Recombinant:Article Title: Coincidence Detection of Membrane Stretch and Extracellular pH by the Proton-Sensing Receptor OGR1 (GPR68).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-His tag Santa Cruz Cat#sc-8036; RRID: AB_627727 Goat polyclonal anti-GAPDH Santa Cruz Cat#sc-20357; RRID: AB_641107 Mouse monoclonal anti-a-Tubulin Santa Cruz Cat#sc-32293; RRID: AB_628412 Alexa 488-conjugated anti-mouse IgG antibodies ThermoFisher Scientific Cat# R37114; RRID: AB_2556542 Alexa 488-conjugated, mouse monoclonal anti-Fibronectin abcam Cat#ab198933; RRID: AB_562114 Chemicals, Peptides, and Recombinant Proteins Fura-2 AM Thermo Fisher Scientific Cat#F1221 Oregon Green BAPTA-1 Thermo Fisher Scientific Cat#06807 histamine Tocris Cat#3545 carbachol Tocris Cat#2810 bradykinin Tocris Cat#3004 Endothelin-1 Sigma Cat#E7764; CAS Number: 117399-94-7 Latrunculin A Tocris Cat#3973 Cytochalasin D Sigma Cat#C8273; CAS Number: 22144-77-0 Jasplakinolide Tocris Cat#2792 Forskolin Sigma Cat#F6886; CAS Number: 66575-29-9 TRITC-conjugated Rhodamine Phalloidin ThermoFisher Scientific Cat# R415; RRID: AB_2572408 DAPI ThermoFisher Scientific Cat#D1306; RRID:AB_2307445 Critical Commercial Assays cAMP ELISA kit Cell Biolabs Cat#ABIN577668 RhoA/Rac1/Cdc42 activation assay combo kit Cell Biolabs Cat#ABIN2345083 Experimental Models: Cell Lines DAOY cells (HTB-186) ATTC Cat#HTB-186; RRID:CVCL_1167 HEK293 cells ATTC Cat#CRL-1573; RRID:CVCL_0045 MG63 cells Dr Philippa Hulley, Oxford University, Oxford, UK RRID:CVCL_0426 hOGR1 HEK cells Dr Klaus Seuwen, Novartis, Switzerland https://doi.org/10.1038/nature01905 Reference 15 Human brain vascular pericytes ScienCell Cat#1200 Oligonucleotides 50-AAGGAGCTGCTGACCAGCATCTACTTCCT-30 Origene TF312636A shOGR1_A 50-TGCTCACCAGCTTCAACTGCGTCGCCGAC-30 Origene TF312636B shOGR1-B 50-GTGCTCAGCACCGTGGTCATCTTCCTGGC-30 Origene TF312636C shOGR1_C 50-CCGTGCTCTACTGCTTCGTCAGCGAGACC-30 Origene TF312636D shOGR1-D Mm00558545_s1 qPCR primers for murine OGR1 TaqMan Gene Expression Assay ThermoFisher Scientific Cat#4331182 Software and Algorithms Igor Pro 6.30 WaveMetrics https://www.wavemetrics.com/downloads/ current Instat 2.03 GraphPad Software https://www.graphpad.com/scientific- software/instat/ FIJI NIH https://fiji.sc/ Driver software for custom built stretch machine Zaber Console https://www.zaber.com/zaber-software e1 Current Biology 28, 1–9.e1–e4, December 3, 2018 ..
Article Title: HDAC5 enhances IRF3 activation and is targeted for degradation by protein C6 from orthopoxviruses including Monkeypox virus and Variola virus.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-HDAC5 SANTA CRUZ Cat# Sc133106; RRID:AB_2116793 Mouse anti-a-tubulin SANTA CRUZ Cat# Sc-69970; RRID:AB_2303941 Mouse anti-HA BioLegend Cat# 901501; RRID:AB_2565006 Mouse anti-D8 Laboratory of Geoffrey L Smith Parkinson and Smith, 199455 Rabbit anti-FLAG Sigma-Aldrich Cat# F7425; RRID:AB_439687 Rabbit anti-phospho-IRF3 (Ser386) Cell Signaling Cat# 4947S; RRID:AB_823547 Rabbit anti-actin Sigma-Aldrich Cat# A2066; RRID:AB_476693 Rabbit anti-C6 Laboratory of Geoffrey L Smith Unterholzner et al., 201137 IRDye 800CW Goat anti-Mouse IgG LICOR Cat# 926-32210: RRID:AB_621842 IRDye 800CW Goat anti-Rabbit IgG LICOR Cat# 926-32211; RRID:AB_621843 IRDye 680RD Goat anti-Rabbit IgG LICOR Cat# 926-68071; RRID:AB_10956166 IRDye 680RD Goat anti-Mouse IgG LICOR Cat# 926-68070; RRID:AB_10956588 Alexa Fluor 546 Goat anti-Rabbit IgG (H + L) Invitrogen Cat# A-11035; RRID:AB_2534093 Alexa Fluor 488 Donkey anti-Mouse IgG (H + L) Invitrogen Cat# R37114; RRID:AB_2556542 Bacterial and virus strains RPXV strain Utrecht Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CPXV strain Brighton Red Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CPXV-E Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CMLV strain CMS Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 MPXV_CVR MRC-University of GlasgowCenter for Virus Research Zhao et al., 202313 Sendai Virus Cantell strain Steve Goodbourn, St George’s Hospital Medical School, University of London N/A Chemicals, peptides, and recombinant proteins 40, 6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) ThermoFisher D1306 Opti-MEMTM reduced serum medium ThermoFisher 31985070 TransIT-LT1 transfection reagent Mirus MIR 2306 TNF-a Peprotech 300-001A IL-1b Peprotech 200-01A IFN-a Peprotech 300-02AA IFN-g Peprotech 300–02 cOmpleteTM Protease Inhibitor Cocktail Roche 11697498001 phosphatase inhibitor PhosSTOPTM Roche 4906845001 ANTI-FLAG M2 Affinity Gel MERCK A2220 Anti-HA-Agarose MERCK A2095 Strep-Tactin XT 4Flow resin iba 2-5010-002 Glutathione Sepharose 4B GST-tagged protein purification resin Cytiva 17075605 MG132 Sigma-Aldrich SML1135 DMEM ThermoFisher 41966029 10 x MEM ThermoFisher 11430030 Opti-MEMTM I Reduced Serum Medium ThermoFisher 31985070 (Continued on next page) Cell Reports 43, 113788, March 26, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sodium Bicarbonate 7.5% solution ThermoFisher 25080094 L-Glutamine ThermoFisher 25030–081 FBS PAN Biotech UK P40-37500HI Penicillin-Streptomycin ThermoFisher 15140122 Puromycin (solution) InvivoGen ant-pr-1 Paraformaldehyde 16% Aqueous Solution, EM Grade Electron Microscopy Sciences 15711 Coelenterazine (Renilla Luciferase substrate) Nanolight Technology 303 D-Luciferine Nanolight Technology 306 Co-enzyme A Nanolight Technology 309 Fast SYBRTM Green Master Mix ThermoFisher 4385612 RNaseOUTTM Recombinant Ribonuclease Inhibitor ThermoFisher 10777019 SuperScriptTM III Reverse Transcriptase ThermoFisher 18080093 Oligo(dT)20 Primer InvitrogenTM ThermoFisher 18418020 dNTP ThermoFisher R0181 Passive Lysis 5X Buffer Promega E1941 Critical commercial assays Plasmid DNA sequencing SourceBioscience N/A Experimental models: Cell lines HeLa (human cervical adenocarcinoma epithelial cell line) ATCC CCL-2 H5KO1 Laboratory of Geoffrey L Smith Soday et al., 201912 H5KO2 Laboratory of Geoffrey L Smith Soday et al., 201912 HEK-293T (human embryo kidney epithelial cell line) ATCC CRL-11268 H5KO4 Laboratory of Geoffrey L Smith Soday et al., 201912 H5KO3 Laboratory of Geoffrey L Smith Soday et al., 201912 T-REx-293 Life Technologies R71007 HFFF Laboratory of Michael Weekes Soday et al., 201912
Article Title: Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat anti SOX10 Santa Cruz Cat#sc-17342; RRID:AB_2195374 Mouse anti SOX10 Santa Cruz Cat#sc-365692; RRID:AB_10844002 Mouse anti HOXC9 Abcam Cat#ab50839; RRID:AB_880494 Rabbit anti HOXD13 Abcam Cat#ab19866; RRID:AB_733004 Mouse anti Ki67 Dako Cat# M7240; RRID:AB_2142367 Mouse anti CDX2 BioGenex Cat#MU392A-5UC; RRID:AB_2650531 Goat anti Bra/T R&D Systems Cat#AF2085; RRID:AB_2200235 Rabbit anti SOX2 Cell signaling Tech Cat#35795; RRID:AB_2195767 PE conjugated Mouse Anti-Human CDX-2 BD Biosciences Cat#563428; RRID:AB_2738198) APC-conjugated Human/Mouse Bra/T R&D Systems Cat#IC2085A; RRID:AB_2891298 Alexa Fluor 488 Mouse anti-Sox2 Clone O30-678 BD Biosciences Cat#561593; RRID:AB_10894382 Rabbit anti SNAI2 Cell signaling Tech Cat#9585; RRID:AB_2239535 Rabbit anti TUJ1 Covance Cat#MMS-435P; RRID:AB_2313773 Chicken anti TUJ1 Abcam Cat#ab107216; RRID:AB_10899689 Mouse anti TUJ1 Biolegend Cat#801201; RRID:AB_2313773 Rabbit anti GABA Sigma Cat#A2052; RRID:AB_477652 Mouse anti TH Immunostar Cat#22941; RRID:AB_572268 Rabbit anti nNOS Millipore Cat#07-571; RRID:AB_11211970 Goat anti CHAT Millipore Cat#AB144P; RRID:AB_2079751 Rabbit anti 5’HT Sigma Cat#S5545; RRID:AB_477522 Rabbit anti SST Millipore Cat#mab354; RRID:AB_2255365 Rabbit anti DBH ImmunoStar Cat#22806; RRID:AB_572229 Rabbit ISL1 Developmental Studies Hybridoma Bank Cat#39.4D5; RRID:AB_2314683 Rabbit anti S100-beta Abcam Cat# ab52642; RRID:AB_882426 PE/Cy7 conjugated CD49D Biolegend Cat#304314; RRID:AB_10643278 APC conjugated CD49D Biolegend Cat#304308; RRID:AB_2130041 PE conjugated HNK1 Biolegend Cat#359611; RRID:AB_2562758 APC conjugated P75NTR Biolegend Cat#345107; RRID:AB_10639737 APC conjugated c-kit (CD117) eBioscience Cat#17-1179-42; RRID:AB_10596820 Chicken anti GFP Abcam Cat#ab13970; RRID:AB_300798 Rabbit anti RFP Rockland Cat#600-401-379; RRID:AB_2209751 Mouse anti Stem121 TaKaRa Cat#Y40410; RRID:AB_2801314 Mouse anti RET R&D systems Cat#MAB718-100; RRID:AB_2232594 Rabbit anti EDNRB Biorbyt Cat#orb37019; RRID:AB_10995764 Anti-rabbit IgG, HRP-linked Cell Signaling Tech Cat#7074S; RRID:AB_2099233 Rabbit anti LaminB1 Abcam Cat#ab16048; RRID:AB_443298 Human anti ANNA-1 Gift from Dr V. Lennon (King et al., 1999) Donkey anti-Human IgG H&L (AMCA) Jackson Immuno Cat# 709-155-149; RRID: AB_2340529 Donkey anti-Human Dylight 405 Jackson Immuno Cat# 709-475-149; RRID: AB_2340553 Donkey anti-goat IgG H&L (Alexa Fluor 488) Invitrogen Cat#A11055; RRID:AB_2534102 (Continued on next page) Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Donkey anti-mouse IgG H&L (Alexa Fluor 488) Invitrogen Cat# R37114; RRID:AB_2556542 Donkey anti-rabbit IgG H&L (Alexa Fluor 488) Invitrogen Cat#A21206; RRID:AB_2535792 Donkey anti-mouse IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A31570; RRID:AB_2536180 Donkey anti-rabbit IgG H&L (Alexa Fluor 568) Invitrogen Cat#A10042; RRID:AB_2534017 Donkey anti-goat IgG H&L (Alexa Fluor 568) Invitrogen Cat#A11057; RRID:AB_142581 Donkey anti-mouse IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31571; RRID:AB_162542 Donkey anti-rabbit IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31573; RRID:AB_2536183 Goat anti-chicken IgG H&L (Alexa Fluor 488) Thermo Fisher Cat#A11039; RRID:AB_142924 Goat anti-chicken IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A32932; RRID:AB_2762844 Chemicals, peptides, and recombinant proteins EDTA-free Protease Inhibitor Sigma Cat#11836170001 Y-27632 R&D Systems Cat#1524 SB431542 R&D Systems Cat#1614 BMP4 R&D Systems Cat#314-BP CHIR R&D Systems Cat#4423 RA Sigma Cat#R2625 FGF2 R&D Systems Cat#233-FB/CF Growth/Differentiation Factor-11, BMP-11 Peprotech Cat#120-11 EDN3 American Peptide company Cat#88-5-10B AGN Tocris Cat#5758 GDNF Peprotech Cat#450-10 AA Sigma Cat#4034-100g SHH R&D Systems Cat#464-SH NGF Peprotech Cat#450-01 BDNF R&D Systems Cat#248-BDB SCF R&D Systems Cat#255-SC-MTO cAMP Sigma Cat#D0627 E8 medium Thermo Fisher Cat#A1517001 E6 medium Thermo Fisher Cat#A1516401 DMEM/F12 Thermo