Recombinant:
Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Article Title: Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis
Article Snippet: .. Hydrogen peroxide 30% Science Supply Australia Cat# HA154/500ML Sodium citrate tribasic dihydrate Sigma Aldrich Cat# S4641 Jo urn al Pr e-p roo f UltraPureTM Ethylenediaminetetraacetic Acid, Disodium Salt, Dihydrate (Na2EDTA.2H2O) Thermo Fisher Scientific Cat# 15576028 Liquid 3, 3-diaminobenzidine (DAB)+ 2-component system Agilent Technologies Australia Cat# K346811-2 Normal goat serum Thermo Fisher Scientific Cat# 31872 TritonTM X-100 Sigma Aldrich Cat# X100-100ML DMEM-F12 Thermo Fisher Scientific Cat# 11320033 L-glutamine Thermo Fisher Scientific Cat# A2916801 Fetal Bovine Serum, heat inactivated Thermo Fisher Scientific Cat# 10100147 Deoxyribonuclease I (DNase I) Worthington Biochemical corporation Cat# LS002140 Trypsin (2.5%) Thermo Fisher Scientific Cat# 15090-046 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 HEPES Thermo Fisher Scientific Cat# 15630080 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 RNAsecureTM RNase Inactivation reagent Thermo Fisher Scientific Cat# AM7006 Critical commercial assays ReliaPrep RNA Tissue Miniprep System - Fibrous Tissue protocol Promega Cat# Z6112 High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat# 4368814 AllPrep DNA/RNA/Protein Mini kit Qiagen Cat# 80004 TapeStation D1K ScreenTape assay Agilent Cat# 5067-5363, 5067- 5361 Stranded Total RNA Prep kit with Ribo-Zero Plus Illumina Cat# 20040529 MycoAlert® Mycoplasma Detection Kit Lonza Cat# LT07-318 GenePrint® 10 System Promega Cat# B9510 TruSeq RNA Library Preparation Kit v2 Illumina Cat# RS-122-2001, RS122-2002 Deposited data RNA-seq data This paper GSE306906 Experimental models: Cell lines KM12 Camps et al.43 SW48 ATCC CCL-231 RKO ATCC CRL-2577 LIM1215 Cell Bank Australia CBA-1215 Co115 Carrel et al.44 Vaco5 McBain et al.45 Jo urn al Pr -pr oo f Experimental models: Organisms/strains Mouse: FVB BrafV637E/+ Dankort et al.46 Jackson Stock Number: 017837 Mouse: C57bl/6 VillinCreERT2 el Marjou et al.37 Jackson Stock Number: 020282 Mouse: C57bl/6 Fosl1lox/lox Eferl et al.38 N/A Mouse: C57bl/6 Col1a1tet-O-Fosl1; Rosa26LSL-rtTA Hasenfuss et al.29 N/A Oligonucleotides Primers for real-time quantitative PCR See Table S1 for full sequences N/A Recombinant DNA Software and algorithms Aperio ImageScope software v12.0.1.5027 Leica Biosystems https://www.leicabiosyste ms.com/en-au/digitalpathology/manage/aperio -imagescope/ HALO software version 3.4 Indica Labs, USA https://learn.indicalab.co m/ GraphPad Prism v8.0 GraphPad Software https://www.graphpad.co m/ STAR Dobin et al.39 https://github.com/alexdo bin/STAR. .. R R Project for Statistical Computing https://www.r-project.org/ GSEA v4.1.0 Subramanian et al.40 https://www.gseamsigdb.org Other ViiATM 7 Real Time PCR system Applied Biosystems Cat# 4453534 Leica Biosystems RM2245 Leica Biosystems https://www.leicabiosyste ms.com/en-au/histologyequipment/microtomes/lei ca-rm2245/ EprediaTM SuperFrostTM Plus Adhesion Control Microscope Slide Fisher Scientific Cat# 22-042-941 Jo urn al Pr e-p roo f MasterCycler EP Thermal Cycler Eppendorf https://www.gmiinc.com/product/eppendo rf-mastercycler-epthermal-cycler-range/ Aperio AT2 Slide Scanner Leica Biosystems N/A NovaSeq 6000 System Illumina https://sapac.illumina.com /systems/sequencingplatforms/novaseq.html Jo urn al Pr e-p roo f
Single Cell:
Sequencing:
Bicinchoninic Acid Protein Assay:
Article Title: Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chloroform Millipore Sigma Cat#1.02444; CAS: 67-66-3 Potassium Chloride Thermo Fisher Scientific Cat#BP366; CAS: 7447-40-7 Cis-10-Heptadecenoic Acid Millipore Sigma Cat#H8896; CAS: 29743-97-3 n-Hexane Millipore Sigma Cat#1.03701; CAS: 110-54-3 Methyl Acetate Millipore Sigma Cat#186325; CAS: 79-20-9 Acetonitrile, Optima LC/MS Grade Thermo Fisher Scientific Cat#A955: CAS: 75-05-8 Potassium Hydroxide Millipore Sigma Cat#484016; CAS: 1310-58-3 Formic Acid Millipore Sigma Cat#FX0440; CAS: 64-18-6 2,3,4,5,6-Pentafluorobenzyl Bromide Millipore Sigma Cat#90257; CAS: 1765-40-8 N,N-Diisopropylethylamine Millipore Sigma Cat#D125806; CAS: 7087-68-5 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Scientific Cat#78440 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34096 PowerUp SYBR Green Master Mix Thermo Fisher Scientific Cat#A25741 2,2-Diphenyl-1-picrylhydrazyl Millipore Sigma Cat#D9132; CAS: 1898-66-4 C11 BODIPY 581/591 Thermo Fisher Scientific Cat#D3861 40,6-Diamidino-2-phenylindole Invitrogen Cat#D1306 Lipofectamine 2000 Invitrogen Cat#11668027 SYTOX Green Nucleic Acid Stain Invitrogen Cat#S7020 Trypan Blue Bio-Rad Cat#1450021 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Quick-DNA Miniprep Plus Kit Zymo Research Cat#D4068 ZymoPURE II Plasmid Midiprep Kit Zymo Research Cat#D4200-A QIAprep Spin Miniprep Kit Qiagen Cat#27104 iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat#1725035 Deposited data Raw unprocessed fatty acid and lipidomics mass spectrometry data This paper MassIVE: MSV000095863; https://massive. ucsd.edu/ProteoSAFe/dataset.jsp? accession=MSV000095863 Uncropped Western blot images This paper Mendeley Data: https://doi.org/10.17632/ 95wwrptr59.1 Experimental models: Cell lines Human: A549 ATCC Cat#CCL-185 Human: HeLa ATCC Cat#CCL-2 Human: Panc1 ATCC Cat#CRL-1469 Human: H2199 ATCC Cat#CRL-5803 Human: MIA PaCa-2 ATCC Cat#CRL-1420 Human: 293T ATCC Cat#CRL-3216 Human: A549 sgNTC This paper N/A Human: A549 sgATGL #3.1 This paper N/A Human: