC line WiCell Research Institute James A. Thomson et al., 1998 Human:Mel1 INSGFP/W hESC line Kindly provided by Dr. Edouard G. Stanley Suzanne J Micallef et al., 2011 Human:HUES4 PDXeG hESC line Kindly provided by Dr. Henrik Semb Jacqueline Ameri et al., 2017 Human: GCaMP_CRISPRi hiPSC line Kindly provided by Dr. Bruce Conklin and Dr. Knut Woltjen Mohammad A. Mandegar et al., 2016 Oligonucleotides See Table S2 Integrated DNA Technologies https://www.idtdna.com/pages/ Software and algorithms GraphPad Prism 9.0 GraphPad https://www.graphpad.com/ Fiji/ImageJ Schneider et al.47 https://imagej.nih.gov/ij/ Zen Microscopy Software Zeiss https://www.zeiss.com/microscopy/int/ products/microscope-software/zen.html/ FlowJo v10 FlowJo, LLC http://www.flowjo.com/ BioRender BioRender https://app.biorender.com VisualParadigm Online VisualParadigm https://online.visual-paradigm.com Report ll OPEN ACCESS ..
Lysis:Article Title: Differentiation of stem cell-derived pancreatic progenitors into insulin-secreting islet clusters in a multiwell-based static 3D culture system.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Alexa Fluor 647 mouse IgG1k, isotype control BD Biosciences Cat# 557714; RRID: AB_396823 Biological samples Human islets ADI Islet Core https://www.epicore.ualberta.ca/IsletCore/ Chemicals, peptides, and recombinant proteins Matrigel, hESC-qualified Corning Cat# 08-774-552 TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604021 Accutase STEMCELL Technologies Cat# 07920 Gentle Cell Dissociation Reagent STEMCELL Technologies Cat# 07174 Y-27632 STEMCELL Technologies Cat# 72304 STEMdiffTM Pancreatic Progenitor Kit STEMCELL Technologies Cat# 05120 mTeSR1 Complete Kit STEMCELL Technologies Cat# 85850 DPBS, without Ca2+ and Mg2+ Sigma-Aldrich Cat# D8537 DMEM/F-12, HEPES Thermo Fisher Scientific Cat# 11330-032 MCDB131 medium Life technologies Cat# 10372019 CMRL 1066, Supplemented, CIT modification Corning Cat# 98-304-CV Glutamax Thermo Fisher Scientific Cat# 35050061 ITS-X Thermo Fisher Scientific Cat# 51500056 NaHCO3 Sigma-Aldrich Cat# S6297 D-glucose Sigma-Aldrich Cat# G8769 Fatty acid-free BSA Proliant Cat# 68700 GDF-8 PeproTech Cat# 120-00 MCX-928 Janssen Internal compound N/A CHIR99021 Sigma-Aldrich Cat# SML1046 L-ascorbic acid Sigma-Aldrich Cat# A4544 FGF-7 R&D Systems Cat# 251-KG SANT-1 Sigma-Aldrich Cat# S4572 Retinoid acid, all-trans Sigma-Aldrich Cat# R2625 LDN193189 STEMCELL Technologies Cat# 72147 TPPB Tocris Cat# 5343/1 Triiodothyronine (T3) Sigma-Aldrich Cat# T6397 ALK5 inhibitor II Cayman Chemicals Cat# 14794 Zinc sulfate Sigma-Aldrich Cat# Z0251 Heparin Sigma-Aldrich Cat# H3149 Gamma secretase inhibitor XX (GSi XX) Sigma-Aldrich Cat# 565789 N-acetyl cysteine (NAC) Sigma-Aldrich Cat# A9165 Trolox Sigma-Aldrich Cat# 648471 R428 Cayman Chemicals Cat# 21523 ZM447439 (ZM) SelleckChem Cat# S1103 WNT4 Biorbyt Cat# orb358133 Forskolin (FSK) STEMCELL Technologies Cat# 72114 Critical commercial assays MycoSEQ Mycoplasma Detection Kit Life technologies Cat# 4399363 Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Live/Dead Viability/Cytotoxicity Kit Life technologies Cat# L3224 Human Insulin ELISA Kit ALPCO Cat# 80-INSHU-E01.1 Glucagon ELISA Kit Thermo Fisher Scientific Cat# EHGCG Ultralow Attachment Flat Bottom 96-well plate Corning Costar (VWR) Cat# CLS3474 AggrewellTM 400, 24-well plate STEMCELL Technologies Cat# 34415 (Continued on next page) Cell Reports Methods 3, 100466, May 22, 2023 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER AggrewellTM 800, 24-well plate STEMCELL Technologies Cat# 34815 Anti-Adherence Rinsing Solution STEMCELL Technologies