Fisher Cat#21331020 Neurobasal medium Gibco Cat#21103049 N2 Stem Cell Technologies Cat#07156 B27 Life Technologies Cat#17504044 L-glutamine Gibco Cat#25030-164 MEM non-essential amino acids (NEAA) Sigma Cat#M7145 4’,6-diamidino-2-phenylindole (DAPI) Invitrogen Cat#D1306 Critical commercial assays CytoSelect 24-Well Cell Invasion Assay, Basement Cell Biolabs Cat#CBA-110 iScript Reverse Transcription Supermix for RT-qPCR Biorad Cat#1708840 SsoFast EvaGreen Supermix Biorad Cat#1725201 NuPAGE 4-12% Bis-Tris Protein Gels, 1.5 mm, 15-wells Thermo Scientific Cat#NP0336BOX Trilogy Cell Marque Cat#920P-06 Deposited data RNA seq data This study GEO: GSE199439 ATAC seq data This study GEO: GSE199440 CUT and RUN data This study GEO: GSE199441 (Continued on next page) ll OPEN ACCESS Article e2 Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Human embryonic stem cell (hESC) lines H9 (WA-09) (Thomson et al., 1998)98 RRID:CVCL_9773 Human embryonic stem cell (hESC) lines H1 (WA-01) (Thomson et al., 1998)98 RRID:CVCL_9771 Human embryonic stem cell (hESC) lines HUES6 (Cowan et al., 2004)99 RRID:CVCL_B194 Human embryonic stem cell (hESC) lines MEL1 (Adewumi et al., 2007)100 N/A Induced pluripotent stem cell (iPSCs) lines 348.7, 706.3 and 864.3 Cornacchia et al.101 N/A H9 derived SOX10::GFP reporter line Chambers et al.16 N/A H9 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H1 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H9 derived mCherry reporter line This study N/A H9 derived GFP reporter line This study N/A Experimental models: Organisms/strains Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) JAX 005557 Mouse: B6.129S7-Ednrb tm1Ywa/FrykJ JAX 021933 Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ)Ednrb tm1Ywa/FrykJ This Study N/A Oligonucleotides Hs_SOX10_1_SG QuantiTect primer assay Qiagen QT00055405 Hs_FOXD3_1_SG QuantiTect Primer Assay Qiagen QT00221928 Hs_SOX2_1_SG QuantiTect Primer Assay Qiagen QT00237601 Hs_CDX2_1_SG QuantiTect primer assay Qiagen QT00037807 Hs_T_1_SG QuantiTect Primer Assay Qiagen QT00062314 Hs_GAPDH_1_SG QuantiTect Primer Assay Qiagen QT00079247 Hs_POU5F1_1_SG QuantiTect Primer Assay Qiagen QT00210840 Hs_NANOG_1_SG QuantiTect Primer Assay Qiagen QT01025850 Hs_WNT3A_1_SG QuantiTect Primer Assay Qiagen QT00220542 Hs_EDNRB_1_SG QuantiTect Primer Assay Qiagen QT00014343 All other primers are listed in Table S1 Qiagen and IDT N/A Software and algorithms FIJI Open source Schindelin et al.102 https://imagej.net/software/fiji Flow Jo FlowJo LLC https://www.flowjo.com DESeq2 Love et al.103 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Prism 9 GraphPad Software https://www.graphpad.com Biorender Biorender https://biorender.com Caseviewer 3dhistech https://www.3dhistech.com/ solutions/caseviewer/ Matlab R2014a Open source https://www.mathworks.com/ company/newsroom/mathworksannounces-release-2014a-of-thematlab-and-simulink-product-families.html ll OPEN ACCESSArticle
Article Title: Sushi domain-containing protein 4 controls synaptic plasticity and motor learning
Article Snippet: Key resources table Reagent type (species) or resource Designation Source or reference Identifiers Additional information Gene (Mus musculus) Susd4 NCBI Gene ID: 96935 chr1:182,764,895–182,896,591 Strain (Mus musculus) Susd4 knockout mice Lexicon Genetics Incorporated, Tang et al., 2010 B6:129S5-Susd4tm1Lex Strain (Mus musculus) Htr5b-GFP mouse line Gene Expression Nervous System Atlas (GENSAT) Project STOCK Tg (Htr5b-EGFP)BZ265Gsat/Mmmh Strain (Mus musculus) L7Cre mouse line Jackson Laboratories B6.129-Tg(Pcp2-cre)2Mpin/J Stock number 004146 Cell line (Homo sapiens) HEK293H Gibco Cat# 11631–017 Cell line (Homo sapiens) HeLA Sigma Cat# 93021013 Antibody Mouse monoclonal antiCABP Swant Cat# 300 (1:1000) Antibody Rabbit polyclonal antiCABP Swant Cat# CB38 (1:1000) Antibody Mouse monoclonal antiGFP Abcam Cat# ab1218 (1:1000) Antibody Rabbit polyclonal antiGFP Abcam Cat# ab6556 (1:1000) Antibody Mouse monoclonal antiGLUA2, clone 6C4 Millipore and BD Cat# MAB397 and Cat# 556341 (1:500) Antibody Rabbit monoclonal antiGLUA2 Abcam Cat# ab206293 (1:1000) Antibody Rabbit polyclonal antiGLURd1/2 Millipore Cat# AB2285 (1:1000) Antibody Rat monoclonal anti-HA Roche Life Cat# 11867423001 (1:1000) Antibody Rabbit monoclonal antiITCH Cell Signaling Technology Cat# 12117 (1:1000) Antibody Rabbit polyclonal antiNEDD4 Millipore Cat# 07–049 (1:100,000) Antibody Guinea pig polyclonal antiVGLUT1 Millipore Cat# AB5905 (1:5000) Antibody Guinea pig polyclonal antiVGLUT2 Millipore Cat# AB2251 (1:5000) Antibody Rabbit polyclonal antiWWP1 Proteintech Cat# 13587–1-AP (1:2000) Continued on next page González-Calvo, Iyer, et al. eLife 2021;10:e65712. .. DOI: https://doi.org/10.7554/eLife.65712 17 of 34 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Donkey polyclonal antigoat Alexa Fluor 568 Invitrogen Cat# A11057 (1:1000) Antibody Donkey antimouse Alexa Fluor 488 Invitrogen Cat# R37114 (1:1000) Antibody Donkey polyclonal antimouse Alexa Fluor 568 Invitrogen #A10037 (1:1000) Antibody Donkey polyclonal antirabbit Alexa Fluor 488 Invitrogen Cat# A21206 (1:1000) Antibody Donkey polyclonal antirat Alexa Fluor 594 Invitrogen #A21209 (1:1000) Antibody Donkey polyclonal antirat Alexa Fluor 568 Abcam Cat# 175475 (1:1000) Antibody Goat polyclonal anti-guinea Pig Alexa Fluor 488 Invitrogen Cat# A110-73 (1:1000) Antibody Goat polyclonal anti-guinea Pig Alexa Fluor 647 Invitrogen Cat# A21450 (1:1000) Antibody Goat polyclonal anti-mouse HRP Jackson Immune Research Laboratories Cat# 115-035-174 (1:10,000) Antibody Goat polyclonal anti-rat HRP Jackson Immune Research Laboratories #112-035-175 (1:10,000) Antibody Sheep polyclonal antidigoxigenin alkaline phosphatase Roche Life Science Cat# 11093274910 (1:2000 - 1:5000) Antibody Mouse monoclonal antibACTIN HRP, clone AC-15 Abcam Cat# ab49900 (1:25,000) Recombinant DNA reagent pHA-SUSD4GFP This paper From pEGFP-N1 (Addgene, Cat# 6085–1) Recombinant DNA reagent pHA-SUSD4 This paper Recombinant DNA reagent pHA-SUSD4-D NT This paper Recombinant DNA reagent pHA-SUSD4-NT This paper Recombinant DNA reagent HA-SUSD4-DPY This paper Recombinant DNA reagent HA-SUSD4-DLY This paper Continued on next page González-Calvo, Iyer, et al. eLife 2021;10:e65712. .. DOI: https://doi.org/10.7554/eLife.65712 18 of 34 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Recombinant DNA reagent HA-SUSD4-DPY/ LY This paper Recombinant DNA reagent pIRES2-eGFP Addgene Cat# 6029–1 Recombinant DNA reagent pCAG-PVRL3a This paper From pCAG-mGFP (Addgene, Cat# 14757) Sequencedbased reagent Susd4_WT_F This paper PCR primers CTG TGG TTT CAA CTG GCG CTG TG Sequencedbased reagent Susd4_WT_R This paper PCR primers GCT GCC GGT GGG TGT GCG AAC CTA Sequencedbased reagent Susd4_KO_F This paper PCR primers TTG GCG GTT TCG CTA AAT AC Sequencedbased reagent Susd4_KO_R This paper PCR primers GGA GCT CGT TAT CGC TAT GAC Sequencedbased reagent Htr5b-GFP_F PCR primers TTG GCG CGC CTC CAA CAG GAT GTT AAC AAC Sequencedbased reagent Htr5b-GFP_R PCR primers CGC CCT CGC CGG ACA CGC TGA AC Sequencedbased reagent L7cre_1 PCR primers GGT GAC GGT CAG TAA ATT GGA C Sequencedbased reagent L7cre_2 PCR primers CAC TTC TGA CTT GCA CTT TCC TTG G Sequencedbased reagent L7cre_3 PCR primers TTC TTC AAG CTG CCC AGC AGA GAG C Chemical compound, drug Picrotoxin Sigma-Aldrich Cat# P1675 Chemical compound, drug D-AP5 Tocris Cat# 0106 Chemical compound, drug CGP52432 Tocris Cat# 1246 Chemical compound, drug JNJ16259685 Tocris Cat# 2333 Chemical compound, drug DPCPX Tocris Cat# 0439 Chemical compound, drug AM251 Tocris Cat# 1117 Software, algorithm Sinaptiqs Antoine Valera Software written in Python http://synaptiqs. wixsite.com/synaptiqs Other Hoechst 33342 Sigma Cat# 14533 Recombinant viral particles hSYN-DIO-HASUSD4-2AeGFP-WPRE Vector biolabs AAV2 particles
Enzyme-linked Immunosorbent Assay:Article Title: Coincidence Detection of Membrane Stretch and Extracellular pH by the Proton-Sensing Receptor OGR1 (GPR68).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-His tag Santa Cruz Cat#sc-8036; RRID: AB_627727 Goat polyclonal anti-GAPDH Santa Cruz Cat#sc-20357; RRID: AB_641107 Mouse monoclonal anti-a-Tubulin Santa Cruz Cat#sc-32293; RRID: AB_628412 Alexa 488-conjugated anti-mouse IgG antibodies ThermoFisher Scientific Cat# R37114; RRID: AB_2556542 Alexa 488-conjugated, mouse monoclonal anti-Fibronectin abcam Cat#ab198933; RRID: AB_562114 Chemicals, Peptides, and Recombinant Proteins Fura-2 AM Thermo Fisher Scientific Cat#F1221 Oregon Green BAPTA-1 Thermo Fisher Scientific Cat#06807 histamine Tocris Cat#3545 carbachol Tocris Cat#2810 bradykinin Tocris Cat#3004 Endothelin-1 Sigma Cat#E7764; CAS Number: 117399-94-7 Latrunculin A Tocris Cat#3973 Cytochalasin D Sigma Cat#C8273; CAS Number: 22144-77-0 Jasplakinolide Tocris Cat#2792 Forskolin Sigma Cat#F6886; CAS Number: 66575-29-9 TRITC-conjugated Rhodamine Phalloidin ThermoFisher Scientific Cat# R415; RRID: AB_2572408 DAPI ThermoFisher Scientific Cat#D1306; RRID:AB_2307445 Critical Commercial Assays cAMP ELISA kit Cell Biolabs Cat#ABIN577668 RhoA/Rac1/Cdc42 activation assay combo kit Cell Biolabs Cat#ABIN2345083 Experimental Models: Cell Lines DAOY cells (HTB-186) ATTC Cat#HTB-186; RRID:CVCL_1167 HEK293 cells ATTC Cat#CRL-1573; RRID:CVCL_0045 MG63 cells Dr Philippa Hulley, Oxford University, Oxford, UK RRID:CVCL_0426 hOGR1 HEK cells Dr Klaus Seuwen, Novartis, Switzerland https://doi.org/10.1038/nature01905 Reference 15 Human brain vascular pericytes ScienCell Cat#1200 Oligonucleotides 50-AAGGAGCTGCTGACCAGCATCTACTTCCT-30 Origene TF312636A shOGR1_A 50-TGCTCACCAGCTTCAACTGCGTCGCCGAC-30 Origene TF312636B shOGR1-B 50-GTGCTCAGCACCGTGGTCATCTTCCTGGC-30 Origene TF312636C shOGR1_C 50-CCGTGCTCTACTGCTTCGTCAGCGAGACC-30 Origene TF312636D shOGR1-D Mm00558545_s1 qPCR primers for murine OGR1 TaqMan Gene Expression Assay ThermoFisher Scientific Cat#4331182 Software and Algorithms Igor Pro 6.30 WaveMetrics https://www.wavemetrics.com/downloads/ current Instat 2.03 GraphPad Software https://www.graphpad.com/scientific- software/instat/ FIJI NIH https://fiji.sc/ Driver software for custom built stretch machine Zaber Console https://www.zaber.com/zaber-software e1 Current Biology 28, 1–9.e1–e4, December 3, 2018 ..