A549 sgATGL #5.1 This paper N/A Human: A549 sgFADS2 #1.1 This paper N/A Human: A549 sgAGPS #1.1 This paper N/A Human: A549 sgAGPS #4.1 This paper N/A Oligonucleotides See Table S1 N/A N/A (Continued on next page) Cell Chemical Biology 32, 1–15.e1–e6, February 20, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Ran et al.52 Addgene Plasmid #48138 Software and algorithms Microsoft Excel 16.87 Microsoft Corporation https://www.microsoft.com/en-us/ microsoft-365/excel R 4.3.1 The R Project https://www.r-project.org/ Prism 10.2.3 GraphPad https://www.graphpad.com/features FlowJo 10.10.0 Becton Dickinson https://www.flowjo.com/ LipidSearch 5.0 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/multi-omics-dataanalysis/lipid-search-software.html El-Maven 0.12 Agrawal et al.46 https://github.com/ElucidataInc/ElMaven Skyline 23.1.0.455 Adams et al.48 https://skyline.ms/project/home/software/ Skyline/begin.view IsoCorrectoR Heinrich et al.49 https://www.bioconductor.org/packages/ release/bioc/html/IsoCorrectoR.html CRISPResso2 Clement et al.53 http://crispresso2.pinellolab.org/ submission
Lysis:
Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Article Title: Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis
Article Snippet: .. Hydrogen peroxide 30% Science Supply Australia Cat# HA154/500ML Sodium citrate tribasic dihydrate Sigma Aldrich Cat# S4641 Jo urn al Pr e-p roo f UltraPureTM Ethylenediaminetetraacetic Acid, Disodium Salt, Dihydrate (Na2EDTA.2H2O) Thermo Fisher Scientific Cat# 15576028 Liquid 3, 3-diaminobenzidine (DAB)+ 2-component system Agilent Technologies Australia Cat# K346811-2 Normal goat serum Thermo Fisher Scientific Cat# 31872 TritonTM X-100 Sigma Aldrich Cat# X100-100ML DMEM-F12 Thermo Fisher Scientific Cat# 11320033 L-glutamine Thermo Fisher Scientific Cat# A2916801 Fetal Bovine Serum, heat inactivated Thermo Fisher Scientific Cat# 10100147 Deoxyribonuclease I (DNase I) Worthington Biochemical corporation Cat# LS002140 Trypsin (2.5%) Thermo Fisher Scientific Cat# 15090-046 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 HEPES Thermo Fisher Scientific Cat# 15630080 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 RNAsecureTM RNase Inactivation reagent Thermo Fisher Scientific Cat# AM7006 Critical commercial assays ReliaPrep RNA Tissue Miniprep System - Fibrous Tissue protocol Promega Cat# Z6112 High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat# 4368814 AllPrep DNA/RNA/Protein Mini kit Qiagen Cat# 80004 TapeStation D1K ScreenTape assay Agilent Cat# 5067-5363, 5067- 5361 Stranded Total RNA Prep kit with Ribo-Zero Plus Illumina Cat# 20040529 MycoAlert® Mycoplasma Detection Kit Lonza Cat# LT07-318 GenePrint® 10 System Promega Cat# B9510 TruSeq RNA Library Preparation Kit v2 Illumina Cat# RS-122-2001, RS122-2002 Deposited data RNA-seq data This paper GSE306906 Experimental models: Cell lines KM12 Camps et al.43 SW48 ATCC CCL-231 RKO ATCC CRL-2577 LIM1215 Cell Bank Australia CBA-1215 Co115 Carrel et al.44 Vaco5 McBain et al.45 Jo urn al Pr -pr oo f Experimental models: Organisms/strains Mouse: FVB BrafV637E/+ Dankort et al.46 Jackson Stock Number: 017837 Mouse: C57bl/6 VillinCreERT2 el Marjou et al.37 Jackson Stock Number: 020282 Mouse: C57bl/6 Fosl1lox/lox Eferl et al.38 N/A Mouse: C57bl/6 Col1a1tet-O-Fosl1; Rosa26LSL-rtTA Hasenfuss et al.29 N/A Oligonucleotides Primers for real-time quantitative PCR See Table S1 for full sequences N/A Recombinant DNA Software and algorithms Aperio ImageScope software v12.0.1.5027 Leica Biosystems https://www.leicabiosyste ms.com/en-au/digitalpathology/manage/aperio -imagescope/ HALO software version 3.4 Indica Labs, USA https://learn.indicalab.co m/ GraphPad Prism v8.0 GraphPad Software https://www.graphpad.co m/ STAR Dobin et al.39 https://github.com/alexdo bin/STAR. .. R R Project for Statistical Computing https://www.r-project.org/ GSEA v4.1.0 Subramanian et al.40 https://www.gseamsigdb.org Other ViiATM 7 Real Time PCR system Applied Biosystems Cat# 4453534 Leica Biosystems RM2245 Leica Biosystems https://www.leicabiosyste ms.com/en-au/histologyequipment/microtomes/lei ca-rm2245/ EprediaTM SuperFrostTM Plus Adhesion Control Microscope Slide Fisher Scientific Cat# 22-042-941 Jo urn al Pr e-p roo f MasterCycler EP Thermal Cycler Eppendorf https://www.gmiinc.com/product/eppendo rf-mastercycler-epthermal-cycler-range/ Aperio AT2 Slide Scanner Leica Biosystems N/A NovaSeq 6000 System Illumina https://sapac.illumina.com /systems/sequencingplatforms/novaseq.html Jo urn al Pr e-p roo f
Article Title: Generation and characterization of a chronic in vitro model to study the early stage of metabolic dysfunction-associated steatotic liver disease (MASLD).
Article Snippet: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic and progressive liver disease with an increasing global burden that starts with an early stage of simple steatosis (MASL) which frequently progresses to liver cirrhosis and hepatocellular carcinoma (HCC).. Despite its widespread occurrence, the MASL or steatotic stage, characterized by excessive fat accumulation in the liver and considered reversible and benign, has not been extensively studied.. To study MASL effectively, it is imperative to have a clinically relevant model system that focuses solely on steatosis, in a progressive and time-dependent manner, recapitulating molecular changes associated with human disease.
Article Title: Single extracellular vesicle detection assay identifies membrane-associated α-synuclein as an early-stage biomarker in Parkinson's disease.