Cat# 07010 QIAzol lysis reagent Qiagen Cat# 79306 RNeasy Mini Kit Qiagen Cat# 74106 iScriptTM gDNA Clear cDNA Synthesis kit Bio-Rad Cat# 1725035 SsoFastTM EvaGreen Supermix Bio-Rad Cat# 1725202 UltraPure DNase/RNase-Free Distilled Water Life technologies Cat# 10977-015 Dithizone Sigma-Aldrich Cat# 43820-50G 4% Paraformaldehyde (PFA) solution in PBS Santa Cruz Biotechnology Cat# sc-281692 100% Triton X-100 Thermo Fisher Scientific Cat# BP151-100 Bovine serum albumin (BSA) Thermo Fisher Scientific Cat# BP1600-100 DAPI Sigma-Aldrich Cat# D9542 RIPA Lysis Buffer, 10X Sigma-Aldrich Cat# 20-188 Cell-Tak Cell and Tissue Adhesive Corning Cat# 354240 Experimental models: Cell lines Human: H1 hESC line WiCell Research Institute James A. Thomson et al., 1998 Human:Mel1 INSGFP/W hESC line Kindly provided by Dr. Edouard G. Stanley Suzanne J Micallef et al., 2011 Human:HUES4 PDXeG hESC line Kindly provided by Dr. Henrik Semb Jacqueline Ameri et al., 2017 Human: GCaMP_CRISPRi hiPSC line Kindly provided by Dr. Bruce Conklin and Dr. Knut Woltjen Mohammad A. Mandegar et al., 2016 Oligonucleotides See Table S2 Integrated DNA Technologies https://www.idtdna.com/pages/ Software and algorithms GraphPad Prism 9.0 GraphPad https://www.graphpad.com/ Fiji/ImageJ Schneider et al.47 https://imagej.nih.gov/ij/ Zen Microscopy Software Zeiss https://www.zeiss.com/microscopy/int/ products/microscope-software/zen.html/ FlowJo v10 FlowJo, LLC http://www.flowjo.com/ BioRender BioRender https://app.biorender.com VisualParadigm Online VisualParadigm https://online.visual-paradigm.com ..
Adhesive:Article Title: Differentiation of stem cell-derived pancreatic progenitors into insulin-secreting islet clusters in a multiwell-based static 3D culture system.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Alexa Fluor 647 mouse IgG1k, isotype control BD Biosciences Cat# 557714; RRID: AB_396823 Biological samples Human islets ADI Islet Core https://www.epicore.ualberta.ca/IsletCore/ Chemicals, peptides, and recombinant proteins Matrigel, hESC-qualified Corning Cat# 08-774-552 TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604021 Accutase STEMCELL Technologies Cat# 07920 Gentle Cell Dissociation Reagent STEMCELL Technologies Cat# 07174 Y-27632 STEMCELL Technologies Cat# 72304 STEMdiffTM Pancreatic Progenitor Kit STEMCELL Technologies Cat# 05120 mTeSR1 Complete Kit STEMCELL Technologies Cat# 85850 DPBS, without Ca2+ and Mg2+ Sigma-Aldrich Cat# D8537 DMEM/F-12, HEPES Thermo Fisher Scientific Cat# 11330-032 MCDB131 medium Life technologies Cat# 10372019 CMRL 1066, Supplemented, CIT modification Corning Cat# 98-304-CV Glutamax Thermo Fisher Scientific Cat# 35050061 ITS-X Thermo Fisher Scientific Cat# 51500056 NaHCO3 Sigma-Aldrich Cat# S6297 D-glucose Sigma-Aldrich Cat# G8769 Fatty acid-free BSA Proliant Cat# 68700 GDF-8 PeproTech Cat# 120-00 MCX-928 Janssen Internal compound N/A CHIR99021 Sigma-Aldrich Cat# SML1046 L-ascorbic acid Sigma-Aldrich Cat# A4544 FGF-7 R&D Systems Cat# 251-KG SANT-1 Sigma-Aldrich Cat# S4572 Retinoid acid, all-trans Sigma-Aldrich Cat# R2625 LDN193189 STEMCELL Technologies Cat# 72147 TPPB Tocris Cat# 5343/1 Triiodothyronine (T3) Sigma-Aldrich Cat# T6397 ALK5 inhibitor II Cayman Chemicals Cat# 14794 Zinc sulfate Sigma-Aldrich Cat# Z0251 Heparin Sigma-Aldrich Cat# H3149 Gamma secretase inhibitor XX (GSi XX) Sigma-Aldrich Cat# 565789 N-acetyl cysteine (NAC) Sigma-Aldrich Cat# A9165 Trolox Sigma-Aldrich Cat# 648471 R428 Cayman Chemicals Cat# 21523 ZM447439 (ZM) SelleckChem Cat# S1103 WNT4 Biorbyt Cat# orb358133 Forskolin (FSK) STEMCELL Technologies Cat# 72114 Critical commercial