Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Purified anti-Pax-6 antibody, Poly19013 | BioLegend | 901301; RRID: AB_2565003 |
| Anti-β-Tubulin III Antibody, mouse monoclonal, 2G10 (TUJ1) | Sigma-Aldrich | T8578; RRID: AB_1841228 |
| PRKG1 polyclonal antibody | Proteintech | 21646-1-AP; RRID: AB_2878897 |
| Anti-Phosphorylated Vimentin (Ser55) mAb | MBL Life Science | D076-3; RRID: AB_592963 |
| Anti-Nestin monoclonal antibody, clone 10C2 (mouse) | Millipore | MAB5326; RRID: AB_2251134 |
| Occludin Monoclonal Antibody (OC-3F10) | Invitrogen | 33-1500; RRID: AB_2533101 |
| ZO-1 Polyclonal antibody | Proteintech | 21773-1-AP; RRID:AB_10733242 |
| Cleaved Caspase-3 (Asp175) Antibody | Cell Signaling Technology | 9661 |
| Anti-Iba1 antibody [EPR16589] - Mouse IgG1 (Chimeric) | Abcam | Ab283319; RRID:AB_2924797 |
| ATP6 polyclonal antibody | Immunological Science | AB-83828 |
| Anti-GAPDH antibody [6C5] | Abcam | Ab8245; RRID:AB_2107448 |
| Anti-β-actin Antibody, mouse monoclonal | Abcam | ab8226; RRID: AB_30637 |
| PRKG1 antibody, rabbit polyclonal | Cell Signaling | 3248 |
| mTOR-Ser2448 antibody, rabbit polyclonal | Cell Signaling | 2971; RRID: AB_330970 |
| p-AMPKa-Thr174 antibody, rabbit polyclonal | Cell Signaling | 2535 |
| p-PGC1a-Ser571 antibody, rabbit polyclonal | Biotechne | AF6650; RRID: AB_10890391 |
| p-4EBP-1 antibody, rabbit polyclonal | Cell Signaling | 2855 |
| PGC1a antibody, rabbit polyclonal | Novus Bio | NBP1-04676; RRID: AB_1522118 |
| AMPKa antibody, rabbit polyclonal | Cell Signaling | 2532; RRID: AB_330331 |
| 4EBP-1 antibody, rabbit polyclonal | Cell Signaling | 9644 |
| mTOR antibody, rabbit polyclonal | Cell Signaling | 2972; RRID: AB_330978 |
| GAPDH antibody, rabbit polyclonal | Abcam | ab181602; RRID: AB_2630358 |
| Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 488 | Invitrogen | A-21206; RRID: AB_2535792 |
| Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 633 | Invitrogen | A-21050 |
| Goat Anti-Mouse IgG (H + L)-HRP Conjugate | BioRad | 1706516; RRID: AB_2921252 |
| Anti-Rabbit IgG (H+L), HRP Conjugate | Promega | W4018 |
| Anti-Mitofilin antibody [EPR8749] (MIC60) | Abcam | Ab137057; RRID: AB_3676556 |
| Anti-ACTN2 Antibody (alpha-actinin) | Sigma-Aldrich | A7811; RRID: AB_476766 |
| ATP5B | Sigma-Aldrich | HPA001528 |
| NDUFA9 | Invitrogen | 459100 |
| SDH-B | Abcam | ab14714 |
| UQCRSF1 | Abcam | ab14746 |
| DCX antibody | Cell signaling | 4604 |
| Chemicals, peptides, and recombinant proteins | ||
| StemMACS™ iPS-Brew XF, human | Miltenyi Biotec | 130-104-368 |
| mTeSR™ Plus | STEMCELL Technologies | 100-0276 |
| KnockOut-DMEM | Gibco | 10829-018 |
| KnockOut™ serum replacement | Gibco | 10828-028 |
| DMEM/F/12 | Gibco | 31330038 |
| DMEM glucose-free | Gibco | 11966025 |
| Glasgow-MEM | Gibco | 11710035 |
| Neurobasal A-Medium glucose-free | Gibco | A2477501 |
| Neurobasal | Gibco | 21103-049 |