Activation Assay:Article Title: Coincidence Detection of Membrane Stretch and Extracellular pH by the Proton-Sensing Receptor OGR1 (GPR68).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-His tag Santa Cruz Cat#sc-8036; RRID: AB_627727 Goat polyclonal anti-GAPDH Santa Cruz Cat#sc-20357; RRID: AB_641107 Mouse monoclonal anti-a-Tubulin Santa Cruz Cat#sc-32293; RRID: AB_628412 Alexa 488-conjugated anti-mouse IgG antibodies ThermoFisher Scientific Cat# R37114; RRID: AB_2556542 Alexa 488-conjugated, mouse monoclonal anti-Fibronectin abcam Cat#ab198933; RRID: AB_562114 Chemicals, Peptides, and Recombinant Proteins Fura-2 AM Thermo Fisher Scientific Cat#F1221 Oregon Green BAPTA-1 Thermo Fisher Scientific Cat#06807 histamine Tocris Cat#3545 carbachol Tocris Cat#2810 bradykinin Tocris Cat#3004 Endothelin-1 Sigma Cat#E7764; CAS Number: 117399-94-7 Latrunculin A Tocris Cat#3973 Cytochalasin D Sigma Cat#C8273; CAS Number: 22144-77-0 Jasplakinolide Tocris Cat#2792 Forskolin Sigma Cat#F6886; CAS Number: 66575-29-9 TRITC-conjugated Rhodamine Phalloidin ThermoFisher Scientific Cat# R415; RRID: AB_2572408 DAPI ThermoFisher Scientific Cat#D1306; RRID:AB_2307445 Critical Commercial Assays cAMP ELISA kit Cell Biolabs Cat#ABIN577668 RhoA/Rac1/Cdc42 activation assay combo kit Cell Biolabs Cat#ABIN2345083 Experimental Models: Cell Lines DAOY cells (HTB-186) ATTC Cat#HTB-186; RRID:CVCL_1167 HEK293 cells ATTC Cat#CRL-1573; RRID:CVCL_0045 MG63 cells Dr Philippa Hulley, Oxford University, Oxford, UK RRID:CVCL_0426 hOGR1 HEK cells Dr Klaus Seuwen, Novartis, Switzerland https://doi.org/10.1038/nature01905 Reference 15 Human brain vascular pericytes ScienCell Cat#1200 Oligonucleotides 50-AAGGAGCTGCTGACCAGCATCTACTTCCT-30 Origene TF312636A shOGR1_A 50-TGCTCACCAGCTTCAACTGCGTCGCCGAC-30 Origene TF312636B shOGR1-B 50-GTGCTCAGCACCGTGGTCATCTTCCTGGC-30 Origene TF312636C shOGR1_C 50-CCGTGCTCTACTGCTTCGTCAGCGAGACC-30 Origene TF312636D shOGR1-D Mm00558545_s1 qPCR primers for murine OGR1 TaqMan Gene Expression Assay ThermoFisher Scientific Cat#4331182 Software and Algorithms Igor Pro 6.30 WaveMetrics https://www.wavemetrics.com/downloads/ current Instat 2.03 GraphPad Software https://www.graphpad.com/scientific- software/instat/ FIJI NIH https://fiji.sc/ Driver software for custom built stretch machine Zaber Console https://www.zaber.com/zaber-software e1 Current Biology 28, 1–9.e1–e4, December 3, 2018 ..
Real-time Polymerase Chain Reaction:Article Title: Coincidence Detection of Membrane Stretch and Extracellular pH by the Proton-Sensing Receptor OGR1 (GPR68).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-His tag Santa Cruz Cat#sc-8036; RRID: AB_627727 Goat polyclonal anti-GAPDH Santa Cruz Cat#sc-20357; RRID: AB_641107 Mouse monoclonal anti-a-Tubulin Santa Cruz Cat#sc-32293; RRID: AB_628412 Alexa 488-conjugated anti-mouse IgG antibodies ThermoFisher Scientific Cat# R37114; RRID: AB_2556542 Alexa 488-conjugated, mouse monoclonal anti-Fibronectin abcam Cat#ab198933; RRID: AB_562114 Chemicals, Peptides, and Recombinant Proteins Fura-2 AM Thermo Fisher Scientific Cat#F1221 Oregon Green BAPTA-1 Thermo Fisher Scientific Cat#06807 histamine Tocris Cat#3545 carbachol Tocris Cat#2810 bradykinin Tocris Cat#3004 Endothelin-1 Sigma Cat#E7764; CAS Number: 117399-94-7 Latrunculin A Tocris Cat#3973 Cytochalasin D Sigma Cat#C8273; CAS Number: 22144-77-0 Jasplakinolide Tocris Cat#2792 Forskolin Sigma Cat#F6886; CAS Number: 66575-29-9 TRITC-conjugated Rhodamine Phalloidin ThermoFisher Scientific Cat# R415; RRID: AB_2572408 DAPI ThermoFisher Scientific Cat#D1306; RRID:AB_2307445 Critical Commercial Assays cAMP ELISA kit Cell Biolabs Cat#ABIN577668 RhoA/Rac1/Cdc42 activation assay combo kit Cell Biolabs Cat#ABIN2345083 Experimental Models: Cell Lines DAOY cells (HTB-186) ATTC Cat#HTB-186; RRID:CVCL_1167 HEK293 cells ATTC Cat#CRL-1573; RRID:CVCL_0045 MG63 cells Dr Philippa Hulley, Oxford University, Oxford, UK RRID:CVCL_0426 hOGR1 HEK cells Dr Klaus Seuwen, Novartis, Switzerland https://doi.org/10.1038/nature01905 Reference 15 Human brain vascular pericytes ScienCell Cat#1200 Oligonucleotides 50-AAGGAGCTGCTGACCAGCATCTACTTCCT-30 Origene TF312636A shOGR1_A 50-TGCTCACCAGCTTCAACTGCGTCGCCGAC-30 Origene TF312636B shOGR1-B 50-GTGCTCAGCACCGTGGTCATCTTCCTGGC-30 Origene TF312636C shOGR1_C 50-CCGTGCTCTACTGCTTCGTCAGCGAGACC-30 Origene TF312636D shOGR1-D Mm00558545_s1 qPCR primers for murine OGR1 TaqMan Gene Expression Assay ThermoFisher Scientific Cat#4331182 Software and Algorithms Igor Pro 6.30 WaveMetrics https://www.wavemetrics.com/downloads/ current Instat 2.03 GraphPad Software https://www.graphpad.com/scientific- software/instat/ FIJI NIH https://fiji.sc/ Driver software for custom built stretch machine Zaber Console https://www.zaber.com/zaber-software e1 Current Biology 28, 1–9.e1–e4, December 3, 2018 ..
Gene Expression:Article Title: Coincidence Detection of Membrane Stretch and Extracellular pH by the Proton-Sensing Receptor OGR1 (GPR68).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-His tag Santa Cruz Cat#sc-8036; RRID: AB_627727 Goat polyclonal anti-GAPDH Santa Cruz Cat#sc-20357; RRID: AB_641107 Mouse monoclonal anti-a-Tubulin Santa Cruz Cat#sc-32293; RRID: AB_628412 Alexa 488-conjugated anti-mouse IgG antibodies ThermoFisher Scientific Cat# R37114; RRID: AB_2556542 Alexa 488-conjugated, mouse monoclonal anti-Fibronectin abcam Cat#ab198933; RRID: AB_562114 Chemicals, Peptides, and Recombinant Proteins Fura-2 AM Thermo Fisher Scientific Cat#F1221 Oregon Green BAPTA-1 Thermo Fisher Scientific Cat#06807 histamine Tocris Cat#3545 carbachol Tocris Cat#2810 bradykinin Tocris Cat#3004 Endothelin-1 Sigma Cat#E7764; CAS Number: 117399-94-7 Latrunculin A Tocris Cat#3973 Cytochalasin D Sigma Cat#C8273; CAS Number: 22144-77-0 Jasplakinolide Tocris Cat#2792 Forskolin Sigma Cat#F6886; CAS Number: 66575-29-9 TRITC-conjugated Rhodamine Phalloidin ThermoFisher Scientific Cat# R415; RRID: AB_2572408 DAPI ThermoFisher Scientific Cat#D1306; RRID:AB_2307445 Critical Commercial Assays cAMP ELISA kit Cell Biolabs Cat#ABIN577668 RhoA/Rac1/Cdc42 activation assay combo kit Cell Biolabs Cat#ABIN2345083 Experimental Models: Cell Lines DAOY cells (HTB-186) ATTC Cat#HTB-186; RRID:CVCL_1167 HEK293 cells ATTC Cat#CRL-1573; RRID:CVCL_0045 MG63 cells Dr Philippa Hulley, Oxford University, Oxford, UK RRID:CVCL_0426 hOGR1 HEK cells Dr Klaus Seuwen, Novartis, Switzerland https://doi.org/10.1038/nature01905 Reference 15 Human brain vascular pericytes ScienCell Cat#1200 Oligonucleotides 50-AAGGAGCTGCTGACCAGCATCTACTTCCT-30 Origene TF312636A shOGR1_A 50-TGCTCACCAGCTTCAACTGCGTCGCCGAC-30 Origene TF312636B shOGR1-B 50-GTGCTCAGCACCGTGGTCATCTTCCTGGC-30 Origene TF312636C shOGR1_C 50-CCGTGCTCTACTGCTTCGTCAGCGAGACC-30 Origene TF312636D shOGR1-D Mm00558545_s1 qPCR primers for murine OGR1 TaqMan Gene Expression Assay ThermoFisher Scientific Cat#4331182 Software and Algorithms Igor Pro 6.30 WaveMetrics https://www.wavemetrics.com/downloads/ current Instat 2.03 GraphPad Software https://www.graphpad.com/scientific- software/instat/ FIJI NIH https://fiji.sc/ Driver software for custom built stretch machine Zaber Console https://www.zaber.com/zaber-software e1 Current Biology 28, 1–9.e1–e4, December 3, 2018 ..
Software:Article Title: Coincidence Detection of Membrane Stretch and Extracellular pH by the Proton-Sensing Receptor OGR1 (GPR68).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-His tag Santa Cruz Cat#sc-8036; RRID: AB_627727 Goat polyclonal anti-GAPDH Santa Cruz Cat#sc-20357; RRID: AB_641107 Mouse monoclonal anti-a-Tubulin Santa Cruz Cat#sc-32293; RRID: AB_628412 Alexa 488-conjugated anti-mouse IgG antibodies ThermoFisher Scientific Cat# R37114; RRID: AB_2556542 Alexa 488-conjugated, mouse monoclonal anti-Fibronectin abcam Cat#ab198933; RRID: AB_562114 Chemicals, Peptides, and Recombinant Proteins Fura-2 AM Thermo Fisher Scientific Cat#F1221 Oregon Green BAPTA-1 Thermo Fisher Scientific Cat#06807 histamine Tocris Cat#3545 carbachol Tocris Cat#2810 bradykinin Tocris Cat#3004 Endothelin-1 Sigma Cat#E7764; CAS Number: 117399-94-7 Latrunculin A Tocris Cat#3973 Cytochalasin D Sigma Cat#C8273; CAS Number: 22144-77-0 Jasplakinolide Tocris Cat#2792 Forskolin Sigma Cat#F6886; CAS Number: 66575-29-9 TRITC-conjugated Rhodamine Phalloidin ThermoFisher Scientific Cat# R415; RRID: AB_2572408 DAPI ThermoFisher Scientific Cat#D1306; RRID:AB_2307445 Critical Commercial Assays cAMP ELISA kit Cell Biolabs Cat#ABIN577668 RhoA/Rac1/Cdc42 activation assay combo kit Cell Biolabs Cat#ABIN2345083 Experimental Models: Cell Lines DAOY cells (HTB-186) ATTC Cat#HTB-186; RRID:CVCL_1167 HEK293 cells ATTC Cat#CRL-1573; RRID:CVCL_0045 MG63 cells Dr Philippa Hulley, Oxford University, Oxford, UK RRID:CVCL_0426 hOGR1 HEK cells Dr Klaus Seuwen, Novartis, Switzerland https://doi.org/10.1038/nature01905 Reference 15 Human brain vascular pericytes ScienCell Cat#1200 Oligonucleotides 50-AAGGAGCTGCTGACCAGCATCTACTTCCT-30 Origene TF312636A shOGR1_A 50-TGCTCACCAGCTTCAACTGCGTCGCCGAC-30 Origene TF312636B shOGR1-B 50-GTGCTCAGCACCGTGGTCATCTTCCTGGC-30 Origene TF312636C shOGR1_C 50-CCGTGCTCTACTGCTTCGTCAGCGAGACC-30 Origene TF312636D shOGR1-D Mm00558545_s1 qPCR primers for murine OGR1 TaqMan Gene Expression Assay ThermoFisher Scientific Cat#4331182 Software and Algorithms Igor Pro 6.30 WaveMetrics https://www.wavemetrics.com/downloads/ current Instat 2.03 GraphPad Software https://www.graphpad.com/scientific- software/instat/ FIJI NIH https://fiji.sc/ Driver software for custom built stretch machine Zaber Console https://www.zaber.com/zaber-software e1 Current Biology 28, 1–9.e1–e4, December 3, 2018 ..