Article Snippet: Software and algorithms AutoCAD Autodesk https://www.autodesk.com/products/ autocad/overview?term=1-YEAR; RRID:SCR_021072 NIS-Elements Nikon https://www.nikoninstruments.com/ Products/Software; RRID:SCR_014329 Fiji ImageJ GNU General Public License https://ImageJ.net/software/fiji; RRID: SCR_002285 CODI ONI https://alto.codi.bio/ GraphPad Prism GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 Biorender Biorender www.biorender.com; RRID:SCR_018361 Other mTeSRTM1 Stem Cell Technologies Cat# 85857 Versene solution Thermo Fisher Scientific Cat# 15040066 GeltrexTM LDEV-free reduced growth factor basement membrane matrix Thermo Fisher Scientific Cat# A1413202 DMEM - high glucose Sigma Cat# D5671 Fetal Bovine Serum (FBS) Sigma Cat# F7524 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 (Continued on next page) e2 Cell Reports Medicine 6, 101999, March 18, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER GlutaMAXTM Supplement Thermo Fisher Scientific Cat# 35050061 Antibiotic-Antimycotic (100X) Thermo Fisher Scientific Cat# 15240062 TrypLETM Express Enzyme (1X), phenol red Thermo Fisher Scientific Cat# 12605036 HaltTM protease and phosphatase inhibitor cocktail Thermo Fisher Scientific Cat# 78444 Encapsulated superparamagnetic microspheres polymer-COOH (Glacial Blue) Bangs Laboratories Cat# MEGB002 Encapsulated superparamagnetic microspheres polymer-COOH (Flash Red) Bangs Laboratories Cat# MEFR002 Bovine serum albumin (BSA) Sigma Cat# A7030 EZ-LinkTM Micro Sulfo-NHS-LC-Biotinylation Kit Thermo Fisher Scientific Cat# 21935 SU-8 3025 Permanent negative epoxy photoresist Kayaku Cat# SU-8 3025 SYLGARDTM 184 Silicone Elastomer Kit Dow-Corning Cat# PDMS184 RIPA lysis and extraction buffer Thermo Fisher Scientific Cat# 89901 Amersham ECL prime western blotting detection reagent Cytiva Cat# RPN2232 HBSS Thermo Fisher Scientific Cat# 88284 Alexa Fluor 647Conjugation Kit (Fast) - Lightning-Link Abcam Cat# 269823 Alexa Fluor 488 Conjugation Kit (Fast) - Lightning-Link Abcam Cat# 236553 NEBuilder HiFi DNA Assembly Master Mix New England Biolabs Cat# E2621S OPEN ACCESS ..
Article Title: Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chloroform Millipore Sigma Cat#1.02444; CAS: 67-66-3 Potassium Chloride Thermo Fisher Scientific Cat#BP366; CAS: 7447-40-7 Cis-10-Heptadecenoic Acid Millipore Sigma Cat#H8896; CAS: 29743-97-3 n-Hexane Millipore Sigma Cat#1.03701; CAS: 110-54-3 Methyl Acetate Millipore Sigma Cat#186325; CAS: 79-20-9 Acetonitrile, Optima LC/MS Grade Thermo Fisher Scientific Cat#A955: CAS: 75-05-8 Potassium Hydroxide Millipore Sigma Cat#484016; CAS: 1310-58-3 Formic Acid Millipore Sigma Cat#FX0440; CAS: 64-18-6 2,3,4,5,6-Pentafluorobenzyl Bromide Millipore Sigma Cat#90257; CAS: 1765-40-8 N,N-Diisopropylethylamine Millipore Sigma Cat#D125806; CAS: 7087-68-5 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Scientific Cat#78440 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34096 PowerUp SYBR Green Master Mix Thermo Fisher Scientific Cat#A25741 2,2-Diphenyl-1-picrylhydrazyl Millipore Sigma Cat#D9132; CAS: 1898-66-4 C11 BODIPY 581/591 Thermo Fisher Scientific Cat#D3861 40,6-Diamidino-2-phenylindole Invitrogen Cat#D1306 Lipofectamine 2000 Invitrogen Cat#11668027 SYTOX Green Nucleic Acid Stain Invitrogen Cat#S7020 Trypan Blue Bio-Rad Cat#1450021 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Quick-DNA Miniprep Plus Kit Zymo Research Cat#D4068 ZymoPURE II Plasmid Midiprep Kit Zymo Research Cat#D4200-A QIAprep Spin Miniprep Kit Qiagen Cat#27104 iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat#1725035 Deposited data Raw unprocessed fatty acid and lipidomics mass spectrometry data This paper MassIVE: MSV000095863; https://massive. ucsd.edu/ProteoSAFe/dataset.jsp? accession=MSV000095863 Uncropped Western blot images This paper Mendeley Data: https://doi.org/10.17632/ 95wwrptr59.1 Experimental models: Cell lines Human: A549 ATCC Cat#CCL-185 Human: HeLa ATCC Cat#CCL-2 Human: Panc1 ATCC Cat#CRL-1469 Human: H2199 ATCC Cat#CRL-5803 Human: MIA PaCa-2 ATCC Cat#CRL-1420 Human: 293T ATCC Cat#CRL-3216 Human: A549 sgNTC This paper N/A Human: A549 sgATGL #3.1 This paper N/A Human: A549 sgATGL #5.1 This paper N/A Human: A549 sgFADS2 #1.1 This paper N/A Human: A549 sgAGPS #1.1 This paper N/A Human: A549 sgAGPS #4.1 This paper N/A Oligonucleotides See Table S1 N/A N/A (Continued on next page) Cell Chemical Biology 32, 1–15.e1–e6, February 20, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Ran et al.52 Addgene Plasmid #48138 Software and algorithms Microsoft Excel 16.87 Microsoft Corporation https://www.microsoft.com/en-us/ microsoft-365/excel R 4.3.1 The R Project https://www.r-project.org/ Prism 10.2.3 GraphPad https://www.graphpad.com/features FlowJo 10.10.0 Becton Dickinson https://www.flowjo.com/ LipidSearch 5.0 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/multi-omics-dataanalysis/lipid-search-software.html El-Maven 0.12 Agrawal et al.46 https://github.com/ElucidataInc/ElMaven Skyline 23.1.0.455 Adams et al.48 https://skyline.ms/project/home/software/ Skyline/begin.view IsoCorrectoR Heinrich et al.49 https://www.bioconductor.org/packages/ release/bioc/html/IsoCorrectoR.html CRISPResso2 Clement et al.53 http://crispresso2.pinellolab.org/ submission
Magnetic Cell Separation:
Blocking Assay:
Extraction:
Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Article Title: Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis
Article Snippet: .. Hydrogen peroxide 30% Science Supply Australia Cat# HA154/500ML Sodium citrate tribasic dihydrate Sigma Aldrich Cat# S4641 Jo urn al Pr e-p roo f UltraPureTM Ethylenediaminetetraacetic Acid, Disodium Salt, Dihydrate (Na2EDTA.2H2O) Thermo Fisher Scientific Cat# 15576028 Liquid 3, 3-diaminobenzidine (DAB)+ 2-component system Agilent Technologies Australia Cat# K346811-2 Normal goat serum Thermo Fisher Scientific Cat# 31872 TritonTM X-100 Sigma Aldrich Cat# X100-100ML DMEM-F12 Thermo Fisher Scientific Cat# 11320033 L-glutamine Thermo Fisher Scientific Cat# A2916801 Fetal Bovine Serum, heat inactivated Thermo Fisher Scientific Cat# 10100147 Deoxyribonuclease I (DNase I) Worthington Biochemical corporation Cat# LS002140 Trypsin (2.5%) Thermo Fisher Scientific Cat# 15090-046 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 HEPES Thermo Fisher Scientific Cat# 15630080 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 RNAsecureTM RNase Inactivation reagent Thermo Fisher Scientific Cat# AM7006 Critical commercial assays ReliaPrep RNA Tissue Miniprep System - Fibrous Tissue protocol Promega Cat# Z6112 High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat# 4368814 AllPrep DNA/RNA/Protein Mini kit Qiagen Cat# 80004 TapeStation D1K ScreenTape assay Agilent Cat# 5067-5363, 5067- 5361 Stranded Total RNA Prep kit with Ribo-Zero Plus Illumina Cat# 20040529 MycoAlert® Mycoplasma Detection Kit Lonza Cat# LT07-318 GenePrint® 10 System Promega Cat# B9510 TruSeq RNA Library Preparation Kit v2 Illumina Cat# RS-122-2001, RS122-2002 Deposited data RNA-seq data This paper GSE306906 Experimental models: Cell lines KM12 Camps et al.43 SW48 ATCC CCL-231 RKO ATCC CRL-2577 LIM1215 Cell Bank Australia CBA-1215 Co115 Carrel et al.44 Vaco5 McBain et al.45 Jo urn al Pr -pr oo f Experimental models: Organisms/strains Mouse: FVB BrafV637E/+ Dankort et al.46 Jackson Stock Number: 017837 Mouse: C57bl/6 VillinCreERT2 el Marjou et al.37 Jackson Stock Number: 020282 Mouse: C57bl/6 Fosl1lox/lox Eferl et al.38 N/A Mouse: C57bl/6 Col1a1tet-O-Fosl1; Rosa26LSL-rtTA Hasenfuss et al.29 N/A Oligonucleotides Primers for real-time quantitative PCR See Table S1 for full sequences N/A Recombinant DNA Software and algorithms Aperio ImageScope software v12.0.1.5027 Leica Biosystems https://www.leicabiosyste ms.com/en-au/digitalpathology/manage/aperio -imagescope/ HALO software version 3.4 Indica Labs, USA https://learn.indicalab.co m/ GraphPad Prism v8.0 GraphPad Software https://www.graphpad.co m/ STAR Dobin et al.39 https://github.com/alexdo bin/STAR. .. R R Project for Statistical Computing https://www.r-project.org/ GSEA v4.1.0 Subramanian et al.40 https://www.gseamsigdb.org Other ViiATM 7 Real Time PCR system Applied Biosystems Cat# 4453534 Leica Biosystems RM2245 Leica Biosystems https://www.leicabiosyste ms.com/en-au/histologyequipment/microtomes/lei ca-rm2245/ EprediaTM SuperFrostTM Plus Adhesion Control Microscope Slide Fisher Scientific Cat# 22-042-941 Jo urn al Pr e-p roo f MasterCycler EP Thermal Cycler Eppendorf https://www.gmiinc.com/product/eppendo rf-mastercycler-epthermal-cycler-range/ Aperio AT2 Slide Scanner Leica Biosystems N/A NovaSeq 6000 System Illumina https://sapac.illumina.com /systems/sequencingplatforms/novaseq.html Jo urn al Pr e-p roo f
Article Title: Generation and characterization of a chronic in vitro model to study the early stage of metabolic dysfunction-associated steatotic liver disease (MASLD).
Article Snippet: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic and progressive liver disease with an increasing global burden that starts with an early stage of simple steatosis (MASL) which frequently progresses to liver cirrhosis and hepatocellular carcinoma (HCC).. Despite its widespread occurrence, the MASL or steatotic stage, characterized by excessive fat accumulation in the liver and considered reversible and benign, has not been extensively studied.. To study MASL effectively, it is imperative to have a clinically relevant model system that focuses solely on steatosis, in a progressive and time-dependent manner, recapitulating molecular changes associated with human disease.
Article Title: Single extracellular vesicle detection assay identifies membrane-associated α-synuclein as an early-stage biomarker in Parkinson's disease.
Article Snippet: Software and algorithms AutoCAD Autodesk https://www.autodesk.com/products/ autocad/overview?term=1-YEAR; RRID:SCR_021072 NIS-Elements Nikon https://www.nikoninstruments.com/ Products/Software; RRID:SCR_014329 Fiji ImageJ GNU General Public License https://ImageJ.net/software/fiji; RRID: SCR_002285 CODI ONI https://alto.codi.bio/ GraphPad Prism GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 Biorender Biorender www.biorender.com; RRID:SCR_018361 Other mTeSRTM1 Stem Cell Technologies Cat# 85857 Versene solution Thermo Fisher Scientific Cat# 15040066 GeltrexTM LDEV-free reduced growth factor basement membrane matrix Thermo Fisher Scientific Cat# A1413202 DMEM - high glucose Sigma Cat# D5671 Fetal Bovine Serum (FBS) Sigma Cat# F7524 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 (Continued on next page) e2 Cell Reports Medicine 6, 101999, March 18, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER GlutaMAXTM Supplement Thermo Fisher Scientific Cat# 35050061 Antibiotic-Antimycotic (100X) Thermo Fisher Scientific Cat# 15240062 TrypLETM Express Enzyme (1X), phenol red Thermo Fisher Scientific Cat# 12605036 HaltTM protease and phosphatase inhibitor cocktail Thermo Fisher Scientific Cat# 78444 Encapsulated superparamagnetic microspheres polymer-COOH (Glacial Blue) Bangs Laboratories Cat# MEGB002 Encapsulated superparamagnetic microspheres polymer-COOH (Flash Red) Bangs Laboratories Cat# MEFR002 Bovine serum albumin (BSA) Sigma Cat# A7030 EZ-LinkTM Micro Sulfo-NHS-LC-Biotinylation Kit Thermo Fisher Scientific Cat# 21935 SU-8 3025 Permanent negative epoxy photoresist Kayaku Cat# SU-8 3025 SYLGARDTM 184 Silicone Elastomer Kit Dow-Corning Cat# PDMS184 RIPA lysis and extraction buffer Thermo Fisher Scientific Cat# 89901 Amersham ECL prime western blotting detection reagent Cytiva Cat# RPN2232 HBSS Thermo Fisher Scientific Cat# 88284 Alexa Fluor 647Conjugation Kit (Fast) - Lightning-Link Abcam Cat# 269823 Alexa Fluor 488 Conjugation Kit (Fast) - Lightning-Link Abcam Cat# 236553 NEBuilder HiFi DNA Assembly Master Mix New England Biolabs Cat# E2621S OPEN ACCESS ..