| Non-essential amino acids (MEM-NEAA) 100X | Gibco | 11140-050 |
| Sodium Pyruvate | Gibco | 11360070 |
| B-27 with Vitamin A (50×) | Gibco | 17504044 |
| B-27 without Vitamin A (50×) | Gibco | 12587010 |
| N2 Supplement (100×) | Gibco | 17502-048 |
| DPBS, no calcium, co magnesium | Gibco | 14190144 |
| Accutase | Thermo Fisher Scientific; Sigma-Aldrich | A1110501; A6964-100ML |
| UltraPure™ 0,5 M EDTA | Invitrogen | 11568896 |
| ROCK inhibitor Y-27632 | Enzo Life Sciences | ALX-270-333-M005 |
| MycoZap Plus-CL | Lonza | VZA-2012 |
| Pen/Strep | Gibco | 15140122 |
| GlutaMAX | Gibco | 35050061 |
| L-glutamine | Gibco | 25030081 |
| FBS | Gibco | 10270106 |
| Matrigel, Growth Factor reduced | Corning | 356231 |
| Geltrex™ Reduced-Growth Factor Basement-Membrane Matrix, LDEV-free, stem-cell qualified | Gibco | A1413302 |
| Laminin | Sigma Aldrich | L2020 |
| Chemically Defined Lipid Concentrate | Gibco | 11905031 |
| Anti-Adherence Rinsing Solution | STEMCELL Technologies | 07010 |
| Purmorphamine | Sigma Aldrich; Miltenyi Biotec | 540220; 130-104-465 |
| CHIR99021 | Sigma Aldrich | SML1046 |
| Dorsomorphine | Sigma-Aldrich | P5499 |
| SB431542 | Miltenyi Biotec | 130-105-336 |
| GDNF | R & D System | 212-GD-010 |
| BDNF | MACS Miltenyi | 130-096-811 |
| EGF | R & D System | 236-EG-200 |
| FGF2 | R & D System | 3718-FB-100 |
| Db-cAMP | StemCell Technologies | 73886 |
| Recombinant Human NT-3 | Peprotech / Biozol | 450-03 |
| FGF8-a | R&D systems | 4745-F8-050 |
| TGFbeta 3 | StemCell Technologies | 78156 |
| (+)-sodium L-ascorbate (Vitamin C) | Sigma Aldrich | A4034 |
| Human Recombinant Activin A | StemCell Technologies | 78001.1 |
| cis-4,7,10,13,16,19-Docosahexaensäure (DHA) | Sigma-Aldrich | D2534 |
| WNT antagonist IWR1 | EMD Millipore Corp | 681669 |
| Heparin | Merck | 375095 |
| 2-mercaptoethanol | Gibco | 31350010 |
| Doxycycline hydrochloride (DOX) | Sigma Aldrich | D3072 |
| DMSO | Sigma-Aldrich | D2650-100ML |
| SuperSignal West Pico PLUS Chemiluminescent Substrate | Thermo Fisher Scientific | |
| 16% Paraformaldehyde (PFA) | Thermo Fisher Scientific | 28906 |
| Hoechst 33342 | Invitrogen | H3570 |
| Donkey serum | Merck Millipore | S30 |
| Triton-X-100 | Sigma-Aldrich | 93443; 93426 |
| Tween 20 | Sigma-Aldrich | P1504 |
| abberior STAR 635 (STAR RED) | Abberior | ST635-1002 |
| DAPI | Sigma-Aldrich | D9542 |
| MitoProbe™ TMRM Assay Kit for Flow Cytometry | Invitrogen | M20036 |
| Incucyte dye red | Sartorius | 4717 |
| Calcein AM Viability Dye® | Invitrogen™ | C1430 |
| MitoSpy™ Orange | BioLegend | 424803 |
| Sildenafil-d3 | CDN isotopes | D-6366 |
| HpaII | NEB | R0171 |
| StuI | NEB | R0187 |
| XbaI | NEB | R0145 |
| FCCP | Biozol | SEL-S8276 |
| Antimycin A | Sigma-Aldrich | A8674 |
| Oligomycin | Sigma-Aldrich | O4876-5MG |
| CCCP | Sigma-Aldrich | 555602 |
| Propidium iodide | Invitrogen | P1304MP |
| Sildenafil citrate | Sigma | SML3033 |
| KT5823 | Biomol | LKT-K7602.100 |