assays MycoSEQ Mycoplasma Detection Kit Life technologies Cat# 4399363 Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Live/Dead Viability/Cytotoxicity Kit Life technologies Cat# L3224 Human Insulin ELISA Kit ALPCO Cat# 80-INSHU-E01.1 Glucagon ELISA Kit Thermo Fisher Scientific Cat# EHGCG Ultralow Attachment Flat Bottom 96-well plate Corning Costar (VWR) Cat# CLS3474 AggrewellTM 400, 24-well plate STEMCELL Technologies Cat# 34415 (Continued on next page) Cell Reports Methods 3, 100466, May 22, 2023 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER AggrewellTM 800, 24-well plate STEMCELL Technologies Cat# 34815 Anti-Adherence Rinsing Solution STEMCELL Technologies Cat# 07010 QIAzol lysis reagent Qiagen Cat# 79306 RNeasy Mini Kit Qiagen Cat# 74106 iScriptTM gDNA Clear cDNA Synthesis kit Bio-Rad Cat# 1725035 SsoFastTM EvaGreen Supermix Bio-Rad Cat# 1725202 UltraPure DNase/RNase-Free Distilled Water Life technologies Cat# 10977-015 Dithizone Sigma-Aldrich Cat# 43820-50G 4% Paraformaldehyde (PFA) solution in PBS Santa Cruz Biotechnology Cat# sc-281692 100% Triton X-100 Thermo Fisher Scientific Cat# BP151-100 Bovine serum albumin (BSA) Thermo Fisher Scientific Cat# BP1600-100 DAPI Sigma-Aldrich Cat# D9542 RIPA Lysis Buffer, 10X Sigma-Aldrich Cat# 20-188 Cell-Tak Cell and Tissue Adhesive Corning Cat# 354240 Experimental models: Cell lines Human: H1 hESC line WiCell Research Institute James A. Thomson et al., 1998 Human:Mel1 INSGFP/W hESC line Kindly provided by Dr. Edouard G. Stanley Suzanne J Micallef et al., 2011 Human:HUES4 PDXeG hESC line Kindly provided by Dr. Henrik Semb Jacqueline Ameri et al., 2017 Human: GCaMP_CRISPRi hiPSC line Kindly provided by Dr. Bruce Conklin and Dr. Knut Woltjen Mohammad A. Mandegar et al., 2016 Oligonucleotides See Table S2 Integrated DNA Technologies https://www.idtdna.com/pages/ Software and algorithms GraphPad Prism 9.0 GraphPad https://www.graphpad.com/ Fiji/ImageJ Schneider et al.47 https://imagej.nih.gov/ij/ Zen Microscopy Software Zeiss https://www.zeiss.com/microscopy/int/ products/microscope-software/zen.html/ FlowJo v10 FlowJo, LLC http://www.flowjo.com/ BioRender BioRender https://app.biorender.com VisualParadigm Online VisualParadigm https://online.visual-paradigm.com ..
Microscopy:Article Title: Differentiation of stem cell-derived pancreatic progenitors into insulin-secreting islet clusters in a multiwell-based static 3D culture system.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Alexa Fluor 647 mouse IgG1k, isotype control BD Biosciences Cat# 557714; RRID: AB_396823 Biological samples Human islets ADI Islet Core https://www.epicore.ualberta.ca/IsletCore/ Chemicals, peptides, and recombinant proteins Matrigel, hESC-qualified Corning Cat# 08-774-552 TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604021 Accutase STEMCELL Technologies Cat# 07920 Gentle Cell Dissociation Reagent STEMCELL Technologies Cat# 07174 Y-27632 STEMCELL Technologies Cat# 72304 STEMdiffTM Pancreatic Progenitor Kit STEMCELL Technologies Cat# 05120 mTeSR1 Complete Kit STEMCELL Technologies Cat# 85850 DPBS, without Ca2+ and Mg2+ Sigma-Aldrich Cat# D8537 DMEM/F-12, HEPES Thermo Fisher Scientific Cat# 11330-032 MCDB131 medium Life technologies Cat# 10372019 CMRL 1066, Supplemented, CIT modification Corning Cat# 98-304-CV Glutamax Thermo Fisher Scientific Cat# 35050061 ITS-X Thermo Fisher Scientific Cat# 51500056 NaHCO3 Sigma-Aldrich Cat# S6297 D-glucose Sigma-Aldrich Cat# G8769 Fatty acid-free BSA Proliant Cat# 68700 GDF-8 PeproTech Cat# 120-00 MCX-928 Janssen Internal compound N/A CHIR99021 Sigma-Aldrich Cat# SML1046 L-ascorbic acid