Virus:Article Title: HDAC5 enhances IRF3 activation and is targeted for degradation by protein C6 from orthopoxviruses including Monkeypox virus and Variola virus.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-HDAC5 SANTA CRUZ Cat# Sc133106; RRID:AB_2116793 Mouse anti-a-tubulin SANTA CRUZ Cat# Sc-69970; RRID:AB_2303941 Mouse anti-HA BioLegend Cat# 901501; RRID:AB_2565006 Mouse anti-D8 Laboratory of Geoffrey L Smith Parkinson and Smith, 199455 Rabbit anti-FLAG Sigma-Aldrich Cat# F7425; RRID:AB_439687 Rabbit anti-phospho-IRF3 (Ser386) Cell Signaling Cat# 4947S; RRID:AB_823547 Rabbit anti-actin Sigma-Aldrich Cat# A2066; RRID:AB_476693 Rabbit anti-C6 Laboratory of Geoffrey L Smith Unterholzner et al., 201137 IRDye 800CW Goat anti-Mouse IgG LICOR Cat# 926-32210: RRID:AB_621842 IRDye 800CW Goat anti-Rabbit IgG LICOR Cat# 926-32211; RRID:AB_621843 IRDye 680RD Goat anti-Rabbit IgG LICOR Cat# 926-68071; RRID:AB_10956166 IRDye 680RD Goat anti-Mouse IgG LICOR Cat# 926-68070; RRID:AB_10956588 Alexa Fluor 546 Goat anti-Rabbit IgG (H + L) Invitrogen Cat# A-11035; RRID:AB_2534093 Alexa Fluor 488 Donkey anti-Mouse IgG (H + L) Invitrogen Cat# R37114; RRID:AB_2556542 Bacterial and virus strains RPXV strain Utrecht Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CPXV strain Brighton Red Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CPXV-E Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CMLV strain CMS Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 MPXV_CVR MRC-University of GlasgowCenter for Virus Research Zhao et al., 202313 Sendai Virus Cantell strain Steve Goodbourn, St George’s Hospital Medical School, University of London N/A Chemicals, peptides, and recombinant proteins 40, 6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) ThermoFisher D1306 Opti-MEMTM reduced serum medium ThermoFisher 31985070 TransIT-LT1 transfection reagent Mirus MIR 2306 TNF-a Peprotech 300-001A IL-1b Peprotech 200-01A IFN-a Peprotech 300-02AA IFN-g Peprotech 300–02 cOmpleteTM Protease Inhibitor Cocktail Roche 11697498001 phosphatase inhibitor PhosSTOPTM Roche 4906845001 ANTI-FLAG M2 Affinity Gel MERCK A2220 Anti-HA-Agarose MERCK A2095 Strep-Tactin XT 4Flow resin iba 2-5010-002 Glutathione Sepharose 4B GST-tagged protein purification resin Cytiva 17075605 MG132 Sigma-Aldrich SML1135 DMEM ThermoFisher 41966029 10 x MEM ThermoFisher 11430030 Opti-MEMTM I Reduced Serum Medium ThermoFisher 31985070 (Continued on next page) Cell Reports 43, 113788, March 26, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sodium Bicarbonate 7.5% solution ThermoFisher 25080094 L-Glutamine ThermoFisher 25030–081 FBS PAN Biotech UK P40-37500HI Penicillin-Streptomycin ThermoFisher 15140122 Puromycin (solution) InvivoGen ant-pr-1 Paraformaldehyde 16% Aqueous Solution, EM Grade Electron Microscopy Sciences 15711 Coelenterazine (Renilla Luciferase substrate) Nanolight Technology 303 D-Luciferine Nanolight Technology 306 Co-enzyme A Nanolight Technology 309 Fast SYBRTM Green Master Mix ThermoFisher 4385612 RNaseOUTTM Recombinant Ribonuclease Inhibitor ThermoFisher 10777019 SuperScriptTM III Reverse Transcriptase ThermoFisher 18080093 Oligo(dT)20 Primer InvitrogenTM ThermoFisher 18418020 dNTP ThermoFisher R0181 Passive Lysis 5X Buffer Promega E1941 Critical commercial assays Plasmid DNA sequencing SourceBioscience N/A Experimental models: Cell lines HeLa (human cervical adenocarcinoma epithelial cell line) ATCC CCL-2 H5KO1 Laboratory of Geoffrey L Smith Soday et al., 201912 H5KO2 Laboratory of Geoffrey L Smith Soday et al., 201912 HEK-293T (human embryo kidney epithelial cell line) ATCC CRL-11268 H5KO4 Laboratory of Geoffrey L Smith Soday et al., 201912 H5KO3 Laboratory of Geoffrey L Smith Soday et al., 201912 T-REx-293 Life Technologies R71007 HFFF Laboratory of Michael Weekes Soday et al., 201912
Transfection:Article Title: HDAC5 enhances IRF3 activation and is targeted for degradation by protein C6 from orthopoxviruses including Monkeypox virus and Variola virus.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-HDAC5 SANTA CRUZ Cat# Sc133106; RRID:AB_2116793 Mouse anti-a-tubulin SANTA CRUZ Cat# Sc-69970; RRID:AB_2303941 Mouse anti-HA BioLegend Cat# 901501; RRID:AB_2565006 Mouse anti-D8 Laboratory of Geoffrey L Smith Parkinson and Smith, 199455 Rabbit anti-FLAG Sigma-Aldrich Cat# F7425; RRID:AB_439687 Rabbit anti-phospho-IRF3 (Ser386) Cell Signaling Cat# 4947S; RRID:AB_823547 Rabbit anti-actin Sigma-Aldrich Cat# A2066; RRID:AB_476693 Rabbit anti-C6 Laboratory of Geoffrey L Smith Unterholzner et al., 201137 IRDye 800CW Goat anti-Mouse IgG LICOR Cat# 926-32210: RRID:AB_621842 IRDye 800CW Goat anti-Rabbit IgG LICOR Cat# 926-32211; RRID:AB_621843 IRDye 680RD Goat anti-Rabbit IgG LICOR Cat# 926-68071; RRID:AB_10956166 IRDye 680RD Goat anti-Mouse IgG LICOR Cat# 926-68070; RRID:AB_10956588 Alexa Fluor 546 Goat anti-Rabbit IgG (H + L) Invitrogen Cat# A-11035; RRID:AB_2534093 Alexa Fluor 488 Donkey anti-Mouse IgG (H + L) Invitrogen Cat# R37114; RRID:AB_2556542 Bacterial and virus strains RPXV strain Utrecht Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CPXV strain Brighton Red Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CPXV-E Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CMLV strain CMS Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 MPXV_CVR MRC-University of GlasgowCenter for Virus Research Zhao et al., 202313 Sendai Virus Cantell strain Steve Goodbourn, St George’s Hospital Medical School, University of London N/A Chemicals, peptides, and recombinant proteins 40, 6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) ThermoFisher D1306 Opti-MEMTM reduced serum medium ThermoFisher 31985070 TransIT-LT1 transfection reagent Mirus MIR 2306 TNF-a Peprotech 300-001A IL-1b Peprotech 200-01A IFN-a Peprotech 300-02AA IFN-g Peprotech 300–02 cOmpleteTM Protease Inhibitor Cocktail Roche 11697498001 phosphatase inhibitor PhosSTOPTM Roche 4906845001 ANTI-FLAG M2 Affinity Gel MERCK A2220 Anti-HA-Agarose MERCK A2095 Strep-Tactin XT 4Flow resin iba 2-5010-002 Glutathione Sepharose 4B GST-tagged protein purification resin Cytiva 17075605 MG132 Sigma-Aldrich SML1135 DMEM ThermoFisher 41966029 10 x MEM ThermoFisher 11430030 Opti-MEMTM I Reduced Serum Medium ThermoFisher 31985070 (Continued on next page) Cell Reports 43, 113788, March 26, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sodium Bicarbonate 7.5% solution ThermoFisher 25080094 L-Glutamine ThermoFisher 25030–081 FBS PAN Biotech UK P40-37500HI Penicillin-Streptomycin ThermoFisher 15140122 Puromycin (solution) InvivoGen ant-pr-1 Paraformaldehyde 16% Aqueous Solution, EM Grade Electron Microscopy Sciences 15711 Coelenterazine (Renilla Luciferase substrate) Nanolight Technology 303 D-Luciferine Nanolight Technology 306 Co-enzyme A Nanolight Technology 309 Fast SYBRTM Green Master Mix ThermoFisher 4385612 RNaseOUTTM Recombinant Ribonuclease Inhibitor ThermoFisher 10777019 SuperScriptTM III Reverse Transcriptase ThermoFisher 18080093 Oligo(dT)20 Primer InvitrogenTM ThermoFisher 18418020 dNTP ThermoFisher R0181 Passive Lysis 5X Buffer Promega E1941 Critical commercial assays Plasmid DNA sequencing SourceBioscience N/A Experimental models: Cell lines HeLa (human cervical adenocarcinoma epithelial cell line) ATCC CCL-2 H5KO1 Laboratory of Geoffrey L Smith Soday et al., 201912 H5KO2 Laboratory of Geoffrey L Smith Soday et al., 201912 HEK-293T (human embryo kidney epithelial cell line) ATCC CRL-11268 H5KO4 Laboratory of Geoffrey L Smith Soday et al., 201912 H5KO3 Laboratory of Geoffrey L Smith Soday et al., 201912 T-REx-293 Life Technologies R71007 HFFF Laboratory of Michael Weekes Soday et al., 201912
Protease Inhibitor:Article Title: HDAC5 enhances IRF3 activation and is targeted for degradation by protein C6 from orthopoxviruses including Monkeypox virus and Variola virus.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-HDAC5 SANTA CRUZ Cat# Sc133106; RRID:AB_2116793 Mouse anti-a-tubulin SANTA CRUZ Cat# Sc-69970; RRID:AB_2303941 Mouse anti-HA BioLegend Cat# 901501; RRID:AB_2565006 Mouse anti-D8 Laboratory of Geoffrey L Smith Parkinson and Smith, 199455 Rabbit anti-FLAG Sigma-Aldrich Cat# F7425; RRID:AB_439687 Rabbit anti-phospho-IRF3 (Ser386) Cell Signaling Cat# 4947S; RRID:AB_823547 Rabbit anti-actin Sigma-Aldrich Cat# A2066; RRID:AB_476693 Rabbit anti-C6 Laboratory of Geoffrey L Smith Unterholzner et al., 201137 IRDye 800CW Goat anti-Mouse IgG LICOR Cat# 926-32210: RRID:AB_621842 IRDye 800CW Goat anti-Rabbit IgG LICOR Cat# 926-32211; RRID:AB_621843 IRDye 680RD Goat anti-Rabbit IgG LICOR Cat# 926-68071; RRID:AB_10956166 IRDye 680RD Goat anti-Mouse IgG LICOR Cat# 926-68070; RRID:AB_10956588 Alexa Fluor 546 Goat anti-Rabbit IgG (H + L) Invitrogen Cat# A-11035; RRID:AB_2534093 Alexa Fluor 488 Donkey anti-Mouse IgG (H + L) Invitrogen Cat# R37114; RRID:AB_2556542 Bacterial and virus strains RPXV strain Utrecht Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CPXV strain Brighton Red Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CPXV-E Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CMLV strain CMS Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 MPXV_CVR MRC-University of GlasgowCenter for Virus Research Zhao et al., 202313 Sendai Virus Cantell strain Steve Goodbourn, St George’s Hospital Medical School, University of London N/A Chemicals, peptides, and recombinant proteins 40, 6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) ThermoFisher D1306 Opti-MEMTM reduced serum medium ThermoFisher 31985070 TransIT-LT1 transfection reagent Mirus MIR 2306 TNF-a Peprotech 300-001A IL-1b Peprotech 200-01A IFN-a Peprotech 300-02AA IFN-g Peprotech 300–02 cOmpleteTM Protease Inhibitor Cocktail Roche 11697498001 phosphatase inhibitor PhosSTOPTM Roche 4906845001 ANTI-FLAG M2 Affinity Gel MERCK A2220 Anti-HA-Agarose MERCK A2095 Strep-Tactin XT 4Flow resin iba 2-5010-002 Glutathione Sepharose 4B GST-tagged protein purification resin Cytiva 17075605 MG132 Sigma-Aldrich SML1135 DMEM ThermoFisher 41966029 10 x MEM ThermoFisher 11430030 Opti-MEMTM I Reduced Serum Medium ThermoFisher 31985070 (Continued on next page) Cell Reports 43, 113788, March 26, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sodium Bicarbonate 7.5% solution ThermoFisher 25080094 L-Glutamine ThermoFisher 25030–081 FBS PAN Biotech UK P40-37500HI Penicillin-Streptomycin ThermoFisher 15140122 Puromycin (solution) InvivoGen ant-pr-1 Paraformaldehyde 16% Aqueous Solution, EM Grade Electron Microscopy Sciences 15711 Coelenterazine (Renilla Luciferase substrate) Nanolight Technology 303 D-Luciferine Nanolight Technology 306 Co-enzyme A Nanolight Technology 309 Fast SYBRTM Green Master Mix ThermoFisher 4385612 RNaseOUTTM Recombinant Ribonuclease Inhibitor ThermoFisher 10777019 SuperScriptTM III Reverse Transcriptase ThermoFisher 18080093 Oligo(dT)20 Primer InvitrogenTM ThermoFisher 18418020 dNTP ThermoFisher R0181 Passive Lysis 5X Buffer Promega E1941 Critical commercial assays Plasmid DNA sequencing SourceBioscience N/A Experimental models: Cell lines HeLa (human cervical adenocarcinoma epithelial cell line) ATCC CCL-2 H5KO1 Laboratory of Geoffrey L Smith Soday et al., 201912 H5KO2 Laboratory of Geoffrey L Smith Soday et al., 201912 HEK-293T (human embryo kidney epithelial cell line) ATCC CRL-11268 H5KO4 Laboratory of Geoffrey L Smith Soday et al., 201912 H5KO3 Laboratory of Geoffrey L Smith Soday et al., 201912 T-REx-293 Life Technologies R71007 HFFF Laboratory of Michael Weekes Soday et al., 201912