Article Title: Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chloroform Millipore Sigma Cat#1.02444; CAS: 67-66-3 Potassium Chloride Thermo Fisher Scientific Cat#BP366; CAS: 7447-40-7 Cis-10-Heptadecenoic Acid Millipore Sigma Cat#H8896; CAS: 29743-97-3 n-Hexane Millipore Sigma Cat#1.03701; CAS: 110-54-3 Methyl Acetate Millipore Sigma Cat#186325; CAS: 79-20-9 Acetonitrile, Optima LC/MS Grade Thermo Fisher Scientific Cat#A955: CAS: 75-05-8 Potassium Hydroxide Millipore Sigma Cat#484016; CAS: 1310-58-3 Formic Acid Millipore Sigma Cat#FX0440; CAS: 64-18-6 2,3,4,5,6-Pentafluorobenzyl Bromide Millipore Sigma Cat#90257; CAS: 1765-40-8 N,N-Diisopropylethylamine Millipore Sigma Cat#D125806; CAS: 7087-68-5 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Scientific Cat#78440 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34096 PowerUp SYBR Green Master Mix Thermo Fisher Scientific Cat#A25741 2,2-Diphenyl-1-picrylhydrazyl Millipore Sigma Cat#D9132; CAS: 1898-66-4 C11 BODIPY 581/591 Thermo Fisher Scientific Cat#D3861 40,6-Diamidino-2-phenylindole Invitrogen Cat#D1306 Lipofectamine 2000 Invitrogen Cat#11668027 SYTOX Green Nucleic Acid Stain Invitrogen Cat#S7020 Trypan Blue Bio-Rad Cat#1450021 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Quick-DNA Miniprep Plus Kit Zymo Research Cat#D4068 ZymoPURE II Plasmid Midiprep Kit Zymo Research Cat#D4200-A QIAprep Spin Miniprep Kit Qiagen Cat#27104 iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat#1725035 Deposited data Raw unprocessed fatty acid and lipidomics mass spectrometry data This paper MassIVE: MSV000095863; https://massive. ucsd.edu/ProteoSAFe/dataset.jsp? accession=MSV000095863 Uncropped Western blot images This paper Mendeley Data: https://doi.org/10.17632/ 95wwrptr59.1 Experimental models: Cell lines Human: A549 ATCC Cat#CCL-185 Human: HeLa ATCC Cat#CCL-2 Human: Panc1 ATCC Cat#CRL-1469 Human: H2199 ATCC Cat#CRL-5803 Human: MIA PaCa-2 ATCC Cat#CRL-1420 Human: 293T ATCC Cat#CRL-3216 Human: A549 sgNTC This paper N/A Human: A549 sgATGL #3.1 This paper N/A Human: A549 sgATGL #5.1 This paper N/A Human: A549 sgFADS2 #1.1 This paper N/A Human: A549 sgAGPS #1.1 This paper N/A Human: A549 sgAGPS #4.1 This paper N/A Oligonucleotides See Table S1 N/A N/A (Continued on next page) Cell Chemical Biology 32, 1–15.e1–e6, February 20, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Ran et al.52 Addgene Plasmid #48138 Software and algorithms Microsoft Excel 16.87 Microsoft Corporation https://www.microsoft.com/en-us/ microsoft-365/excel R 4.3.1 The R Project https://www.r-project.org/ Prism 10.2.3 GraphPad https://www.graphpad.com/features FlowJo 10.10.0 Becton Dickinson https://www.flowjo.com/ LipidSearch 5.0 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/multi-omics-dataanalysis/lipid-search-software.html El-Maven 0.12 Agrawal et al.46 https://github.com/ElucidataInc/ElMaven Skyline 23.1.0.455 Adams et al.48 https://skyline.ms/project/home/software/ Skyline/begin.view IsoCorrectoR Heinrich et al.49 https://www.bioconductor.org/packages/ release/bioc/html/IsoCorrectoR.html CRISPResso2 Clement et al.53 http://crispresso2.pinellolab.org/ submission
Protein Extraction:Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Transfection:Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Reverse Transcription:Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Article Title: Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis
Article Snippet: .. Hydrogen peroxide 30% Science Supply Australia Cat# HA154/500ML Sodium citrate tribasic dihydrate Sigma Aldrich Cat# S4641 Jo urn al Pr e-p roo f UltraPureTM Ethylenediaminetetraacetic Acid, Disodium Salt, Dihydrate (Na2EDTA.2H2O) Thermo Fisher Scientific Cat# 15576028 Liquid 3, 3-diaminobenzidine (DAB)+ 2-component system Agilent Technologies Australia Cat# K346811-2 Normal goat serum Thermo Fisher Scientific Cat# 31872 TritonTM X-100 Sigma Aldrich Cat# X100-100ML DMEM-F12 Thermo Fisher Scientific Cat# 11320033 L-glutamine Thermo Fisher Scientific Cat# A2916801 Fetal Bovine Serum, heat inactivated Thermo Fisher Scientific Cat# 10100147 Deoxyribonuclease I (DNase I) Worthington Biochemical corporation Cat# LS002140 Trypsin (2.5%) Thermo Fisher Scientific Cat# 15090-046 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 HEPES Thermo Fisher Scientific Cat# 15630080 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 RNAsecureTM RNase Inactivation reagent Thermo Fisher Scientific Cat# AM7006 Critical commercial assays ReliaPrep RNA Tissue Miniprep System - Fibrous Tissue protocol Promega Cat# Z6112 High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat# 4368814 AllPrep DNA/RNA/Protein Mini kit Qiagen Cat# 80004 TapeStation D1K ScreenTape assay Agilent Cat# 5067-5363, 5067- 5361 Stranded Total RNA Prep kit with Ribo-Zero Plus Illumina Cat# 20040529 MycoAlert® Mycoplasma Detection Kit Lonza Cat# LT07-318 GenePrint® 10 System Promega Cat# B9510 TruSeq RNA Library Preparation Kit v2 Illumina Cat# RS-122-2001, RS122-2002 Deposited data RNA-seq data This paper GSE306906 Experimental models: Cell lines KM12 Camps et al.43 SW48 ATCC CCL-231 RKO ATCC CRL-2577 LIM1215 Cell Bank Australia CBA-1215 Co115 Carrel et al.44 Vaco5 McBain et al.45 Jo urn al Pr -pr oo f Experimental models: Organisms/strains Mouse: FVB BrafV637E/+ Dankort et al.46 Jackson Stock Number: 017837 Mouse: C57bl/6 VillinCreERT2 el Marjou et al.37 Jackson Stock Number: 020282 Mouse: C57bl/6 Fosl1lox/lox Eferl et al.38 N/A Mouse: C57bl/6 Col1a1tet-O-Fosl1; Rosa26LSL-rtTA Hasenfuss et al.29 N/A Oligonucleotides Primers for real-time quantitative PCR See Table S1 for full sequences N/A Recombinant DNA Software and algorithms Aperio ImageScope software v12.0.1.5027 Leica Biosystems https://www.leicabiosyste ms.com/en-au/digitalpathology/manage/aperio -imagescope/ HALO software version 3.4 Indica Labs, USA https://learn.indicalab.co m/ GraphPad Prism v8.0 GraphPad Software https://www.graphpad.co m/ STAR Dobin et al.39 https://github.com/alexdo bin/STAR. .. R R Project for Statistical Computing https://www.r-project.org/ GSEA v4.1.0 Subramanian et al.40 https://www.gseamsigdb.org Other ViiATM 7 Real Time PCR system Applied Biosystems Cat# 4453534 Leica Biosystems RM2245 Leica Biosystems https://www.leicabiosyste ms.com/en-au/histologyequipment/microtomes/lei ca-rm2245/ EprediaTM SuperFrostTM Plus Adhesion Control Microscope Slide Fisher Scientific Cat# 22-042-941 Jo urn al Pr e-p roo f MasterCycler EP Thermal Cycler Eppendorf https://www.gmiinc.com/product/eppendo rf-mastercycler-epthermal-cycler-range/ Aperio AT2 Slide Scanner Leica Biosystems N/A NovaSeq 6000 System Illumina https://sapac.illumina.com /systems/sequencingplatforms/novaseq.html Jo urn al Pr e-p roo f
Enzyme-linked Immunosorbent Assay:Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