Sigma-Aldrich Cat# A4544 FGF-7 R&D Systems Cat# 251-KG SANT-1 Sigma-Aldrich Cat# S4572 Retinoid acid, all-trans Sigma-Aldrich Cat# R2625 LDN193189 STEMCELL Technologies Cat# 72147 TPPB Tocris Cat# 5343/1 Triiodothyronine (T3) Sigma-Aldrich Cat# T6397 ALK5 inhibitor II Cayman Chemicals Cat# 14794 Zinc sulfate Sigma-Aldrich Cat# Z0251 Heparin Sigma-Aldrich Cat# H3149 Gamma secretase inhibitor XX (GSi XX) Sigma-Aldrich Cat# 565789 N-acetyl cysteine (NAC) Sigma-Aldrich Cat# A9165 Trolox Sigma-Aldrich Cat# 648471 R428 Cayman Chemicals Cat# 21523 ZM447439 (ZM) SelleckChem Cat# S1103 WNT4 Biorbyt Cat# orb358133 Forskolin (FSK) STEMCELL Technologies Cat# 72114 Critical commercial assays MycoSEQ Mycoplasma Detection Kit Life technologies Cat# 4399363 Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Live/Dead Viability/Cytotoxicity Kit Life technologies Cat# L3224 Human Insulin ELISA Kit ALPCO Cat# 80-INSHU-E01.1 Glucagon ELISA Kit Thermo Fisher Scientific Cat# EHGCG Ultralow Attachment Flat Bottom 96-well plate Corning Costar (VWR) Cat# CLS3474 AggrewellTM 400, 24-well plate STEMCELL Technologies Cat# 34415 (Continued on next page) Cell Reports Methods 3, 100466, May 22, 2023 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER AggrewellTM 800, 24-well plate STEMCELL Technologies Cat# 34815 Anti-Adherence Rinsing Solution STEMCELL Technologies Cat# 07010 QIAzol lysis reagent Qiagen Cat# 79306 RNeasy Mini Kit Qiagen Cat# 74106 iScriptTM gDNA Clear cDNA Synthesis kit Bio-Rad Cat# 1725035 SsoFastTM EvaGreen Supermix Bio-Rad Cat# 1725202 UltraPure DNase/RNase-Free Distilled Water Life technologies Cat# 10977-015 Dithizone Sigma-Aldrich Cat# 43820-50G 4% Paraformaldehyde (PFA) solution in PBS Santa Cruz Biotechnology Cat# sc-281692 100% Triton X-100 Thermo Fisher Scientific Cat# BP151-100 Bovine serum albumin (BSA) Thermo Fisher Scientific Cat# BP1600-100 DAPI Sigma-Aldrich Cat# D9542 RIPA Lysis Buffer, 10X Sigma-Aldrich Cat# 20-188 Cell-Tak Cell and Tissue Adhesive Corning Cat# 354240 Experimental models: Cell lines Human: H1 hESC line WiCell Research Institute James A. Thomson et al., 1998 Human:Mel1 INSGFP/W hESC line Kindly provided by Dr. Edouard G. Stanley Suzanne J Micallef et al., 2011 Human:HUES4 PDXeG hESC line Kindly provided by Dr. Henrik Semb Jacqueline Ameri et al., 2017 Human: GCaMP_CRISPRi hiPSC line Kindly provided by Dr. Bruce Conklin and Dr. Knut Woltjen Mohammad A. Mandegar et al., 2016 Oligonucleotides See Table S2 Integrated DNA Technologies https://www.idtdna.com/pages/ Software and algorithms GraphPad Prism 9.0 GraphPad https://www.graphpad.com/ Fiji/ImageJ Schneider et al.47 https://imagej.nih.gov/ij/ Zen Microscopy Software Zeiss https://www.zeiss.com/microscopy/int/ products/microscope-software/zen.html/ FlowJo v10 FlowJo, LLC http://www.flowjo.com/ BioRender BioRender https://app.biorender.com VisualParadigm Online VisualParadigm https://online.visual-paradigm.com ..
Software:Article Title: Differentiation of stem cell-derived pancreatic progenitors into insulin-secreting islet clusters in a multiwell-based static 3D culture system.