Article Title: Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat anti SOX10 Santa Cruz Cat#sc-17342; RRID:AB_2195374 Mouse anti SOX10 Santa Cruz Cat#sc-365692; RRID:AB_10844002 Mouse anti HOXC9 Abcam Cat#ab50839; RRID:AB_880494 Rabbit anti HOXD13 Abcam Cat#ab19866; RRID:AB_733004 Mouse anti Ki67 Dako Cat# M7240; RRID:AB_2142367 Mouse anti CDX2 BioGenex Cat#MU392A-5UC; RRID:AB_2650531 Goat anti Bra/T R&D Systems Cat#AF2085; RRID:AB_2200235 Rabbit anti SOX2 Cell signaling Tech Cat#35795; RRID:AB_2195767 PE conjugated Mouse Anti-Human CDX-2 BD Biosciences Cat#563428; RRID:AB_2738198) APC-conjugated Human/Mouse Bra/T R&D Systems Cat#IC2085A; RRID:AB_2891298 Alexa Fluor 488 Mouse anti-Sox2 Clone O30-678 BD Biosciences Cat#561593; RRID:AB_10894382 Rabbit anti SNAI2 Cell signaling Tech Cat#9585; RRID:AB_2239535 Rabbit anti TUJ1 Covance Cat#MMS-435P; RRID:AB_2313773 Chicken anti TUJ1 Abcam Cat#ab107216; RRID:AB_10899689 Mouse anti TUJ1 Biolegend Cat#801201; RRID:AB_2313773 Rabbit anti GABA Sigma Cat#A2052; RRID:AB_477652 Mouse anti TH Immunostar Cat#22941; RRID:AB_572268 Rabbit anti nNOS Millipore Cat#07-571; RRID:AB_11211970 Goat anti CHAT Millipore Cat#AB144P; RRID:AB_2079751 Rabbit anti 5’HT Sigma Cat#S5545; RRID:AB_477522 Rabbit anti SST Millipore Cat#mab354; RRID:AB_2255365 Rabbit anti DBH ImmunoStar Cat#22806; RRID:AB_572229 Rabbit ISL1 Developmental Studies Hybridoma Bank Cat#39.4D5; RRID:AB_2314683 Rabbit anti S100-beta Abcam Cat# ab52642; RRID:AB_882426 PE/Cy7 conjugated CD49D Biolegend Cat#304314; RRID:AB_10643278 APC conjugated CD49D Biolegend Cat#304308; RRID:AB_2130041 PE conjugated HNK1 Biolegend Cat#359611; RRID:AB_2562758 APC conjugated P75NTR Biolegend Cat#345107; RRID:AB_10639737 APC conjugated c-kit (CD117) eBioscience Cat#17-1179-42; RRID:AB_10596820 Chicken anti GFP Abcam Cat#ab13970; RRID:AB_300798 Rabbit anti RFP Rockland Cat#600-401-379; RRID:AB_2209751 Mouse anti Stem121 TaKaRa Cat#Y40410; RRID:AB_2801314 Mouse anti RET R&D systems Cat#MAB718-100; RRID:AB_2232594 Rabbit anti EDNRB Biorbyt Cat#orb37019; RRID:AB_10995764 Anti-rabbit IgG, HRP-linked Cell Signaling Tech Cat#7074S; RRID:AB_2099233 Rabbit anti LaminB1 Abcam Cat#ab16048; RRID:AB_443298 Human anti ANNA-1 Gift from Dr V. Lennon (King et al., 1999) Donkey anti-Human IgG H&L (AMCA) Jackson Immuno Cat# 709-155-149; RRID: AB_2340529 Donkey anti-Human Dylight 405 Jackson Immuno Cat# 709-475-149; RRID: AB_2340553 Donkey anti-goat IgG H&L (Alexa Fluor 488) Invitrogen Cat#A11055; RRID:AB_2534102 (Continued on next page) Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Donkey anti-mouse IgG H&L (Alexa Fluor 488) Invitrogen Cat# R37114; RRID:AB_2556542 Donkey anti-rabbit IgG H&L (Alexa Fluor 488) Invitrogen Cat#A21206; RRID:AB_2535792 Donkey anti-mouse IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A31570; RRID:AB_2536180 Donkey anti-rabbit IgG H&L (Alexa Fluor 568) Invitrogen Cat#A10042; RRID:AB_2534017 Donkey anti-goat IgG H&L (Alexa Fluor 568) Invitrogen Cat#A11057; RRID:AB_142581 Donkey anti-mouse IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31571; RRID:AB_162542 Donkey anti-rabbit IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31573; RRID:AB_2536183 Goat anti-chicken IgG H&L (Alexa Fluor 488) Thermo Fisher Cat#A11039; RRID:AB_142924 Goat anti-chicken IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A32932; RRID:AB_2762844 Chemicals, peptides, and recombinant proteins EDTA-free Protease Inhibitor Sigma Cat#11836170001 Y-27632 R&D Systems Cat#1524 SB431542 R&D Systems Cat#1614 BMP4 R&D Systems Cat#314-BP CHIR R&D Systems Cat#4423 RA Sigma Cat#R2625 FGF2 R&D Systems Cat#233-FB/CF Growth/Differentiation Factor-11, BMP-11 Peprotech Cat#120-11 EDN3 American Peptide company Cat#88-5-10B AGN Tocris Cat#5758 GDNF Peprotech Cat#450-10 AA Sigma Cat#4034-100g SHH R&D Systems Cat#464-SH NGF Peprotech Cat#450-01 BDNF R&D Systems Cat#248-BDB SCF R&D Systems Cat#255-SC-MTO cAMP Sigma Cat#D0627 E8 medium Thermo Fisher Cat#A1517001 E6 medium Thermo Fisher Cat#A1516401 DMEM/F12 Thermo Fisher Cat#21331020 Neurobasal medium Gibco Cat#21103049 N2 Stem Cell Technologies Cat#07156 B27 Life Technologies Cat#17504044 L-glutamine Gibco Cat#25030-164 MEM non-essential amino acids (NEAA) Sigma Cat#M7145 4’,6-diamidino-2-phenylindole (DAPI) Invitrogen Cat#D1306 Critical commercial assays CytoSelect 24-Well Cell Invasion Assay, Basement Cell Biolabs Cat#CBA-110 iScript Reverse Transcription Supermix for RT-qPCR Biorad Cat#1708840 SsoFast EvaGreen Supermix Biorad Cat#1725201 NuPAGE 4-12% Bis-Tris Protein Gels, 1.5 mm, 15-wells Thermo Scientific Cat#NP0336BOX Trilogy Cell Marque Cat#920P-06 Deposited data RNA seq data This study GEO: GSE199439 ATAC seq data This study GEO: GSE199440 CUT and RUN data This study GEO: GSE199441 (Continued on next page) ll OPEN ACCESS Article e2 Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Human embryonic stem cell (hESC) lines H9 (WA-09) (Thomson et al., 1998)98 RRID:CVCL_9773 Human embryonic stem cell (hESC) lines H1 (WA-01) (Thomson et al., 1998)98 RRID:CVCL_9771 Human embryonic stem cell (hESC) lines HUES6 (Cowan et al., 2004)99 RRID:CVCL_B194 Human embryonic stem cell (hESC) lines MEL1 (Adewumi et al., 2007)100 N/A Induced pluripotent stem cell (iPSCs) lines 348.7, 706.3 and 864.3 Cornacchia et al.101 N/A H9 derived SOX10::GFP reporter line Chambers et al.16 N/A H9 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H1 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H9 derived mCherry reporter line This study N/A H9 derived GFP reporter line This study N/A Experimental models: Organisms/strains Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) JAX 005557 Mouse: B6.129S7-Ednrb tm1Ywa/FrykJ JAX 021933 Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ)Ednrb tm1Ywa/FrykJ This Study N/A Oligonucleotides Hs_SOX10_1_SG QuantiTect primer assay Qiagen QT00055405 Hs_FOXD3_1_SG QuantiTect Primer Assay Qiagen QT00221928 Hs_SOX2_1_SG QuantiTect Primer Assay Qiagen QT00237601 Hs_CDX2_1_SG QuantiTect primer assay Qiagen QT00037807 Hs_T_1_SG QuantiTect Primer Assay Qiagen QT00062314 Hs_GAPDH_1_SG QuantiTect Primer Assay Qiagen QT00079247 Hs_POU5F1_1_SG QuantiTect Primer Assay Qiagen QT00210840 Hs_NANOG_1_SG QuantiTect Primer Assay Qiagen QT01025850 Hs_WNT3A_1_SG QuantiTect Primer Assay Qiagen QT00220542 Hs_EDNRB_1_SG QuantiTect Primer Assay Qiagen QT00014343 All other primers are listed in Table S1 Qiagen and IDT N/A Software and algorithms FIJI Open source Schindelin et al.102 https://imagej.net/software/fiji Flow Jo FlowJo LLC https://www.flowjo.com DESeq2 Love et al.103 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Prism 9 GraphPad Software https://www.graphpad.com Biorender Biorender https://biorender.com Caseviewer 3dhistech https://www.3dhistech.com/ solutions/caseviewer/ Matlab R2014a Open source https://www.mathworks.com/ company/newsroom/mathworksannounces-release-2014a-of-thematlab-and-simulink-product-families.html ll OPEN ACCESSArticle
Protein Purification:Article Title: HDAC5 enhances IRF3 activation and is targeted for degradation by protein C6 from orthopoxviruses including Monkeypox virus and Variola virus.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-HDAC5 SANTA CRUZ Cat# Sc133106; RRID:AB_2116793 Mouse anti-a-tubulin SANTA CRUZ Cat# Sc-69970; RRID:AB_2303941 Mouse anti-HA BioLegend Cat# 901501; RRID:AB_2565006 Mouse anti-D8 Laboratory of Geoffrey L Smith Parkinson and Smith, 199455 Rabbit anti-FLAG Sigma-Aldrich Cat# F7425; RRID:AB_439687 Rabbit anti-phospho-IRF3 (Ser386) Cell Signaling Cat# 4947S; RRID:AB_823547 Rabbit anti-actin Sigma-Aldrich Cat# A2066; RRID:AB_476693 Rabbit anti-C6 Laboratory of Geoffrey L Smith Unterholzner et al., 201137 IRDye 800CW Goat anti-Mouse IgG LICOR Cat# 926-32210: RRID:AB_621842 IRDye 800CW Goat anti-Rabbit IgG LICOR Cat# 926-32211; RRID:AB_621843 IRDye 680RD Goat anti-Rabbit IgG LICOR Cat# 926-68071; RRID:AB_10956166 IRDye 680RD Goat anti-Mouse IgG LICOR Cat# 926-68070; RRID:AB_10956588 Alexa Fluor 546 Goat anti-Rabbit IgG (H + L) Invitrogen Cat# A-11035; RRID:AB_2534093 Alexa Fluor 488 Donkey anti-Mouse IgG (H + L) Invitrogen Cat# R37114; RRID:AB_2556542 Bacterial and virus strains RPXV strain Utrecht Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CPXV strain Brighton Red Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CPXV-E Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 CMLV strain CMS Laboratory of Geoffrey L Smith Alcamı́ et al., 199556 MPXV_CVR MRC-University of GlasgowCenter for Virus Research Zhao et al., 202313 Sendai Virus Cantell strain Steve Goodbourn, St George’s Hospital Medical School, University of London N/A