cAMP Assay:Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Staining:Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Article Title: Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chloroform Millipore Sigma Cat#1.02444; CAS: 67-66-3 Potassium Chloride Thermo Fisher Scientific Cat#BP366; CAS: 7447-40-7 Cis-10-Heptadecenoic Acid Millipore Sigma Cat#H8896; CAS: 29743-97-3 n-Hexane Millipore Sigma Cat#1.03701; CAS: 110-54-3 Methyl Acetate Millipore Sigma Cat#186325; CAS: 79-20-9 Acetonitrile, Optima LC/MS Grade Thermo Fisher Scientific Cat#A955: CAS: 75-05-8 Potassium Hydroxide Millipore Sigma Cat#484016; CAS: 1310-58-3 Formic Acid Millipore Sigma Cat#FX0440; CAS: 64-18-6 2,3,4,5,6-Pentafluorobenzyl Bromide Millipore Sigma Cat#90257; CAS: 1765-40-8 N,N-Diisopropylethylamine Millipore Sigma Cat#D125806; CAS: 7087-68-5 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Scientific Cat#78440 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34096 PowerUp SYBR Green Master Mix Thermo Fisher Scientific Cat#A25741 2,2-Diphenyl-1-picrylhydrazyl Millipore Sigma Cat#D9132; CAS: 1898-66-4 C11 BODIPY 581/591 Thermo Fisher Scientific Cat#D3861 40,6-Diamidino-2-phenylindole Invitrogen Cat#D1306 Lipofectamine 2000 Invitrogen Cat#11668027 SYTOX Green Nucleic Acid Stain Invitrogen Cat#S7020 Trypan Blue Bio-Rad Cat#1450021 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Quick-DNA Miniprep Plus Kit Zymo Research Cat#D4068 ZymoPURE II Plasmid Midiprep Kit Zymo Research Cat#D4200-A QIAprep Spin Miniprep Kit Qiagen Cat#27104 iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat#1725035 Deposited data Raw unprocessed fatty acid and lipidomics mass spectrometry data This paper MassIVE: MSV000095863; https://massive. ucsd.edu/ProteoSAFe/dataset.jsp? accession=MSV000095863 Uncropped Western blot images This paper Mendeley Data: https://doi.org/10.17632/ 95wwrptr59.1 Experimental models: Cell lines Human: A549 ATCC Cat#CCL-185 Human: HeLa ATCC Cat#CCL-2 Human: Panc1 ATCC Cat#CRL-1469 Human: H2199 ATCC Cat#CRL-5803 Human: MIA PaCa-2 ATCC Cat#CRL-1420 Human: 293T ATCC Cat#CRL-3216 Human: A549 sgNTC This paper N/A Human: A549 sgATGL #3.1 This paper N/A Human: A549 sgATGL #5.1 This paper N/A Human: A549 sgFADS2 #1.1 This paper N/A Human: A549 sgAGPS #1.1 This paper N/A Human: A549 sgAGPS #4.1 This paper N/A Oligonucleotides See Table S1 N/A N/A (Continued on next page) Cell Chemical Biology 32, 1–15.e1–e6, February 20, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Ran et al.52 Addgene Plasmid #48138 Software and algorithms Microsoft Excel 16.87 Microsoft Corporation https://www.microsoft.com/en-us/ microsoft-365/excel R 4.3.1 The R Project https://www.r-project.org/ Prism 10.2.3 GraphPad https://www.graphpad.com/features FlowJo 10.10.0 Becton Dickinson https://www.flowjo.com/ LipidSearch 5.0 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/multi-omics-dataanalysis/lipid-search-software.html El-Maven 0.12 Agrawal et al.46 https://github.com/ElucidataInc/ElMaven Skyline 23.1.0.455 Adams et al.48 https://skyline.ms/project/home/software/ Skyline/begin.view IsoCorrectoR Heinrich et al.49 https://www.bioconductor.org/packages/ release/bioc/html/IsoCorrectoR.html CRISPResso2 Clement et al.53 http://crispresso2.pinellolab.org/ submission
Plasmid Preparation:Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Article Title: Generation and characterization of a chronic in vitro model to study the early stage of metabolic dysfunction-associated steatotic liver disease (MASLD).
Article Snippet: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic and progressive liver disease with an increasing global burden that starts with an early stage of simple steatosis (MASL) which frequently progresses to liver cirrhosis and hepatocellular carcinoma (HCC).. Despite its widespread occurrence, the MASL or steatotic stage, characterized by excessive fat accumulation in the liver and considered reversible and benign, has not been extensively studied.. To study MASL effectively, it is imperative to have a clinically relevant model system that focuses solely on steatosis, in a progressive and time-dependent manner, recapitulating molecular changes associated with human disease.
Article Title: Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chloroform Millipore Sigma Cat#1.02444; CAS: 67-66-3 Potassium Chloride Thermo Fisher Scientific Cat#BP366; CAS: 7447-40-7 Cis-10-Heptadecenoic Acid Millipore Sigma Cat#H8896; CAS: 29743-97-3 n-Hexane Millipore Sigma Cat#1.03701; CAS: 110-54-3 Methyl Acetate Millipore Sigma Cat#186325; CAS: 79-20-9 Acetonitrile, Optima LC/MS Grade Thermo Fisher Scientific Cat#A955: CAS: 75-05-8 Potassium Hydroxide Millipore Sigma Cat#484016; CAS: 1310-58-3 Formic Acid Millipore Sigma Cat#FX0440; CAS: 64-18-6 2,3,4,5,6-Pentafluorobenzyl Bromide Millipore Sigma Cat#90257; CAS: 1765-40-8 N,N-Diisopropylethylamine Millipore Sigma Cat#D125806; CAS: 7087-68-5 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Scientific Cat#78440 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34096 PowerUp SYBR Green Master Mix Thermo Fisher Scientific Cat#A25741 2,2-Diphenyl-1-picrylhydrazyl Millipore Sigma Cat#D9132; CAS: 1898-66-4 C11 BODIPY 581/591 Thermo Fisher Scientific Cat#D3861 40,6-Diamidino-2-phenylindole Invitrogen Cat#D1306 Lipofectamine 2000 Invitrogen Cat#11668027 SYTOX Green Nucleic Acid Stain Invitrogen Cat#S7020 Trypan Blue Bio-Rad Cat#1450021 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Quick-DNA Miniprep Plus Kit Zymo Research Cat#D4068 ZymoPURE II Plasmid Midiprep Kit Zymo Research Cat#D4200-A QIAprep Spin Miniprep Kit Qiagen Cat#27104 iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat#1725035 Deposited data Raw unprocessed fatty acid and lipidomics mass spectrometry data This paper MassIVE: MSV000095863; https://massive. ucsd.edu/ProteoSAFe/dataset.jsp? accession=MSV000095863 Uncropped Western blot images This paper Mendeley Data: https://doi.org/10.17632/ 95wwrptr59.1 Experimental models: Cell lines Human: A549 ATCC Cat#CCL-185 Human: HeLa ATCC Cat#CCL-2 Human: Panc1 ATCC Cat#CRL-1469 Human: H2199 ATCC Cat#CRL-5803 Human: MIA PaCa-2 ATCC Cat#CRL-1420 Human: 293T ATCC Cat#CRL-3216 Human: A549 sgNTC This paper N/A Human: A549 sgATGL #3.1 This paper N/A Human: A549 sgATGL #5.1 This paper N/A Human: A549 sgFADS2 #1.1 This paper N/A Human: A549 sgAGPS #1.1 This paper N/A Human: A549 sgAGPS #4.1 This paper N/A Oligonucleotides See Table S1 N/A N/A (Continued on next page) Cell Chemical Biology 32, 1–15.e1–e6, February 20, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Ran et al.52 Addgene Plasmid #48138 Software and algorithms Microsoft Excel 16.87 Microsoft Corporation https://www.microsoft.com/en-us/ microsoft-365/excel R 4.3.1 The R Project https://www.r-project.org/ Prism 10.2.3 GraphPad https://www.graphpad.com/features FlowJo 10.10.0 Becton Dickinson https://www.flowjo.com/ LipidSearch 5.0 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/multi-omics-dataanalysis/lipid-search-software.html El-Maven 0.12 Agrawal et al.46 https://github.com/ElucidataInc/ElMaven Skyline 23.1.0.455 Adams et al.48 https://skyline.ms/project/home/software/ Skyline/begin.view IsoCorrectoR Heinrich et al.49 https://www.bioconductor.org/packages/ release/bioc/html/IsoCorrectoR.html CRISPResso2 Clement et al.53 http://crispresso2.pinellolab.org/ submission