| 8-Br-cGMP | Sigma-Aldrich | 203820 |
| Sildenafil | Selleckchem | S468402 and S468403 |
| d3-sildenafil | CDN Isotopes | |
| Mowiol with 0.1 % 1,4-Diazabicyclo[2.2.2]octan (DABCO) | Carl Roth | 0713.1 |
| LB Agar | Sigma | L2897 |
| SuperFrost Plus glass slides | VWR | 631-0447 |
| Pro-Long Glass Antifade Mountant | Invitrogen | P36984 |
| oligo d(T)18 primers | Thermo Fisher Scientific | SO132 |
| dNTP mix | Thermo Fisher Scientific | 10319879 |
| Rnase OUT Recombinant Ribonuclease Inhibitor | Invitrogen | 10777-019 |
| M-MLV Reverse Transcriptase (200 U/μL) | Invitrogen | 28025021 |
| Human Endothelial-SFM | Gibco | 11111044 |
| hFGF | Peprotech | 100-18B |
| Retinoic acid | StemCell Technologies | 72262 |
| Collagen IV | Sigma-Aldrich | c5533-5MG |
| Fibronectin | Gibco/ThermoFisher | 33016015 |
| Transwell membranes | Greiner | 662641 |
| Sodium fluorescein | Sigma-Aldrich | F6377-100G |
| Diazepam | Sigma-Aldrich | D0899-100MG |
| Atenolol | Sigma-Aldrich | A7655-1G |
| LysC | Roche | 11420429001 |
| Low melting temperature agar | Gibco | 5517UB |
| Hank’s Balanced Salt Solution (HBSS) | Sigma | H9394 |
| Oregon Green 488 BAPTA-1 AM | Invitrogen | O6807 |
| Deoxy-D-glucose | Apollo Scientific; Sigma-Aldrich | OR3900T; D8375-1g |
| RNase H | Epicentre/ LGC Biosearch Technologies | E0038-5D1 |
| Acetonitrile | Biosolve, ULC/MS-CC/SFC | 001204101BS |
| Trypan Blue Solution | Sigma-Aldrich | T8154 |
| Medium 199 | Life Technologies/ Thermo Fisher Scientific | 22340020 |
| Trypsin | Sigma-Aldrich/Merck | T4799 |
| Medium 199 Modified | Sigma-Aldrich/Merck | M3769 |
| Penicillin-G | Sigma-Aldrich/Merck | P7794 |
| Streptomycin sulfate | Sigma-Aldrich/Merck | S1277 |
| Kanamycin | Sigma-Aldrich/Merck | K1377 |
| FBS Premium plus GI | Life Technologies/ Thermo Fisher Scientific | 01190048M |
| Sodium bicarbonate | Sigma-Aldrich/Merck | S5761 |
| ITS premix - Universal Culture Supplement | Corning | 354351 |
| Hormones (FSH, LH) | Meriofert | 75IU |
| Long-EGF | Gibco/ ThermoFisher Scientific | AF-100-15 |
| bFGF | Gibco/ ThermoFisher Scientific | 100-18B |
| Hyaluronidase | Sigma-Aldrich/Merck | H3506 |
| Protease from Streptomyces griseus | Sigma-Aldrich/Merck | P8811 |
| Cytochalasin B | Sigma-Aldrich/Merck | C6762 |
| D-Mannitolo | Sigma-Aldrich/Merck | M1902 |
| Phytohemagglutinin (Lectin) | Sigma-Aldrich/Merck | L-1668 |
| Cycloheximide | Sigma-Aldrich/Merck | C7698 |
| CaCl2 | Sigma-Aldrich/Merck | C7902 |
| Altrenogest | MSD Animal Health | |
| PGF2-alpha | Fatro S.P.A. | |
| Sodium dithionite | Merck | 1.06505 |
| Cytocrome C | Sigma-Aldrich | C2037 |
| n-dodecil β-D-maltoside | Sigma-Aldrich | D4641 |
| Bovine Serum Albumin Fraction V | Roche Diagnostics | 10735086001 |
| Acetil coenzima A | Merck | 10101907001 |
| Oxaloacetic acid | Sigma-Aldrich | O4126 |
| DTNB (5,5′-dithiobis(2-nitrobenzoic acid): | Sigma-Aldrich | D8130 |
| Critical commercial assays | ||