Chemicals, peptides, and recombinant proteins 40, 6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) ThermoFisher D1306 Opti-MEMTM reduced serum medium ThermoFisher 31985070 TransIT-LT1 transfection reagent Mirus MIR 2306 TNF-a Peprotech 300-001A IL-1b Peprotech 200-01A IFN-a Peprotech 300-02AA IFN-g Peprotech 300–02 cOmpleteTM Protease Inhibitor Cocktail Roche 11697498001 phosphatase inhibitor PhosSTOPTM Roche 4906845001 ANTI-FLAG M2 Affinity Gel MERCK A2220 Anti-HA-Agarose MERCK A2095 Strep-Tactin XT 4Flow resin iba 2-5010-002 Glutathione Sepharose 4B GST-tagged protein purification resin Cytiva 17075605 MG132 Sigma-Aldrich SML1135 DMEM ThermoFisher 41966029 10 x MEM ThermoFisher 11430030 Opti-MEMTM I Reduced Serum Medium ThermoFisher 31985070 (Continued on next page) Cell Reports 43, 113788, March 26, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sodium Bicarbonate 7.5% solution ThermoFisher 25080094 L-Glutamine ThermoFisher 25030–081 FBS PAN Biotech UK P40-37500HI Penicillin-Streptomycin ThermoFisher 15140122 Puromycin (solution) InvivoGen ant-pr-1 Paraformaldehyde 16% Aqueous Solution, EM Grade Electron Microscopy Sciences 15711 Coelenterazine (Renilla Luciferase substrate) Nanolight Technology 303 D-Luciferine Nanolight Technology 306 Co-enzyme A Nanolight Technology 309 Fast SYBRTM Green Master Mix ThermoFisher 4385612 RNaseOUTTM Recombinant Ribonuclease Inhibitor ThermoFisher 10777019 SuperScriptTM III Reverse Transcriptase ThermoFisher 18080093 Oligo(dT)20 Primer InvitrogenTM ThermoFisher 18418020 dNTP ThermoFisher R0181 Passive Lysis 5X Buffer Promega E1941 Critical commercial assays Plasmid DNA sequencing SourceBioscience N/A Experimental models: Cell lines HeLa (human cervical adenocarcinoma epithelial cell line) ATCC CCL-2 H5KO1 Laboratory of Geoffrey L Smith Soday et al., 201912 H5KO2 Laboratory of Geoffrey L Smith Soday et al., 201912 HEK-293T (human embryo kidney epithelial cell line) ATCC CRL-11268 H5KO4 Laboratory of Geoffrey L Smith Soday et al., 201912 H5KO3 Laboratory of Geoffrey L Smith Soday et al., 201912 T-REx-293 Life Technologies R71007 HFFF Laboratory of Michael Weekes Soday et al., 201912
Invasion Assay:Article Title: Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat anti SOX10 Santa Cruz Cat#sc-17342; RRID:AB_2195374 Mouse anti SOX10 Santa Cruz Cat#sc-365692; RRID:AB_10844002 Mouse anti HOXC9 Abcam Cat#ab50839; RRID:AB_880494 Rabbit anti HOXD13 Abcam Cat#ab19866; RRID:AB_733004 Mouse anti Ki67 Dako Cat# M7240; RRID:AB_2142367 Mouse anti CDX2 BioGenex Cat#MU392A-5UC; RRID:AB_2650531 Goat anti Bra/T R&D Systems Cat#AF2085; RRID:AB_2200235 Rabbit anti SOX2 Cell signaling Tech Cat#35795; RRID:AB_2195767 PE conjugated Mouse Anti-Human CDX-2 BD Biosciences Cat#563428; RRID:AB_2738198) APC-conjugated Human/Mouse Bra/T R&D Systems Cat#IC2085A; RRID:AB_2891298 Alexa Fluor 488 Mouse anti-Sox2 Clone O30-678 BD Biosciences Cat#561593; RRID:AB_10894382 Rabbit anti SNAI2 Cell signaling Tech Cat#9585; RRID:AB_2239535 Rabbit anti TUJ1 Covance Cat#MMS-435P; RRID:AB_2313773 Chicken anti TUJ1 Abcam Cat#ab107216; RRID:AB_10899689 Mouse anti TUJ1 Biolegend Cat#801201; RRID:AB_2313773 Rabbit anti GABA Sigma Cat#A2052; RRID:AB_477652 Mouse anti TH Immunostar Cat#22941; RRID:AB_572268 Rabbit anti nNOS Millipore Cat#07-571; RRID:AB_11211970 Goat anti CHAT Millipore Cat#AB144P; RRID:AB_2079751 Rabbit anti 5’HT Sigma Cat#S5545; RRID:AB_477522 Rabbit anti SST Millipore Cat#mab354; RRID:AB_2255365 Rabbit anti DBH ImmunoStar Cat#22806; RRID:AB_572229 Rabbit ISL1 Developmental Studies Hybridoma Bank Cat#39.4D5; RRID:AB_2314683 Rabbit anti S100-beta Abcam Cat# ab52642; RRID:AB_882426 PE/Cy7 conjugated CD49D Biolegend Cat#304314; RRID:AB_10643278 APC conjugated CD49D Biolegend Cat#304308; RRID:AB_2130041 PE conjugated HNK1 Biolegend Cat#359611; RRID:AB_2562758 APC conjugated P75NTR Biolegend Cat#345107; RRID:AB_10639737 APC conjugated c-kit (CD117) eBioscience Cat#17-1179-42; RRID:AB_10596820 Chicken anti GFP Abcam Cat#ab13970; RRID:AB_300798 Rabbit anti RFP Rockland Cat#600-401-379; RRID:AB_2209751 Mouse anti Stem121 TaKaRa Cat#Y40410; RRID:AB_2801314 Mouse anti RET R&D systems Cat#MAB718-100; RRID:AB_2232594 Rabbit anti EDNRB Biorbyt Cat#orb37019; RRID:AB_10995764 Anti-rabbit IgG, HRP-linked Cell Signaling Tech Cat#7074S; RRID:AB_2099233 Rabbit anti LaminB1 Abcam Cat#ab16048; RRID:AB_443298 Human anti ANNA-1 Gift from Dr V. Lennon (King et al., 1999) Donkey anti-Human IgG H&L (AMCA) Jackson Immuno Cat# 709-155-149; RRID: AB_2340529 Donkey anti-Human Dylight 405 Jackson Immuno Cat# 709-475-149; RRID: AB_2340553 Donkey anti-goat IgG H&L (Alexa Fluor 488) Invitrogen Cat#A11055; RRID:AB_2534102 (Continued on next page) Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Donkey anti-mouse IgG H&L (Alexa Fluor 488) Invitrogen Cat# R37114; RRID:AB_2556542 Donkey anti-rabbit IgG H&L (Alexa Fluor 488) Invitrogen Cat#A21206; RRID:AB_2535792 Donkey anti-mouse IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A31570; RRID:AB_2536180 Donkey anti-rabbit IgG H&L (Alexa Fluor 568) Invitrogen Cat#A10042; RRID:AB_2534017 Donkey anti-goat IgG H&L (Alexa Fluor 568) Invitrogen Cat#A11057; RRID:AB_142581 Donkey anti-mouse IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31571; RRID:AB_162542 Donkey anti-rabbit IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31573; RRID:AB_2536183 Goat anti-chicken IgG H&L (Alexa Fluor 488) Thermo Fisher Cat#A11039; RRID:AB_142924 Goat anti-chicken IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A32932; RRID:AB_2762844 Chemicals, peptides, and recombinant proteins EDTA-free Protease Inhibitor Sigma Cat#11836170001 Y-27632 R&D Systems Cat#1524 SB431542 R&D Systems Cat#1614 BMP4 R&D Systems Cat#314-BP CHIR R&D Systems Cat#4423 RA Sigma Cat#R2625 FGF2 R&D Systems Cat#233-FB/CF Growth/Differentiation Factor-11, BMP-11 Peprotech Cat#120-11 EDN3 American Peptide company Cat#88-5-10B AGN Tocris Cat#5758 GDNF Peprotech Cat#450-10 AA Sigma Cat#4034-100g SHH R&D Systems Cat#464-SH NGF Peprotech Cat#450-01 BDNF R&D Systems Cat#248-BDB SCF R&D Systems Cat#255-SC-MTO cAMP Sigma Cat#D0627 E8 medium Thermo Fisher Cat#A1517001 E6 medium Thermo Fisher Cat#A1516401 DMEM/F12 Thermo Fisher Cat#21331020 Neurobasal medium Gibco Cat#21103049 N2 Stem Cell Technologies Cat#07156 B27 Life Technologies Cat#17504044 L-glutamine Gibco Cat#25030-164 MEM non-essential amino acids (NEAA) Sigma Cat#M7145 4’,6-diamidino-2-phenylindole (DAPI) Invitrogen Cat#D1306 Critical commercial assays CytoSelect 24-Well Cell Invasion Assay, Basement Cell Biolabs Cat#CBA-110 iScript Reverse Transcription Supermix for RT-qPCR Biorad Cat#1708840 SsoFast EvaGreen Supermix Biorad Cat#1725201 NuPAGE 4-12% Bis-Tris Protein Gels, 1.5 mm, 15-wells Thermo Scientific Cat#NP0336BOX Trilogy Cell Marque Cat#920P-06 Deposited data RNA seq data This study GEO: GSE199439 ATAC seq data This study GEO: GSE199440 CUT and RUN data This study GEO: GSE199441 (Continued on next page) ll OPEN ACCESS Article e2 Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Human embryonic stem cell (hESC) lines H9 (WA-09) (Thomson et al., 1998)98 RRID:CVCL_9773 Human embryonic stem cell (hESC) lines H1 (WA-01) (Thomson et al., 1998)98 RRID:CVCL_9771 Human embryonic stem cell (hESC) lines HUES6 (Cowan et al., 2004)99 RRID:CVCL_B194 Human embryonic stem cell (hESC) lines MEL1 (Adewumi et al., 2007)100 N/A Induced pluripotent stem cell (iPSCs) lines 348.7, 706.3 and 864.3 Cornacchia et al.101 N/A H9 derived SOX10::GFP reporter line Chambers et al.16 N/A H9 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H1 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H9 derived mCherry reporter line This study N/A H9 derived GFP reporter line This study N/A Experimental models: Organisms/strains Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) JAX 005557 Mouse: B6.129S7-Ednrb tm1Ywa/FrykJ JAX 021933 Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ)Ednrb tm1Ywa/FrykJ This Study N/A Oligonucleotides Hs_SOX10_1_SG QuantiTect primer assay Qiagen QT00055405 Hs_FOXD3_1_SG QuantiTect Primer Assay Qiagen QT00221928 Hs_SOX2_1_SG QuantiTect Primer Assay Qiagen QT00237601 Hs_CDX2_1_SG QuantiTect primer assay Qiagen QT00037807 Hs_T_1_SG QuantiTect Primer Assay Qiagen QT00062314 Hs_GAPDH_1_SG QuantiTect Primer Assay Qiagen QT00079247 Hs_POU5F1_1_SG QuantiTect Primer Assay Qiagen QT00210840 Hs_NANOG_1_SG QuantiTect Primer Assay Qiagen QT01025850 Hs_WNT3A_1_SG QuantiTect Primer Assay Qiagen QT00220542 Hs_EDNRB_1_SG QuantiTect Primer Assay Qiagen QT00014343 All other primers are listed in Table S1 Qiagen and IDT N/A Software and algorithms FIJI Open source Schindelin et al.102 https://imagej.net/software/fiji Flow Jo FlowJo LLC https://www.flowjo.com DESeq2 Love et al.103 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Prism 9 GraphPad Software https://www.graphpad.com Biorender Biorender https://biorender.com Caseviewer 3dhistech https://www.3dhistech.com/ solutions/caseviewer/ Matlab R2014a Open source https://www.mathworks.com/ company/newsroom/mathworksannounces-release-2014a-of-thematlab-and-simulink-product-families.html ll OPEN ACCESSArticle