Generated:Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Software:Article Title: Engineered commensals for targeted nose-to-brain drug delivery.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER D(+)-SUCROSE Sigma-Aldrich Cat# 84100-1KG Tissue-Tek O.C.T. .. Compound Tissue-Tek Cat# 4583 M-PER Mammalian Protein Extraction Reagent Thermo Fisher Scientific Cat# 78501 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Hoechst - Molecular Probes NucBlue Live ReadyProbes Reagent Thermo Fisher Scientific Cat# R37605 Trichloroacetic acid Sigma-Aldrich Cat# TCIT0369 GoScript(TM) Reverse transcription Mix Promega Cat# A2791 TRIzol Thermo Fisher Scientific Cat# 15596018 Isoflurane Baxter SG2L9100 Kanamycin Gold Biotechnology Cat# K-120-25 Carbenicillin Gold Biotechnology Cat# C-103-25 Erythromycin Fisher Scientific Cat# BP920-25 Penicillin-Streptomycin Solution 100X - 100ml Atlantis Bioscience Pte Ltd Cat# L0022-100 Trypsin 0.25% EDTA Thermo Fisher Scientific Cat# 25200056 Critical commercial assays a-MSH ELISA kit Phoenix Pharmaceuticals Cat# EK-043-01 cAMP Assay Kit Abcam Cat# ab65355 Nano-Glo HiBiT Extracellular Detection System Promega Cat# N2420 Triglyceride-Glo Assay Promega Cat# J3160 H&E Staining Kit (Hematoxylin and Eosin) Abcam Cat# ab245880 Red Oli O staining Sigma-Aldrich Cat# MAK560 Experimental models: Cell lines RPMI 2650 cell CLS Cell Lines Service RRID: CVCL_1664 CHO-K1 cell Leibniz Institute DSMZ RRID: CVCL_0214 NS0 cell Merck RRID: CVCL_3940 HEK 293T cells American Type Culture Collection (ATCC) RRID: CVCL_4U22 Neuro2A cells American Type Culture Collection (ATCC) RRID: CVCL_0470 GT1-7 cells Merck RRID: CVCL_0281 Experimental models: Organisms/strains Mouse: C57BL/6NTac Taconic RRID: IMSR_TAC:B6 Recombinant DNA pcDNA-LpR plasmid Generated this study N/A pcDNA-TrkB40 plasmid Addgene Cat# 24088 pET30b plasmid Merck Cat# 69910-3 pHSSC256 Shen et al.51 N/A pLCNICK Addgene Cat# 84653 Software and algorithms IVIS spectrum PerkinElmer RRID: SCR_018621 Leica Las X Leica Microsystems RRID: SCR_013673 Graphpad Prism 10 Graphpad N/A CytExpert 2.4 Beckman N/A Synthego Synthego www.synthego.com Biorender Biorender www.biorender.com Benchling Benchling www.benchling.com (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–18.e1–e6, March 20, 2025 Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Other LB broth powder BD DIFCO Cat# 244620 MRS media BD DIFCO Cat# 288130 M 17 Broth Sigma-Aldrich Cat# 56156-500G-F DMEM medium Thermo Fisher Scientific Cat# 11995065 EMEM medium Thermo Fisher Scientific Cat# 32561037 Fetal Bovine Serum Atlantis Bioscience Pte Ltd Cat# S1810 Transwels - Millicell Standing Cell Culture Inserts Merck Cat# PIHP01250 Epredia HP35 Disposable Microtome Blades SciMed Cat# 3153735 Gene Pulser/MicroPulser Electroporation Cuvettes, 0.2 cm Gap Bio-Rad Cat# 1652086 HiTrap Heparin HP affinity columns Cytiva Cat# 28936549 HisTrap HP His tag protein purification columns Cytiva Cat# 17524801 Amicon Ultra Centrifugal Filters Merck Cat# UFC901024 Rodent Diet With 60 kcal% Fat Research Diets Inc Cat# D12492i L. plantarum WCFS1 reference proteome for protein ID Uniprot Uniprot ID: UP000000432 ll OPEN ACCESS Please cite this article in press as: Shen et al., Engineered commensals for targeted nose-to-brain drug delivery, Cell (2025), https://doi.org/ 10.1016/j.cell.2025.01.017
Article Title: Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis
Article Snippet: .. Hydrogen peroxide 30% Science Supply Australia Cat# HA154/500ML Sodium citrate tribasic dihydrate Sigma Aldrich Cat# S4641 Jo urn al Pr e-p roo f UltraPureTM Ethylenediaminetetraacetic Acid, Disodium Salt, Dihydrate (Na2EDTA.2H2O) Thermo Fisher Scientific Cat# 15576028 Liquid 3, 3-diaminobenzidine (DAB)+ 2-component system Agilent Technologies Australia Cat# K346811-2 Normal goat serum Thermo Fisher Scientific Cat# 31872 TritonTM X-100 Sigma Aldrich Cat# X100-100ML DMEM-F12 Thermo Fisher Scientific Cat# 11320033 L-glutamine Thermo Fisher Scientific Cat# A2916801 Fetal Bovine Serum, heat inactivated Thermo Fisher Scientific Cat# 10100147 Deoxyribonuclease I (DNase I) Worthington Biochemical corporation Cat# LS002140 Trypsin (2.5%) Thermo Fisher Scientific Cat# 15090-046 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 HEPES Thermo Fisher Scientific Cat# 15630080 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 RNAsecureTM RNase Inactivation reagent Thermo Fisher Scientific Cat# AM7006 Critical commercial assays ReliaPrep RNA Tissue Miniprep System - Fibrous Tissue protocol Promega Cat# Z6112 High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat# 4368814 AllPrep DNA/RNA/Protein Mini kit Qiagen Cat# 80004 TapeStation D1K ScreenTape assay Agilent Cat# 5067-5363, 5067- 5361 Stranded Total RNA Prep kit with Ribo-Zero Plus Illumina Cat# 20040529 MycoAlert® Mycoplasma Detection Kit Lonza Cat# LT07-318 GenePrint® 10 System Promega Cat# B9510 TruSeq RNA Library Preparation Kit v2 Illumina Cat# RS-122-2001, RS122-2002 Deposited data RNA-seq data This paper GSE306906 Experimental models: Cell lines KM12 Camps et al.43 SW48 ATCC CCL-231 RKO ATCC CRL-2577 LIM1215 Cell Bank Australia CBA-1215 Co115 Carrel et al.44 Vaco5 McBain et al.45 Jo urn al Pr -pr oo f Experimental models: Organisms/strains Mouse: FVB BrafV637E/+ Dankort et al.46 Jackson Stock Number: 017837 Mouse: C57bl/6 VillinCreERT2 el Marjou et al.37 Jackson Stock Number: 020282 Mouse: C57bl/6 Fosl1lox/lox Eferl et al.38 N/A Mouse: C57bl/6 Col1a1tet-O-Fosl1; Rosa26LSL-rtTA Hasenfuss et al.29 N/A Oligonucleotides Primers for real-time quantitative PCR See Table S1 for full sequences N/A Recombinant DNA Software and algorithms Aperio ImageScope software v12.0.1.5027 Leica Biosystems https://www.leicabiosyste ms.com/en-au/digitalpathology/manage/aperio -imagescope/ HALO software version 3.4 Indica Labs, USA https://learn.indicalab.co m/ GraphPad Prism v8.0 GraphPad Software https://www.graphpad.co m/ STAR Dobin et al.39 https://github.com/alexdo bin/STAR. .. R R Project for Statistical Computing https://www.r-project.org/ GSEA v4.1.0 Subramanian et al.40 https://www.gseamsigdb.org Other ViiATM 7 Real Time PCR system Applied Biosystems Cat# 4453534 Leica Biosystems RM2245 Leica Biosystems https://www.leicabiosyste ms.com/en-au/histologyequipment/microtomes/lei ca-rm2245/ EprediaTM SuperFrostTM Plus Adhesion Control Microscope Slide Fisher Scientific Cat# 22-042-941 Jo urn al Pr e-p roo f MasterCycler EP Thermal Cycler Eppendorf https://www.gmiinc.com/product/eppendo rf-mastercycler-epthermal-cycler-range/ Aperio AT2 Slide Scanner Leica Biosystems N/A NovaSeq 6000 System Illumina https://sapac.illumina.com /systems/sequencingplatforms/novaseq.html Jo urn al Pr e-p roo f
Article Title: Generation and characterization of a chronic in vitro model to study the early stage of metabolic dysfunction-associated steatotic liver disease (MASLD).