| Lactate-Assay kit | Sigma Aldrich | MAK064 |
| CellTiter-Glo® Luminescent Cell Viability assay | Promega | G7571 |
| Rnase-Free Dnase Set (50) (250) | Qiagen | 79254 |
| RNeasy Mini Kit (50) | Qiagen | 74104 |
| First Strand cDNA Synthesis Kit | Thermo Scientific | K1612 |
| PDS - Papain Dissociation System | Cell Systems | LK003150 |
| Nucleo-Spin Tissue kit | Macherey-Nagel | 740952.50 |
| SYBRTM Green PCR Master Mix | Applied Biosystems | 4364344 |
| Bicinchoninic Acid (BCA) protein assay kit | Thermo Scientific | 23252 |
| NucleoSpin RNA Plus kit | Macherey-Nagel | 740984.50 |
| RNA Cleanup XP beads | Agencourt/Beckman coulter | A66514 |
| TURBO DNase rigorous treatment | Invitrogen | AM1907 |
| TruSeq Stranded Total LT Sample Prep Kit | Illumina | N/A |
| Chromium Single Cell 3' (vNext) Reagent Kit | 10X Genomics | N/A |
| ViaLightTM Plus Kit | Lonza | LT07-221 |
| CyQUANT Cell Proliferation Assay | Invitrogen | C7026 |
| jetPRIME transfection | Polyplus | 101000027 |
| Deposited data | ||
| Bulk RNAses NPCs dataset | This paper | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE292178 GSE292178 Token: kviluouivdmlnmn |
| Bulk RNAseq organoids dataset | This paper | Reviewer only link: https://dataview.ncbi.nlm.nih.gov/object/PRJNA1248577?reviewer=h0vj30jbkanvobfmhpb90nq1nn SRA BioProject ID: PRJNA1248577 Token: ixobgyempjkrzsr |
| Codes | This paper | https://github.com/tpentim/Leigh_Sildenafil_Organoids |
| snRNAseq organoids dataset | This paper | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE293573 GSE293573 Token: ixobgyempjkrzsr |
| Proteomics NPCs dataset | This paper | ProteomeXchange http://proteomecentral.proteomexchange.org PXD059519 Token: Edp2AxzzRPDZ |
| Metabolomics NPCs dataset | This paper | MassIVE: ftp://MSV000097182@massive.ucsd.edu Submission ID: MSV000097182; Account: curemils; Account password: leighpass, |
| Experimental models: Cell lines | ||
| Human iPSC: BIHi043-A | Helmholtz Zentrum München (HMGU) | PMID 29396371 |
| Human iPSC: HHUUKDi009-A | Heinrich-Heine-Universität Düsseldorf (HHUUKD) | PMID 28132834 |
| Human iPSC: CRMi003-A | RUCDR Infinite Biologics | PMID 36459969 |
| Human iPSC: BIHi269-B | Berlin Institute of Health (BIH) | PMID 36669241 |
| Human iPSC: HVRDi004-B | Synthego | PMID 36459969 |
| Human iPSC: IUFi004-A | Cell Applications | PMID 38217996 |
| Human iPSC: BIHi266-A | Berlin Institute of Health (BIH) | PMID 36669241 |
| Human iPSC: WISCi004-B | WiCell | PMID 18029452 |
| Human iPSC: UMGi014-C | University Medical Center Goettingen (UMG) | PMID 33905594 |
| Human iPSC: HHUi001-A | Universitätsklinikum Düsseldorf (HHU) | PMID 28132834 |
| Human iPSC: HHUi002-A | Universitätsklinikum Düsseldorf (HHU) | PMID 28132834 |
| Human iPSC: HHUi003-C | Universitätsklinikum Düsseldorf (HHU) | PMID 36137325 |
| Human iPSC: MDCi008-A | Max Delbrück Center Berlin Buch (MDC) | PMID 35279592 |
| Human iPSC: MDCi009-A | Max Delbrück Center Berlin Buch (MDC) | PMID 35279592 |