Reverse Transcription:Article Title: Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat anti SOX10 Santa Cruz Cat#sc-17342; RRID:AB_2195374 Mouse anti SOX10 Santa Cruz Cat#sc-365692; RRID:AB_10844002 Mouse anti HOXC9 Abcam Cat#ab50839; RRID:AB_880494 Rabbit anti HOXD13 Abcam Cat#ab19866; RRID:AB_733004 Mouse anti Ki67 Dako Cat# M7240; RRID:AB_2142367 Mouse anti CDX2 BioGenex Cat#MU392A-5UC; RRID:AB_2650531 Goat anti Bra/T R&D Systems Cat#AF2085; RRID:AB_2200235 Rabbit anti SOX2 Cell signaling Tech Cat#35795; RRID:AB_2195767 PE conjugated Mouse Anti-Human CDX-2 BD Biosciences Cat#563428; RRID:AB_2738198) APC-conjugated Human/Mouse Bra/T R&D Systems Cat#IC2085A; RRID:AB_2891298 Alexa Fluor 488 Mouse anti-Sox2 Clone O30-678 BD Biosciences Cat#561593; RRID:AB_10894382 Rabbit anti SNAI2 Cell signaling Tech Cat#9585; RRID:AB_2239535 Rabbit anti TUJ1 Covance Cat#MMS-435P; RRID:AB_2313773 Chicken anti TUJ1 Abcam Cat#ab107216; RRID:AB_10899689 Mouse anti TUJ1 Biolegend Cat#801201; RRID:AB_2313773 Rabbit anti GABA Sigma Cat#A2052; RRID:AB_477652 Mouse anti TH Immunostar Cat#22941; RRID:AB_572268 Rabbit anti nNOS Millipore Cat#07-571; RRID:AB_11211970 Goat anti CHAT Millipore Cat#AB144P; RRID:AB_2079751 Rabbit anti 5’HT Sigma Cat#S5545; RRID:AB_477522 Rabbit anti SST Millipore Cat#mab354; RRID:AB_2255365 Rabbit anti DBH ImmunoStar Cat#22806; RRID:AB_572229 Rabbit ISL1 Developmental Studies Hybridoma Bank Cat#39.4D5; RRID:AB_2314683 Rabbit anti S100-beta Abcam Cat# ab52642; RRID:AB_882426 PE/Cy7 conjugated CD49D Biolegend Cat#304314; RRID:AB_10643278 APC conjugated CD49D Biolegend Cat#304308; RRID:AB_2130041 PE conjugated HNK1 Biolegend Cat#359611; RRID:AB_2562758 APC conjugated P75NTR Biolegend Cat#345107; RRID:AB_10639737 APC conjugated c-kit (CD117) eBioscience Cat#17-1179-42; RRID:AB_10596820 Chicken anti GFP Abcam Cat#ab13970; RRID:AB_300798 Rabbit anti RFP Rockland Cat#600-401-379; RRID:AB_2209751 Mouse anti Stem121 TaKaRa Cat#Y40410; RRID:AB_2801314 Mouse anti RET R&D systems Cat#MAB718-100; RRID:AB_2232594 Rabbit anti EDNRB Biorbyt Cat#orb37019; RRID:AB_10995764 Anti-rabbit IgG, HRP-linked Cell Signaling Tech Cat#7074S; RRID:AB_2099233 Rabbit anti LaminB1 Abcam Cat#ab16048; RRID:AB_443298 Human anti ANNA-1 Gift from Dr V. Lennon (King et al., 1999) Donkey anti-Human IgG H&L (AMCA) Jackson Immuno Cat# 709-155-149; RRID: AB_2340529 Donkey anti-Human Dylight 405 Jackson Immuno Cat# 709-475-149; RRID: AB_2340553 Donkey anti-goat IgG H&L (Alexa Fluor 488) Invitrogen Cat#A11055; RRID:AB_2534102 (Continued on next page) Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Donkey anti-mouse IgG H&L (Alexa Fluor 488) Invitrogen Cat# R37114; RRID:AB_2556542 Donkey anti-rabbit IgG H&L (Alexa Fluor 488) Invitrogen Cat#A21206; RRID:AB_2535792 Donkey anti-mouse IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A31570; RRID:AB_2536180 Donkey anti-rabbit IgG H&L (Alexa Fluor 568) Invitrogen Cat#A10042; RRID:AB_2534017 Donkey anti-goat IgG H&L (Alexa Fluor 568) Invitrogen Cat#A11057; RRID:AB_142581 Donkey anti-mouse IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31571; RRID:AB_162542 Donkey anti-rabbit IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31573; RRID:AB_2536183 Goat anti-chicken IgG H&L (Alexa Fluor 488) Thermo Fisher Cat#A11039; RRID:AB_142924 Goat anti-chicken IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A32932; RRID:AB_2762844 Chemicals, peptides, and recombinant proteins EDTA-free Protease Inhibitor Sigma Cat#11836170001 Y-27632 R&D Systems Cat#1524 SB431542 R&D Systems Cat#1614 BMP4 R&D Systems Cat#314-BP CHIR R&D Systems Cat#4423 RA Sigma Cat#R2625 FGF2 R&D Systems Cat#233-FB/CF Growth/Differentiation Factor-11, BMP-11 Peprotech Cat#120-11 EDN3 American Peptide company Cat#88-5-10B AGN Tocris Cat#5758 GDNF Peprotech Cat#450-10 AA Sigma Cat#4034-100g SHH R&D Systems Cat#464-SH NGF Peprotech Cat#450-01 BDNF R&D Systems Cat#248-BDB SCF R&D Systems Cat#255-SC-MTO cAMP Sigma Cat#D0627 E8 medium Thermo Fisher Cat#A1517001 E6 medium Thermo Fisher Cat#A1516401 DMEM/F12 Thermo Fisher Cat#21331020 Neurobasal medium Gibco Cat#21103049 N2 Stem Cell Technologies Cat#07156 B27 Life Technologies Cat#17504044 L-glutamine Gibco Cat#25030-164 MEM non-essential amino acids (NEAA) Sigma Cat#M7145 4’,6-diamidino-2-phenylindole (DAPI) Invitrogen Cat#D1306 Critical commercial assays CytoSelect 24-Well Cell Invasion Assay, Basement Cell Biolabs Cat#CBA-110 iScript Reverse Transcription Supermix for RT-qPCR Biorad Cat#1708840 SsoFast EvaGreen Supermix Biorad Cat#1725201 NuPAGE 4-12% Bis-Tris Protein Gels, 1.5 mm, 15-wells Thermo Scientific Cat#NP0336BOX Trilogy Cell Marque Cat#920P-06 Deposited data RNA seq data This study GEO: GSE199439 ATAC seq data This study GEO: GSE199440 CUT and RUN data This study GEO: GSE199441 (Continued on next page) ll OPEN ACCESS Article e2 Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Human embryonic stem cell (hESC) lines H9 (WA-09) (Thomson et al., 1998)98 RRID:CVCL_9773 Human embryonic stem cell (hESC) lines H1 (WA-01) (Thomson et al., 1998)98 RRID:CVCL_9771 Human embryonic stem cell (hESC) lines HUES6 (Cowan et al., 2004)99 RRID:CVCL_B194 Human embryonic stem cell (hESC) lines MEL1 (Adewumi et al., 2007)100 N/A Induced pluripotent stem cell (iPSCs) lines 348.7, 706.3 and 864.3 Cornacchia et al.101 N/A H9 derived SOX10::GFP reporter line Chambers et al.16 N/A H9 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H1 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H9 derived mCherry reporter line This study N/A H9 derived GFP reporter line This study N/A Experimental models: Organisms/strains Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) JAX 005557 Mouse: B6.129S7-Ednrb tm1Ywa/FrykJ JAX 021933 Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ)Ednrb tm1Ywa/FrykJ This Study N/A Oligonucleotides Hs_SOX10_1_SG QuantiTect primer assay Qiagen QT00055405 Hs_FOXD3_1_SG QuantiTect Primer Assay Qiagen QT00221928 Hs_SOX2_1_SG QuantiTect Primer Assay Qiagen QT00237601 Hs_CDX2_1_SG QuantiTect primer assay Qiagen QT00037807 Hs_T_1_SG QuantiTect Primer Assay Qiagen QT00062314 Hs_GAPDH_1_SG QuantiTect Primer Assay Qiagen QT00079247 Hs_POU5F1_1_SG QuantiTect Primer Assay Qiagen QT00210840 Hs_NANOG_1_SG QuantiTect Primer Assay Qiagen QT01025850 Hs_WNT3A_1_SG QuantiTect Primer Assay Qiagen QT00220542 Hs_EDNRB_1_SG QuantiTect Primer Assay Qiagen QT00014343 All other primers are listed in Table S1 Qiagen and IDT N/A Software and algorithms FIJI Open source Schindelin et al.102 https://imagej.net/software/fiji Flow Jo FlowJo LLC https://www.flowjo.com DESeq2 Love et al.103 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Prism 9 GraphPad Software https://www.graphpad.com Biorender Biorender https://biorender.com Caseviewer 3dhistech https://www.3dhistech.com/ solutions/caseviewer/ Matlab R2014a Open source https://www.mathworks.com/ company/newsroom/mathworksannounces-release-2014a-of-thematlab-and-simulink-product-families.html ll OPEN ACCESSArticle
Quantitative RT-PCR:Article Title: Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat anti SOX10 Santa Cruz Cat#sc-17342; RRID:AB_2195374 Mouse anti SOX10 Santa Cruz Cat#sc-365692; RRID:AB_10844002 Mouse anti HOXC9 Abcam Cat#ab50839; RRID:AB_880494 Rabbit anti HOXD13 Abcam Cat#ab19866; RRID:AB_733004 Mouse anti Ki67 Dako Cat# M7240; RRID:AB_2142367 Mouse anti CDX2 BioGenex Cat#MU392A-5UC; RRID:AB_2650531 Goat anti Bra/T R&D Systems Cat#AF2085; RRID:AB_2200235 Rabbit anti SOX2 Cell signaling Tech Cat#35795; RRID:AB_2195767 PE conjugated Mouse Anti-Human CDX-2 BD Biosciences Cat#563428; RRID:AB_2738198) APC-conjugated Human/Mouse Bra/T R&D Systems Cat#IC2085A; RRID:AB_2891298 Alexa Fluor 488 Mouse anti-Sox2 Clone O30-678 BD Biosciences Cat#561593; RRID:AB_10894382 Rabbit anti SNAI2 Cell signaling Tech Cat#9585; RRID:AB_2239535 Rabbit anti TUJ1 Covance Cat#MMS-435P; RRID:AB_2313773 Chicken anti TUJ1 Abcam Cat#ab107216; RRID:AB_10899689 Mouse anti TUJ1 Biolegend Cat#801201; RRID:AB_2313773 Rabbit anti GABA Sigma Cat#A2052; RRID:AB_477652 Mouse anti TH Immunostar Cat#22941; RRID:AB_572268 Rabbit anti nNOS Millipore Cat#07-571; RRID:AB_11211970 Goat anti CHAT Millipore Cat#AB144P; RRID:AB_2079751 Rabbit anti 5’HT Sigma Cat#S5545; RRID:AB_477522 Rabbit anti SST Millipore Cat#mab354; RRID:AB_2255365 Rabbit anti DBH ImmunoStar Cat#22806; RRID:AB_572229 Rabbit ISL1 Developmental Studies Hybridoma Bank Cat#39.4D5; RRID:AB_2314683 Rabbit anti S100-beta Abcam Cat# ab52642; RRID:AB_882426 PE/Cy7 conjugated CD49D Biolegend Cat#304314; RRID:AB_10643278 APC conjugated CD49D Biolegend Cat#304308; RRID:AB_2130041 PE conjugated HNK1 Biolegend Cat#359611; RRID:AB_2562758 APC conjugated P75NTR Biolegend Cat#345107; RRID:AB_10639737 APC conjugated c-kit (CD117) eBioscience Cat#17-1179-42; RRID:AB_10596820 Chicken anti GFP Abcam Cat#ab13970; RRID:AB_300798 Rabbit anti RFP Rockland Cat#600-401-379; RRID:AB_2209751 Mouse anti Stem121 TaKaRa Cat#Y40410; RRID:AB_2801314 Mouse anti RET R&D systems Cat#MAB718-100; RRID:AB_2232594 Rabbit anti EDNRB Biorbyt Cat#orb37019; RRID:AB_10995764 Anti-rabbit IgG, HRP-linked Cell Signaling Tech Cat#7074S; RRID:AB_2099233 Rabbit anti LaminB1 Abcam Cat#ab16048; RRID:AB_443298 Human anti ANNA-1 Gift from Dr V. Lennon (King et al., 1999) Donkey anti-Human IgG H&L (AMCA) Jackson Immuno Cat# 709-155-149; RRID: AB_2340529 Donkey anti-Human Dylight 405 Jackson Immuno Cat# 709-475-149; RRID: AB_2340553 Donkey anti-goat IgG H&L (Alexa Fluor 488) Invitrogen Cat#A11055; RRID:AB_2534102 (Continued on next page) Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Donkey anti-mouse IgG H&L (Alexa Fluor 488) Invitrogen Cat# R37114; RRID:AB_2556542 Donkey anti-rabbit IgG H&L (Alexa Fluor 488) Invitrogen Cat#A21206; RRID:AB_2535792 Donkey anti-mouse IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A31570; RRID:AB_2536180 Donkey anti-rabbit IgG H&L (Alexa Fluor 568) Invitrogen Cat#A10042; RRID:AB_2534017 Donkey anti-goat IgG H&L (Alexa Fluor 568) Invitrogen Cat#A11057; RRID:AB_142581 Donkey anti-mouse IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31571; RRID:AB_162542 Donkey anti-rabbit IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31573; RRID:AB_2536183 Goat anti-chicken IgG H&L (Alexa Fluor 488) Thermo Fisher Cat#A11039; RRID:AB_142924 Goat anti-chicken IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A32932; RRID:AB_2762844 Chemicals, peptides, and recombinant proteins EDTA-free Protease Inhibitor Sigma Cat#11836170001 Y-27632 R&D Systems Cat#1524 SB431542 R&D Systems Cat#1614 BMP4 R&D Systems Cat#314-BP CHIR R&D Systems Cat#4423 RA Sigma Cat#R2625 FGF2 R&D Systems Cat#233-FB/CF Growth/Differentiation Factor-11, BMP-11 Peprotech Cat#120-11 EDN3 American Peptide company Cat#88-5-10B AGN Tocris Cat#5758 GDNF Peprotech Cat#450-10 AA Sigma Cat#4034-100g SHH R&D Systems Cat#464-SH NGF Peprotech Cat#450-01 BDNF R&D Systems Cat#248-BDB SCF R&D Systems Cat#255-SC-MTO cAMP Sigma Cat#D0627 E8 medium Thermo Fisher Cat#A1517001 E6 medium