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Alexa Fluor 647 mouse IgG1k, isotype control BD Biosciences Cat# 557714; RRID: AB_396823 Biological samples Human islets ADI Islet Core https://www.epicore.ualberta.ca/IsletCore/ Chemicals, peptides, and recombinant proteins Matrigel, hESC-qualified Corning Cat# 08-774-552 TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604021 Accutase STEMCELL Technologies Cat# 07920 Gentle Cell Dissociation Reagent STEMCELL Technologies Cat# 07174 Y-27632 STEMCELL Technologies Cat# 72304 STEMdiffTM Pancreatic Progenitor Kit STEMCELL Technologies Cat# 05120 mTeSR1 Complete Kit STEMCELL Technologies Cat# 85850 DPBS, without Ca2+ and Mg2+ Sigma-Aldrich Cat# D8537 DMEM/F-12, HEPES Thermo Fisher Scientific Cat# 11330-032 MCDB131 medium Life technologies Cat# 10372019 CMRL 1066, Supplemented, CIT modification Corning Cat# 98-304-CV Glutamax Thermo Fisher Scientific Cat# 35050061 ITS-X Thermo Fisher Scientific Cat# 51500056 NaHCO3 Sigma-Aldrich Cat# S6297 D-glucose Sigma-Aldrich Cat# G8769 Fatty acid-free BSA Proliant Cat# 68700 GDF-8 PeproTech Cat# 120-00 MCX-928 Janssen Internal compound N/A CHIR99021 Sigma-Aldrich Cat# SML1046 L-ascorbic acid Sigma-Aldrich Cat# A4544 FGF-7 R&D Systems Cat# 251-KG SANT-1 Sigma-Aldrich Cat# S4572 Retinoid acid, all-trans Sigma-Aldrich Cat# R2625 LDN193189 STEMCELL Technologies Cat# 72147 TPPB Tocris Cat# 5343/1 Triiodothyronine (T3) Sigma-Aldrich Cat# T6397 ALK5 inhibitor II Cayman Chemicals Cat# 14794 Zinc sulfate Sigma-Aldrich Cat# Z0251 Heparin Sigma-Aldrich Cat# H3149 Gamma secretase inhibitor XX (GSi XX) Sigma-Aldrich Cat# 565789 N-acetyl cysteine (NAC) Sigma-Aldrich Cat# A9165 Trolox Sigma-Aldrich Cat# 648471 R428 Cayman Chemicals Cat# 21523 ZM447439 (ZM) SelleckChem Cat# S1103 WNT4 Biorbyt Cat# orb358133 Forskolin (FSK) STEMCELL Technologies Cat# 72114 Critical commercial assays MycoSEQ Mycoplasma Detection Kit Life technologies Cat# 4399363 Fixation/Permeabilization Solution Kit BD Biosciences Cat# 554714 Live/Dead Viability/Cytotoxicity Kit Life technologies Cat# L3224 Human Insulin ELISA Kit ALPCO Cat# 80-INSHU-E01.1 Glucagon ELISA Kit Thermo Fisher Scientific Cat# EHGCG Ultralow Attachment Flat Bottom 96-well plate Corning Costar (VWR) Cat# CLS3474 AggrewellTM 400, 24-well plate STEMCELL Technologies Cat# 34415 (Continued on next page) Cell Reports Methods 3, 100466, May 22, 2023 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER AggrewellTM 800, 24-well plate STEMCELL Technologies Cat# 34815 Anti-Adherence Rinsing Solution STEMCELL Technologies Cat# 07010 QIAzol lysis reagent Qiagen Cat# 79306 RNeasy Mini Kit Qiagen Cat# 74106 iScriptTM gDNA Clear cDNA Synthesis kit Bio-Rad Cat# 1725035 SsoFastTM EvaGreen Supermix Bio-Rad Cat# 1725202 UltraPure DNase/RNase-Free Distilled Water Life technologies Cat# 10977-015 Dithizone Sigma-Aldrich Cat# 43820-50G 4% Paraformaldehyde (PFA) solution in PBS Santa Cruz Biotechnology Cat# sc-281692 100% Triton X-100 Thermo Fisher Scientific Cat# BP151-100 Bovine serum albumin (BSA) Thermo Fisher Scientific Cat# BP1600-100 DAPI Sigma-Aldrich Cat# D9542 RIPA Lysis Buffer, 10X Sigma-Aldrich Cat# 20-188 Cell-Tak Cell and Tissue Adhesive Corning Cat# 354240 Experimental models: Cell lines Human: H1 hESC line WiCell Research Institute James A. Thomson et al., 1998 Human:Mel1 INSGFP/W hESC line Kindly provided by Dr. Edouard G. Stanley Suzanne J Micallef et al., 2011 Human:HUES4 PDXeG hESC line Kindly provided by Dr. Henrik Semb Jacqueline Ameri et al., 2017 Human: GCaMP_CRISPRi hiPSC line Kindly provided by Dr. Bruce Conklin and Dr. Knut Woltjen Mohammad A. Mandegar et al., 2016 Oligonucleotides See Table S2 Integrated DNA Technologies https://www.idtdna.com/pages/ Software and algorithms GraphPad Prism 9.0 GraphPad https://www.graphpad.com/ Fiji/ImageJ Schneider et al.47 https://imagej.nih.gov/ij/ Zen Microscopy Software Zeiss https://www.zeiss.com/microscopy/int/ products/microscope-software/zen.html/ FlowJo v10 FlowJo, LLC http://www.flowjo.com/ BioRender BioRender https://app.biorender.com VisualParadigm Online VisualParadigm https://online.visual-paradigm.com ..