| Human iPSC: MDCi010-A | Max Delbrück Center Berlin Buch (MDC) | PMID 35279592 |
| Human iPSC: BIHi267-B | Berlin Institute of Health (BIH) | PMID 36669241 |
| Human iPSC: C1_mut2 | Max Delbrück Center Berlin Buch (MDC) | PMID 33771987 |
| Human iPSC: E9 | Max Delbrück Center Berlin Buch (MDC) | PMID 36741056 |
| Human iPSC: F3 | Max Delbrück Center Berlin Buch (MDC) | PMID 36741056 |
| Experimental models: Organisms/strains | ||
| Germline Ndufs4 KO, C57/BL6/J background | Reference | PMID: 20534480 |
| SURF1 KO pig, Large White background | Avantea | PMID: 29601977 |
| Oligonucleotides | ||
| ATP6: Forward: CAACCGACTAATCACCACCC, Reverse: GTTGAGCCGTAGATGCCGTC | IDT | N/A |
| ATP6_2: Forward: AACCAATAGCCCTGGCCGTA, Reverse: AGGGCTCATGGTAGGGGTAAA | IDT | N/A |
| GAPDH: Forward: CTGGTAAAGTGGATATTGTTGCCAT, Reverse: TGGAATCATATTGGAACATGTAAACC | IDT | N/A |
| OAZ1: Forward: GGATCCTCAATAGCCACTGC, Reverse: TACAGCAGTGGAGGGAGACC | IDT | N/A |
| NESTIN: Forward: TTCCCTCAGCTTTCAGGAC, Reverse: GAGCAAAGATCCAAGACGC | IDT | N/A |
| PAX6: Forward: CCAGGGCAATCGGTGGTAGT Reverse: ACGGGCACTCCCGCTTATAC | IDT | N/A |
| CTIP: Forward: TGGGTGCCTGCTATGACAAG, Reverse: GATGCCTTTCGTGGGTGAGA | IDT | N/A |
| SOX2: Forward: GTATCAGGAGTTGTCAAGGCAGAG, Reverse: TCCTAGTCTTAAAGAGGCAGCAAAC | IDT | N/A |
| PRKG1: Forward: ACAACTGTACCCGGACAGCGA, Reverse: TCCTCTTGCACCCTGCCTGAT | IDT | N/A |
| OCT4: Forward: GTGGAGGAAGCTGACAACAA, Reverse: ATTCTCCAGGTTGCCTCTCA | IDT | N/A |
| NANOG: Forward: CCTGTGATTTGTGGGCCTG, Reverse: GACAGTCTCCGTGTGAGGCAT | IDT | N/A |
| DBX1: Forward: CTGGGCCTGAAAGACTCGC, Reverse: CCGCTAGACAGGAGTTCGC | ||
| Myco-f1: Forward: CGCCTGAGTAGTACGTTCGC | IDT | N/A |
| Myco-f2: Forward: GCGGTGTGTACAAACCCCGA | IDT | N/A |
| Myco-f3: Forward: TGCCTGAGTAGTCACTTCGC | IDT | N/A |
| Myco-f4: Forward: CGCCTGGGTAGTACATTCGC | IDT | N/A |
| Myco-f5: Forward: CGCCTGAGTAGTAGTCTCGC | IDT | N/A |
| Myco-f6: Forward: TGCCTGGGTAGTACATTCGC | IDT | N/A |
| Myco-r1: Reverse: GCGGTGTGTACAAGACCCGA | IDT | N/A |
| Silencer™ select siRNA PRKG1: Forward: GGAUAGAGGUUCGUUUGAATT, Reverse: UUCAAACGAACCUCUAUCCCT | Ambion | 4392420; assay ID s11131 |
| Silencer ™ select SiRNA negative Control No. 1 | Ambion | 4390843 |
| Software and algorithms | ||
| CellProfiler | https://cellprofiler.org/ 127 | v.4.2.5. |
| GraphPad Prism | GraphPad Software | v.5.01 |
| Adobe Illustrator | Adobe | v.29.6 |
| Cell Ranger | 10x Genomics | v.7.10 |
| Ultivo triple-quadrupole mass spectrometer | Agilent Technologies | https://www.agilent.com/en/product/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-instruments/ultivo-lcms |
| MassHunter Software | Agilent Technologies | N/A |
| MToolBox | v.1 https://github.com/mitoNGS/MToolBox128 | |
| ImageJ | Fiji129 | v1.54g http://imagej.org |
| IGV viewer | IGV | v2.163 https://igv.org |
| CELLCYTE Studio | Cytena | N/A |
| ZEN Microscopy Software | Zeiss | N/A |