Thermo Fisher Cat#A1516401 DMEM/F12 Thermo Fisher Cat#21331020 Neurobasal medium Gibco Cat#21103049 N2 Stem Cell Technologies Cat#07156 B27 Life Technologies Cat#17504044 L-glutamine Gibco Cat#25030-164 MEM non-essential amino acids (NEAA) Sigma Cat#M7145 4’,6-diamidino-2-phenylindole (DAPI) Invitrogen Cat#D1306 Critical commercial assays CytoSelect 24-Well Cell Invasion Assay, Basement Cell Biolabs Cat#CBA-110 iScript Reverse Transcription Supermix for RT-qPCR Biorad Cat#1708840 SsoFast EvaGreen Supermix Biorad Cat#1725201 NuPAGE 4-12% Bis-Tris Protein Gels, 1.5 mm, 15-wells Thermo Scientific Cat#NP0336BOX Trilogy Cell Marque Cat#920P-06 Deposited data RNA seq data This study GEO: GSE199439 ATAC seq data This study GEO: GSE199440 CUT and RUN data This study GEO: GSE199441 (Continued on next page) ll OPEN ACCESS Article e2 Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Human embryonic stem cell (hESC) lines H9 (WA-09) (Thomson et al., 1998)98 RRID:CVCL_9773 Human embryonic stem cell (hESC) lines H1 (WA-01) (Thomson et al., 1998)98 RRID:CVCL_9771 Human embryonic stem cell (hESC) lines HUES6 (Cowan et al., 2004)99 RRID:CVCL_B194 Human embryonic stem cell (hESC) lines MEL1 (Adewumi et al., 2007)100 N/A Induced pluripotent stem cell (iPSCs) lines 348.7, 706.3 and 864.3 Cornacchia et al.101 N/A H9 derived SOX10::GFP reporter line Chambers et al.16 N/A H9 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H1 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H9 derived mCherry reporter line This study N/A H9 derived GFP reporter line This study N/A Experimental models: Organisms/strains Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) JAX 005557 Mouse: B6.129S7-Ednrb tm1Ywa/FrykJ JAX 021933 Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ)Ednrb tm1Ywa/FrykJ This Study N/A Oligonucleotides Hs_SOX10_1_SG QuantiTect primer assay Qiagen QT00055405 Hs_FOXD3_1_SG QuantiTect Primer Assay Qiagen QT00221928 Hs_SOX2_1_SG QuantiTect Primer Assay Qiagen QT00237601 Hs_CDX2_1_SG QuantiTect primer assay Qiagen QT00037807 Hs_T_1_SG QuantiTect Primer Assay Qiagen QT00062314 Hs_GAPDH_1_SG QuantiTect Primer Assay Qiagen QT00079247 Hs_POU5F1_1_SG QuantiTect Primer Assay Qiagen QT00210840 Hs_NANOG_1_SG QuantiTect Primer Assay Qiagen QT01025850 Hs_WNT3A_1_SG QuantiTect Primer Assay Qiagen QT00220542 Hs_EDNRB_1_SG QuantiTect Primer Assay Qiagen QT00014343 All other primers are listed in Table S1 Qiagen and IDT N/A Software and algorithms FIJI Open source Schindelin et al.102 https://imagej.net/software/fiji Flow Jo FlowJo LLC https://www.flowjo.com DESeq2 Love et al.103 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Prism 9 GraphPad Software https://www.graphpad.com Biorender Biorender https://biorender.com Caseviewer 3dhistech https://www.3dhistech.com/ solutions/caseviewer/ Matlab R2014a Open source https://www.mathworks.com/ company/newsroom/mathworksannounces-release-2014a-of-thematlab-and-simulink-product-families.html ll OPEN ACCESSArticle
RNA Sequencing:Article Title: Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat anti SOX10 Santa Cruz Cat#sc-17342; RRID:AB_2195374 Mouse anti SOX10 Santa Cruz Cat#sc-365692; RRID:AB_10844002 Mouse anti HOXC9 Abcam Cat#ab50839; RRID:AB_880494 Rabbit anti HOXD13 Abcam Cat#ab19866; RRID:AB_733004 Mouse anti Ki67 Dako Cat# M7240; RRID:AB_2142367 Mouse anti CDX2 BioGenex Cat#MU392A-5UC; RRID:AB_2650531 Goat anti Bra/T R&D Systems Cat#AF2085; RRID:AB_2200235 Rabbit anti SOX2 Cell signaling Tech Cat#35795; RRID:AB_2195767 PE conjugated Mouse Anti-Human CDX-2 BD Biosciences Cat#563428; RRID:AB_2738198) APC-conjugated Human/Mouse Bra/T R&D Systems Cat#IC2085A; RRID:AB_2891298 Alexa Fluor 488 Mouse anti-Sox2 Clone O30-678 BD Biosciences Cat#561593; RRID:AB_10894382 Rabbit anti SNAI2 Cell signaling Tech Cat#9585; RRID:AB_2239535 Rabbit anti TUJ1 Covance Cat#MMS-435P; RRID:AB_2313773 Chicken anti TUJ1 Abcam Cat#ab107216; RRID:AB_10899689 Mouse anti TUJ1 Biolegend Cat#801201; RRID:AB_2313773 Rabbit anti GABA Sigma Cat#A2052; RRID:AB_477652 Mouse anti TH Immunostar Cat#22941; RRID:AB_572268 Rabbit anti nNOS Millipore Cat#07-571; RRID:AB_11211970 Goat anti CHAT Millipore Cat#AB144P; RRID:AB_2079751 Rabbit anti 5’HT Sigma Cat#S5545; RRID:AB_477522 Rabbit anti SST Millipore Cat#mab354; RRID:AB_2255365 Rabbit anti DBH ImmunoStar Cat#22806; RRID:AB_572229 Rabbit ISL1 Developmental Studies Hybridoma Bank Cat#39.4D5; RRID:AB_2314683 Rabbit anti S100-beta Abcam Cat# ab52642; RRID:AB_882426 PE/Cy7 conjugated CD49D Biolegend Cat#304314; RRID:AB_10643278 APC conjugated CD49D Biolegend Cat#304308; RRID:AB_2130041 PE conjugated HNK1 Biolegend Cat#359611; RRID:AB_2562758 APC conjugated P75NTR Biolegend Cat#345107; RRID:AB_10639737 APC conjugated c-kit (CD117) eBioscience Cat#17-1179-42; RRID:AB_10596820 Chicken anti GFP Abcam Cat#ab13970; RRID:AB_300798 Rabbit anti RFP Rockland Cat#600-401-379; RRID:AB_2209751 Mouse anti Stem121 TaKaRa Cat#Y40410; RRID:AB_2801314 Mouse anti RET R&D systems Cat#MAB718-100; RRID:AB_2232594 Rabbit anti EDNRB Biorbyt Cat#orb37019; RRID:AB_10995764 Anti-rabbit IgG, HRP-linked Cell Signaling Tech Cat#7074S; RRID:AB_2099233 Rabbit anti LaminB1 Abcam Cat#ab16048; RRID:AB_443298 Human anti ANNA-1 Gift from Dr V. Lennon (King et al., 1999) Donkey anti-Human IgG H&L (AMCA) Jackson Immuno Cat# 709-155-149; RRID: AB_2340529 Donkey anti-Human Dylight 405 Jackson Immuno Cat# 709-475-149; RRID: AB_2340553 Donkey anti-goat IgG H&L (Alexa Fluor 488) Invitrogen Cat#A11055; RRID:AB_2534102 (Continued on next page) Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Donkey anti-mouse IgG H&L (Alexa Fluor 488) Invitrogen Cat# R37114; RRID:AB_2556542 Donkey anti-rabbit IgG H&L (Alexa Fluor 488) Invitrogen Cat#A21206; RRID:AB_2535792 Donkey anti-mouse IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A31570; RRID:AB_2536180 Donkey anti-rabbit IgG H&L (Alexa Fluor 568) Invitrogen Cat#A10042; RRID:AB_2534017 Donkey anti-goat IgG H&L (Alexa Fluor 568) Invitrogen Cat#A11057; RRID:AB_142581 Donkey anti-mouse IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31571; RRID:AB_162542 Donkey anti-rabbit IgG H&L (Alexa Fluor 647) Thermo Fisher Cat#A31573; RRID:AB_2536183 Goat anti-chicken IgG H&L (Alexa Fluor 488) Thermo Fisher Cat#A11039; RRID:AB_142924 Goat anti-chicken IgG H&L (Alexa Fluor 555) Thermo Fisher Cat#A32932; RRID:AB_2762844 Chemicals, peptides, and recombinant proteins EDTA-free Protease Inhibitor Sigma Cat#11836170001 Y-27632 R&D Systems Cat#1524 SB431542 R&D Systems Cat#1614 BMP4 R&D Systems Cat#314-BP CHIR R&D Systems Cat#4423 RA Sigma Cat#R2625 FGF2 R&D Systems Cat#233-FB/CF Growth/Differentiation Factor-11, BMP-11 Peprotech Cat#120-11 EDN3 American Peptide company Cat#88-5-10B AGN Tocris Cat#5758 GDNF Peprotech Cat#450-10 AA Sigma Cat#4034-100g SHH R&D Systems Cat#464-SH NGF Peprotech Cat#450-01 BDNF R&D Systems Cat#248-BDB SCF R&D Systems Cat#255-SC-MTO cAMP Sigma Cat#D0627 E8 medium Thermo Fisher Cat#A1517001 E6 medium Thermo Fisher Cat#A1516401 DMEM/F12 Thermo Fisher Cat#21331020 Neurobasal medium Gibco Cat#21103049 N2 Stem Cell Technologies Cat#07156 B27 Life Technologies Cat#17504044 L-glutamine Gibco Cat#25030-164 MEM non-essential amino acids (NEAA) Sigma Cat#M7145 4’,6-diamidino-2-phenylindole (DAPI) Invitrogen Cat#D1306 Critical commercial assays CytoSelect 24-Well Cell Invasion Assay, Basement Cell Biolabs Cat#CBA-110 iScript Reverse Transcription Supermix for RT-qPCR Biorad Cat#1708840 SsoFast EvaGreen Supermix Biorad Cat#1725201 NuPAGE 4-12% Bis-Tris Protein Gels, 1.5 mm, 15-wells Thermo Scientific Cat#NP0336BOX Trilogy Cell Marque Cat#920P-06 Deposited data RNA seq data This study GEO: GSE199439 ATAC seq data This study GEO: GSE199440 CUT and RUN data This study GEO: GSE199441 (Continued on next page) ll OPEN ACCESS Article e2 Cell Stem Cell 30, 264–282.e1–e9, March 2, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Human embryonic stem cell (hESC) lines H9 (WA-09) (Thomson et al., 1998)98 RRID:CVCL_9773 Human embryonic stem cell (hESC) lines H1 (WA-01) (Thomson et al., 1998)98 RRID:CVCL_9771 Human embryonic stem cell (hESC) lines HUES6 (Cowan et al., 2004)99 RRID:CVCL_B194 Human embryonic stem cell (hESC) lines MEL1 (Adewumi et al., 2007)100 N/A Induced pluripotent stem cell (iPSCs) lines 348.7, 706.3 and 864.3 Cornacchia et al.101 N/A H9 derived SOX10::GFP reporter line Chambers et al.16 N/A H9 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H1 derived SOX2::H2B-Tomato/ T::H2B-GFP dual reporter line This study N/A H9 derived mCherry reporter line This study N/A H9 derived GFP reporter line This study N/A Experimental models: Organisms/strains Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) JAX 005557 Mouse: B6.129S7-Ednrb tm1Ywa/FrykJ JAX 021933 Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ)Ednrb tm1Ywa/FrykJ This Study N/A Oligonucleotides Hs_SOX10_1_SG QuantiTect primer assay Qiagen QT00055405 Hs_FOXD3_1_SG QuantiTect Primer Assay Qiagen QT00221928 Hs_SOX2_1_SG QuantiTect Primer Assay Qiagen QT00237601 Hs_CDX2_1_SG QuantiTect primer assay Qiagen QT00037807 Hs_T_1_SG QuantiTect Primer Assay Qiagen QT00062314 Hs_GAPDH_1_SG QuantiTect Primer Assay Qiagen QT00079247 Hs_POU5F1_1_SG QuantiTect Primer Assay Qiagen QT00210840 Hs_NANOG_1_SG QuantiTect Primer Assay Qiagen QT01025850 Hs_WNT3A_1_SG QuantiTect Primer Assay Qiagen QT00220542 Hs_EDNRB_1_SG QuantiTect Primer Assay Qiagen QT00014343 All other primers are listed in Table S1 Qiagen and IDT N/A Software and algorithms FIJI Open source Schindelin et al.102 https://imagej.net/software/fiji Flow Jo FlowJo LLC https://www.flowjo.com DESeq2 Love et al.103 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Prism 9 GraphPad Software https://www.graphpad.com Biorender Biorender https://biorender.com Caseviewer 3dhistech https://www.3dhistech.com/ solutions/caseviewer/ Matlab R2014a Open source https://www.mathworks.com/ company/newsroom/mathworksannounces-release-2014a-of-thematlab-and-simulink-product-families.html ll OPEN ACCESSArticle
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