Staining:Article Title: Endometrial Axin2 + Cells Drive Epithelial Homeostasis, Regeneration, and Cancer following Oncogenic Transformation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Pronase Sigma-Aldrich Cat#10165921001 DNase I Sigma-Aldrich Cat#10104159001 Fetal Bovine Serum Bovogen Cat#SFBS-F L-glutamine HyClone Cat#SH30034.01 Penicillin-streptomycin Thermo Fisher Scientific Cat#15070-063 Matrigel Trevigen Cat#3433-010-01 GlutaMAX (100X) Thermo Fisher Scientific (GIBCO) Cat#35050-061 B27 supplement Thermo Fisher Scientific (GIBCO) Cat#12587-010 N-2 supplement Thermo Fisher Scientific (GIBCO) Cat#17502-048 ITS liquid media supplement Sigma-Aldrich Cat#I3146 Nicotinamide Sigma-Aldrich Cat#N0636 Mouse EGF recombinant Sigma-Aldrich Cat#SRP3196 Human FGF-10 Peprotech Cat#100-26 A83-01 Tocris Cat#2939 TrypLE express Thermo Fisher Scientific (GIBCO) Cat#12604-021 Protein Block Serum Free (Lot#10096977) DAKO Cat#X0909 Ab Diluent with Background Reducing Compoents (Lot#10090973) DAKO Cat#S3022 Doxycycline hyclate (lot#086M4035V) Sigma-Aldrich Cat#D9891 Neutral Red Sigma-Aldrich N3020 Y-27632 dihydrochloride Tocris Cat#1254 DMEM/F12 HAM Sigma-Aldrich Cat#D8437 HBSS/Modified HyClone Cat#SH30031.02 Tamoxifen (Lot#SLBF8049V) Sigma-Aldrich Cat#T5648; CAS#10540-29-1 b-Estradiol (Lot#SLBH0091V) Sigma-Aldrich Cat#E8875; CAS#50-28-2 Progesterone (Lot#SLBG1644V) Sigma-Aldrich Cat#P 0130; CAS#57-83-0 DAPI dilactate Sigma-Aldrich Cat#D9564 Paraformaldehyde 16% solution EM Grade Electron Microscopy Sciences Cat#15710 Xgal (Lot#ES531-B061890) Bioline Cat#BIO-37035 5-Chloro-2‘-Deoxyuridine (Lot#QR10915) MP Biochemicals LLC. .. Cat#105478; CAS#50-90-8 5-Iodo-2‘-Deoxyuridine (Lot#BCBP3111V) Sigma-Aldrich Cat#17152 Diphtheria Toxin (Lot#MKCH2452) Sigma-Aldrich Cat#D0564 Recombinant Murine Wnt-3a Peprotech Cat#315-20 Recombinant Human R-Spondin 1 R&D Systems Cat#4645-RS Noggin Peprotech Cat#120-10C-100 IWR1 Sigma-Aldrich Cat#10161 N,N,N0,N0-Tetrakis(2-Hydroxypropyl) ethylenediamine Sigma-Aldrich Cat #122262 Critical Commercial Assays EnVisionTM+ Dual Link System-HRP (DAB+) (Lot#10095442) DAKO Cat#K4065 Trichrome Stain (Masson) Kit Sigma-Aldrich Cat#HT15 RNeasy Micro Kit QIAGEN Cat#74004 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-rad Cat#172-5034 iTaq Universal SYBR Green Supermix Bio-rad Cat#172-5121 RNAscope 2.5 HD Assay-RED kit Advanced cell Diagnostics Cat# 322350 RNAscope 2.5 HD Detection Reagents-RED Advanced cell Diagnostics Cat# 322360 (Continued on next page) Cell Stem Cell 26, 1–17.e1–e13, February 6, 2020 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER RNAscope H202 & Protease Plus Reagents Advanced cell Diagnostics Cat# 322330 TruSeq PE Cluster Kit v3 Illumina Cat#PE-401-3001 TruSeq SBS Kit v3 Illumina Cat#FC-401-3001 Deposited data RNA-seq data This paper GEO: GSM4156868 RNA-seq data This paper GEO: GSM4156869 RNA-seq data This paper GEO: GSM4156870 RNA-seq data This paper GEO: GSM4156871 RNA-seq data This paper GEO: GSM4156872 RNA-seq data This paper GEO: GSM4156873 Experimental Models: Cell Lines L-WRN cells ATCC Cat#CRL-3276; RRID: CVCL_DA06 Experimental Models: Organisms/Strains Mouse: Pax8rtTA: B6.Cg-Tg(Pax8rtTA2S*M2)1Koes/J The Jackson Laboratory JAX:007176; RRID:IMSR_JAX:007176 Mouse: Axin2rtTA: B6.Cg-Tg(Axin2rtTA2S*M2)7Cos/J The Jackson Laboratory JAX:016997; RRID:IMSR_JAX:016997 Mouse: tetOCre: STOCK Tg(tetO-cre) 1Jaw/J The Jackson Laboratory JAX:006224; RRID:IMSR_JAX:006224 Mouse: tetOH2BJGFP: STOCK Tg(tetOHIST1H2BJ/GFP)47Efu/J The Jackson Laboratory JAX:005104; RRID:IMSR_JAX:005104 Mouse: R26-lacZfl/fl: B6.129S4-Gt(ROSA) 26Sortm1Sor/J The Jackson Laboratory JAX:003474; RRID:IMSR_JAX:003474 Mouse: R26-EYFPfl/fl: B6.129X1-Gt(ROSA) 26Sortm1(EYFP)Cos/J The Jackson Laboratory JAX:006148; RRID:IMSR_JAX:006148 Mouse: Ctnnb1fl/fl: B6.129Ctnnb1tm2Kem/KnwJ The Jackson Laboratory JAX:004152; RRID:IMSR_JAX:004152 Mouse: Ctnnb1fl(ex3)/fl(ex3): C57BL/6NCatnblox(ex3) Harada et al., 1999 Prof Makoto M. Taketo; taketo@mol.f. u-tokyo.ac.jp Mouse: R26Pik3ca,EGFPfl/fl: C57BL/6Gt(ROSA)26Sortm7(Pik3ca*,EGFP)Rsky/J The Jackson Laboratory JAX:012343; RRID:IMSR_JAX:012343 Mouse: R26iDTR: C57BL/6-Gt(ROSA) 26Sortm1(HBEGF)Awai/J The Jackson Laboratory JAX:007900; RRID:IMSR_JAX:007900 Mouse: TCF/Lef:H2B/GFP: STOCK Tg(TCF/Lef1-HIST1H2BB/EGFP)61Hadj/J The Jackson Laboratory JAX:013752; RRID:IMSR_JAX:013752 Oligonucleotides Mouse Axin2 Forward# CGACCCAGTCAATCCTTATCAC (Boretto et al., 2017) N/A Mouse Axin2 Reverse# GGGACTCCATCTACGCTACTG (Boretto et al., 2017) N/A Mouse Gapdh Forward# TGGCAAAGTGGAGATTGTTGCC (Bonnans et al., 2012) N/A Mouse Gapdh Forward# AAGATGGTGATGGGCTTCCCG (Bonnans et al., 2012) N/A RNAscope Negative Control Probe - DapB Advanced cell Diagnostics Cat# 310043 RNAscope Positive Control Probe - Mm-Ppib Advanced cell Diagnostics Cat# 313911 RNAscope Probe-Mm-Axin2 Advanced cell Diagnostics Cat# 400331 RNAscope Probe- Hs-AXIN2 Advanced cell Diagnostics Cat# 400241 (Continued on next page) e3 Cell Stem Cell 26, 1–17.e1–e13, February 6, 2020
RNAscope:Article Title: Endometrial Axin2 + Cells Drive Epithelial Homeostasis, Regeneration, and Cancer following Oncogenic Transformation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Pronase Sigma-Aldrich Cat#10165921001 DNase I Sigma-Aldrich Cat#10104159001 Fetal Bovine Serum Bovogen Cat#SFBS-F L-glutamine HyClone Cat#SH30034.01 Penicillin-streptomycin Thermo Fisher Scientific Cat#15070-063 Matrigel Trevigen Cat#3433-010-01 GlutaMAX (100X) Thermo Fisher Scientific (GIBCO) Cat#35050-061 B27 supplement Thermo Fisher Scientific (GIBCO) Cat#12587-010 N-2 supplement Thermo Fisher Scientific (GIBCO) Cat#17502-048 ITS liquid media supplement Sigma-Aldrich Cat#I3146 Nicotinamide Sigma-Aldrich Cat#N0636 Mouse EGF recombinant Sigma-Aldrich Cat#SRP3196 Human FGF-10 Peprotech Cat#100-26 A83-01 Tocris Cat#2939 TrypLE express Thermo Fisher Scientific (GIBCO) Cat#12604-021 Protein Block Serum Free (Lot#10096977) DAKO Cat#X0909 Ab Diluent with Background Reducing Compoents (Lot#10090973) DAKO Cat#S3022 Doxycycline hyclate (lot#086M4035V) Sigma-Aldrich Cat#D9891 Neutral Red Sigma-Aldrich N3020 Y-27632 dihydrochloride Tocris Cat#1254 DMEM/F12 HAM Sigma-Aldrich Cat#D8437 HBSS/Modified HyClone Cat#SH30031.02 Tamoxifen (Lot#SLBF8049V) Sigma-Aldrich Cat#T5648; CAS#10540-29-1 b-Estradiol (Lot#SLBH0091V) Sigma-Aldrich Cat#E8875; CAS#50-28-2 Progesterone (Lot#SLBG1644V) Sigma-Aldrich Cat#P 0130; CAS#57-83-0 DAPI dilactate Sigma-Aldrich Cat#D9564 Paraformaldehyde 16% solution EM Grade Electron Microscopy Sciences Cat#15710 Xgal (Lot#ES531-B061890) Bioline Cat#BIO-37035 5-Chloro-2‘-Deoxyuridine (Lot#QR10915) MP Biochemicals LLC. .. Cat#105478; CAS#50-90-8 5-Iodo-2‘-Deoxyuridine (Lot#BCBP3111V) Sigma-Aldrich Cat#17152 Diphtheria Toxin (Lot#MKCH2452) Sigma-Aldrich Cat#D0564 Recombinant Murine Wnt-3a Peprotech Cat#315-20 Recombinant Human R-Spondin 1 R&D Systems Cat#4645-RS Noggin Peprotech Cat#120-10C-100 IWR1 Sigma-Aldrich Cat#10161 N,N,N0,N0-Tetrakis(2-Hydroxypropyl) ethylenediamine Sigma-Aldrich Cat #122262 Critical Commercial Assays EnVisionTM+ Dual Link System-HRP (DAB+) (Lot#10095442) DAKO Cat#K4065 Trichrome Stain (Masson) Kit Sigma-Aldrich Cat#HT15 RNeasy Micro Kit QIAGEN Cat#74004 iScriptTM gDNA Clear cDNA Synthesis Kit Bio-rad Cat#172-5034 iTaq Universal SYBR Green Supermix Bio-rad Cat#172-5121 RNAscope 2.5 HD Assay-RED kit Advanced cell Diagnostics Cat# 322350 RNAscope 2.5 HD Detection Reagents-RED Advanced cell Diagnostics Cat# 322360 (Continued on next page) Cell Stem Cell 26, 1–17.e1–e13, February 6, 2020 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER RNAscope H202 & Protease Plus Reagents Advanced cell Diagnostics Cat# 322330 TruSeq PE Cluster Kit v3 Illumina Cat#PE-401-3001 TruSeq SBS Kit v3 Illumina Cat#FC-401-3001 Deposited data RNA-seq data This paper GEO: GSM4156868 RNA-seq data This paper GEO: GSM4156869 RNA-seq data This paper GEO: GSM4156870 RNA-seq data This paper GEO: GSM4156871 RNA-seq data This paper GEO: GSM4156872 RNA-seq data This paper GEO: GSM4156873 Experimental Models: Cell Lines L-WRN cells ATCC Cat#CRL-3276; RRID: CVCL_DA06 Experimental Models: Organisms/Strains Mouse: Pax8rtTA: B6.Cg-Tg(Pax8rtTA2S*M2)1Koes/J The Jackson Laboratory JAX:007176; RRID:IMSR_JAX:007176 Mouse: Axin2rtTA: B6.Cg-Tg(Axin2rtTA2S*M2)7Cos/J The Jackson Laboratory JAX:016997; RRID:IMSR_JAX:016997 Mouse: tetOCre: STOCK Tg(tetO-cre) 1Jaw/J The Jackson Laboratory JAX:006224; RRID:IMSR_JAX:006224 Mouse: tetOH2BJGFP: STOCK Tg(tetOHIST1H2BJ/GFP)47Efu/J The Jackson Laboratory JAX:005104; RRID:IMSR_JAX:005104 Mouse: R26-lacZfl/fl: B6.129S4-Gt(ROSA) 26Sortm1Sor/J The Jackson Laboratory JAX:003474; RRID:IMSR_JAX:003474 Mouse: R26-EYFPfl/fl: B6.129X1-Gt(ROSA) 26Sortm1(EYFP)Cos/J The Jackson Laboratory JAX:006148; RRID:IMSR_JAX:006148 Mouse: Ctnnb1fl/fl: B6.129Ctnnb1tm2Kem/KnwJ The Jackson Laboratory JAX:004152; RRID:IMSR_JAX:004152 Mouse: Ctnnb1fl(ex3)/fl(ex3): C57BL/6NCatnblox(ex3) Harada et al., 1999 Prof Makoto M. Taketo; taketo@mol.f. u-tokyo.ac.jp Mouse: R26Pik3ca,EGFPfl/fl: C57BL/6Gt(ROSA)26Sortm7(Pik3ca*,EGFP)Rsky/J The Jackson Laboratory JAX:012343; RRID:IMSR_JAX:012343 Mouse: R26iDTR: C57BL/6-Gt(ROSA) 26Sortm1(HBEGF)Awai/J The Jackson Laboratory JAX:007900; RRID:IMSR_JAX:007900 Mouse: TCF/Lef:H2B/GFP: STOCK Tg(TCF/Lef1-HIST1H2BB/EGFP)61Hadj/J The Jackson Laboratory JAX:013752; RRID:IMSR_JAX:013752 Oligonucleotides Mouse Axin2 Forward# CGACCCAGTCAATCCTTATCAC (Boretto et al., 2017) N/A Mouse Axin2 Reverse# GGGACTCCATCTACGCTACTG (Boretto et al., 2017) N/A Mouse Gapdh Forward# TGGCAAAGTGGAGATTGTTGCC (Bonnans et al., 2012) N/A Mouse Gapdh Forward# AAGATGGTGATGGGCTTCCCG (Bonnans et al., 2012) N/A RNAscope Negative Control Probe - DapB Advanced cell Diagnostics Cat# 310043 RNAscope Positive Control Probe - Mm-Ppib Advanced cell Diagnostics Cat# 313911 RNAscope Probe-Mm-Axin2 Advanced cell Diagnostics Cat# 400331 RNAscope Probe- Hs-AXIN2 Advanced cell Diagnostics Cat# 400241 (Continued on next page) e3 Cell Stem Cell 26, 1–17.e1–e13, February 6, 2020
Virus:Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat1725035 iTaq SYBR green master mix BIO-RAD Cat#1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
Single Cell:Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat1725035 iTaq SYBR green master mix BIO-RAD Cat#1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
RNA Sequencing:Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat1725035 iTaq SYBR green master mix BIO-RAD Cat#1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
other:Article Title: Coordinated efforts of different actin filament populations are needed for optimal cell wound repair
Article Snippet: Flies and reagents used in this study REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins iTaq Universal SYBR Green Supermix Bio-Rad Cat# 1725120 iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat# 1725034 C3 Exoenzyme Cytoskeleton, Inc. Cat# CT03 Y27632 Tocris Biosciences Cat# 1254 Rabbit anti-DAAM antibody (Matusek et al., 2006) N/A Rabbit anti-Diaphanous antibody (Afshar et al., 2000) N/A Mouse anti-SCAR antibody Developmental Studies Hybridoma Bank (Rodriguez-Mesa et al., 2012) Cat# P1C1SCAR Mouse anti-actin antibody MP Biomedicals Cat# 0869100- CF Mouse anti-alpha-tubulin DSHB Cat#12G10 Mouse monoclonal anti-ATP5A Abcam Cat# ab14748 FM4-64 Invitrogen Cat# T13320
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