| ND-1000 software | Thermo Fisher Scientific | v3.8.1 |
| CFX96 software | Bio-Rad | N/A |
| Image Lab software | Bio-Rad Laboratories | v.6.1 |
| GeneMapper ID | Applied Biosystems | v.3.2.1 |
| ND-1000 software | Thermo Fisher Scientific | v.3.8.1 |
| Xcalibur software | Thermo Fischer Scientific | N/A |
| TraceFinder 5.1 software | Thermo Fischer Scientific | N/A |
| Columbus software | Revvity | v.2.9.0 |
| FlowJo software | FlowJo | v.7.6 |
| OriginPro Software | OriginLab Corporation | N/A |
| nfcore/rnaseq | https://zenodo.org/records/7998767 | v.3.12.0 |
| Trim Galore! | Babraham Bioinformatics https://zenodo.org/records/7598955 | v.0.6.10 |
| STAR aligner | https://github.com/alexdobin/star/releases | v. 2.7.10a |
| Salmon | https://github.com/COMBINE-lab/salmon/releases | v.1.10.1 |
| DESeq2 package | https://github.com/thelovelab/DESeq2 | v. 1.40.2 and v.7.5.1 |
| ClusterProfiler | DOI: 10.18129/B9.bioc.clusterProfiler | v4.8.3 and v4.10.0 |
| org.Hs.eg.db | DOI: 10.18129/B9.bioc.org.Hs.eg.db | v.3.18.0 |
| ggplot2 | https://github.com/tidyverse/ggplot2/releases/tag/v3.5.1 | v.3.5.1 |
| R | The R Project for Statistical Computing | v. 4.4.1 |
| Seurat | https://satijalab.org/seurat/ version: https://github.com/satijalab/seurat/releases | v. 5.1.0 |
| AUCell package | DOI: 10.18129/B9.bioc.AUCell | v. 1.26.0 |
| MsigDB package | https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.5.1/ | v 7.5.1 |
| dplyr | https://cran.r-project.org/web/packages/dplyr/index.html | v. 1.1.4 |
| Dia-NN | https://github.com/vdemichev/DiaNN/releases/tag/1.8.1 | v1.8.1 |
| OmicsNet platform | https://www.omicsnet.ca/ | v.2.0 |
| CytoNCA plugin in Cytoscape | N/A | v.3.10.2 |
| KEGG database | GenomeNet | Release 112.0 |
| IGV viewer | https://igv.org/doc/desktop/ | v2.163 |
| Vevo 2100 analysis software | FUJIFILM VisualSonics | v.1.5 |
| NIS-Elements Advanced Research | Nikon | v.3.2 |
| EZ-C1 Silver | Nikon | v.3.91 |
| MATLAB 2023b | MathWorks | https://de.mathworks.com/products/new_products/release2023b.html |
| IncuCyte Live-Cell Analysis System® | Sartorius | N/A |
| Other | ||
| CytoSmart Cell Counter | Greiner Bio-One | 6749 |
| Orbital Shaker Heidolph Unimax 1010 | Heidolph | 543-12310-00 |
| Operetta® CLS™ | Revvity | HH16000020 |
| 96-well Cell Culture Microplate, PS, F-Bottom, black TC, μCLEAR, 96-well black, clear bottom | Greiner Bio-One | 655090 |
| 96-well Cell Culture Microplate, SCREENSTAR | Greiner | 655866 |
| BIOFLOAT 96 well plate 4PCS | FaCellitate GmbH | F202003 |
| μ-Plate 96 Well Square | Ibidi | 89626 |
| DMS1000 microscope | Leica | N/A |
| Eclipse Ts2 | Nikon | Inverted Microscope |
| ZEISS Axio Observer Apotome 3 | Zeiss | ZEISS Apotome 3: Optical sectioning in widefield fluorescence microscopy |
| Vibratome Microm HM 650 V | Thermo Fisher Scientific | 920120 |
| Ultivo triple-quadrupole mass spectrometer | Agilent Technologies | G6465BA |
| EnSight multimode plate reader | Revvity | N/A |
| Cellcyte X | Cytena | CELLCYTE X™ - Live Cell Imager And Analyzer ∣ CYTENA |
| INFINITY platform | Abberior Instruments | INFINITY - @abberior.rocks |
| Vevo 2700 VisualSonics System | FUJIFILM VisualSonics | N/A |
| Promethion | Sable Systems International | Promethion Core Metabolic and Behavioral Phenotyping Systems |
| Infinite M1000 Pro | TECAN | Tecan ∣ Thermo Fisher Scientific - DE |
| Confocal laser scanning microscope C1 | Nikon Mikroskope Solutions | Nikon's Digital Eclipse C1 Microscope System Delivers High Resolution Confocal Images at Sensible Price ∣ News ∣ Nikon Instruments Inc. |
| Mastercycler X50s | Eppendorf | 6311000010 |
| CFX96™ Real-Time System qPCR machine | Bio-Rad | CFX96 Touch Real-Time PCR Detection System ∣ Bio-Rad |
| ChemiDoc MP Imaging system | Bio-Rad | ChemiDoc MP Imaging System ∣ Bio-Rad |
| Low-attachment U-bottom 96-well plates | Corning | 3474 |
| AggreWell | STEMCELL Technologies | 34815 |
| NovaSeq 6000 system | Illumina | NovaSeq 6000 System ∣ Powerful sequencing with scalable throughput |
| Dionex Ultimate 3000 | Thermo Scientific | UltiMate 3000 HPLC and UHPLC Systems |
| timsTOF SCP mass spectrometer | Bruker Daltonics | timsTOF SCP ∣ Bruker |
| SeQuant ZIC-pHILIC | Merck | 1.50462 |
| LSR-Fortessa X-20 | Becton Dickinson | LSRFortessa™ X-20 ∣ Benchtop Flow Cytometer |
| 384-well black-wall, clear-bottom plates | Revvity | 6007460 |
| Multidrop liquid dispenser | Thermo Fisher Scientific | https://www.thermofisher.com/de/de/home/life-science/lab-equipment/microplate-instruments/multidrop-dispensers.html |
| Rotating incubator Cytomat | Thermo Electron | N/A |
| Echo 550 | LabCyte | N/A |
| Janus MDT | Revvity | YJLM001 |
| Victor Multiple Plate Reader Spectrophotometer | Revvity | HH35000500 |
| Millicell-CM inserts | Millipore | Millicell® Cell Culture Inserts - Zellkulturplatten-Einsätze |
| Eclipse FN-1 | Nikon | ECLIPSE FN1 ∣ Upright Microscopes ∣ Microscope Products ∣ Nikon Instruments Inc. |
| Eclipse 90i | Nikon | upright widefield microscope |
| FLASH 4.0 LT camera | Hamamatsu Photonics | N/A |
| NanoDrop 2000 | Thermo Fisher Scientific | N/A |
| Nanodrop Spectrophotometer ND1000 | peQlab | N/A |
| Aurora Ultimate column | IonOpticks, | N/A |
| H-ESI source probe | Thermo Fisher Scientific | N/A |
| SeQuant ZIC-pHILIC colum | Merck | N/A |
| MSMLS-1EA library | Merck | N/A |
| 1290 Infinity II HPLC | Agilent Technologies | https://www.agilent.com/en/product/liquid-chromatography/hplc-systems/gpc-sec-solutions/1290-infinity-ii-gpc-sec-system |
| Poroshell 120 EC-C18 column | Agilent Technologies | N/A |
| 3,500 Series Genetic Analyzer | Applied Biosystems | RRID:SCR_021901 |
| Seahorse XFe24 Analyzer | Agilent Technologies | |
| Incucyte | Sartorius | |
| Thermal camera | Dongguan Xintai Instrument Co., Ltd, | #HT-18 |
| Chemiluminscent Western Blot imager | Azure byosistem | Azure 300 |