Article Snippet: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic and progressive liver disease with an increasing global burden that starts with an early stage of simple steatosis (MASL) which frequently progresses to liver cirrhosis and hepatocellular carcinoma (HCC).. Despite its widespread occurrence, the MASL or steatotic stage, characterized by excessive fat accumulation in the liver and considered reversible and benign, has not been extensively studied.. To study MASL effectively, it is imperative to have a clinically relevant model system that focuses solely on steatosis, in a progressive and time-dependent manner, recapitulating molecular changes associated with human disease.
RNA Library Preparation:Article Title: Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis
Article Snippet: .. Hydrogen peroxide 30% Science Supply Australia Cat# HA154/500ML Sodium citrate tribasic dihydrate Sigma Aldrich Cat# S4641 Jo urn al Pr e-p roo f UltraPureTM Ethylenediaminetetraacetic Acid, Disodium Salt, Dihydrate (Na2EDTA.2H2O) Thermo Fisher Scientific Cat# 15576028 Liquid 3, 3-diaminobenzidine (DAB)+ 2-component system Agilent Technologies Australia Cat# K346811-2 Normal goat serum Thermo Fisher Scientific Cat# 31872 TritonTM X-100 Sigma Aldrich Cat# X100-100ML DMEM-F12 Thermo Fisher Scientific Cat# 11320033 L-glutamine Thermo Fisher Scientific Cat# A2916801 Fetal Bovine Serum, heat inactivated Thermo Fisher Scientific Cat# 10100147 Deoxyribonuclease I (DNase I) Worthington Biochemical corporation Cat# LS002140 Trypsin (2.5%) Thermo Fisher Scientific Cat# 15090-046 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 HEPES Thermo Fisher Scientific Cat# 15630080 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 RNAsecureTM RNase Inactivation reagent Thermo Fisher Scientific Cat# AM7006 Critical commercial assays ReliaPrep RNA Tissue Miniprep System - Fibrous Tissue protocol Promega Cat# Z6112 High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat# 4368814 AllPrep DNA/RNA/Protein Mini kit Qiagen Cat# 80004 TapeStation D1K ScreenTape assay Agilent Cat# 5067-5363, 5067- 5361 Stranded Total RNA Prep kit with Ribo-Zero Plus Illumina Cat# 20040529 MycoAlert® Mycoplasma Detection Kit Lonza Cat# LT07-318 GenePrint® 10 System Promega Cat# B9510 TruSeq RNA Library Preparation Kit v2 Illumina Cat# RS-122-2001, RS122-2002 Deposited data RNA-seq data This paper GSE306906 Experimental models: Cell lines KM12 Camps et al.43 SW48 ATCC CCL-231 RKO ATCC CRL-2577 LIM1215 Cell Bank Australia CBA-1215 Co115 Carrel et al.44 Vaco5 McBain et al.45 Jo urn al Pr -pr oo f Experimental models: Organisms/strains Mouse: FVB BrafV637E/+ Dankort et al.46 Jackson Stock Number: 017837 Mouse: C57bl/6 VillinCreERT2 el Marjou et al.37 Jackson Stock Number: 020282 Mouse: C57bl/6 Fosl1lox/lox Eferl et al.38 N/A Mouse: C57bl/6 Col1a1tet-O-Fosl1; Rosa26LSL-rtTA Hasenfuss et al.29 N/A Oligonucleotides Primers for real-time quantitative PCR See Table S1 for full sequences N/A Recombinant DNA Software and algorithms Aperio ImageScope software v12.0.1.5027 Leica Biosystems https://www.leicabiosyste ms.com/en-au/digitalpathology/manage/aperio -imagescope/ HALO software version 3.4 Indica Labs, USA https://learn.indicalab.co m/ GraphPad Prism v8.0 GraphPad Software https://www.graphpad.co m/ STAR Dobin et al.39 https://github.com/alexdo bin/STAR. .. R R Project for Statistical Computing https://www.r-project.org/ GSEA v4.1.0 Subramanian et al.40 https://www.gseamsigdb.org Other ViiATM 7 Real Time PCR system Applied Biosystems Cat# 4453534 Leica Biosystems RM2245 Leica Biosystems https://www.leicabiosyste ms.com/en-au/histologyequipment/microtomes/lei ca-rm2245/ EprediaTM SuperFrostTM Plus Adhesion Control Microscope Slide Fisher Scientific Cat# 22-042-941 Jo urn al Pr e-p roo f MasterCycler EP Thermal Cycler Eppendorf https://www.gmiinc.com/product/eppendo rf-mastercycler-epthermal-cycler-range/ Aperio AT2 Slide Scanner Leica Biosystems N/A NovaSeq 6000 System Illumina https://sapac.illumina.com /systems/sequencingplatforms/novaseq.html Jo urn al Pr e-p roo f
RNA Sequencing:Article Title: Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis
Article Snippet: .. Hydrogen peroxide 30% Science Supply Australia Cat# HA154/500ML Sodium citrate tribasic dihydrate Sigma Aldrich Cat# S4641 Jo urn al Pr e-p roo f UltraPureTM Ethylenediaminetetraacetic Acid, Disodium Salt, Dihydrate (Na2EDTA.2H2O) Thermo Fisher Scientific Cat# 15576028 Liquid 3, 3-diaminobenzidine (DAB)+ 2-component system Agilent Technologies Australia Cat# K346811-2 Normal goat serum Thermo Fisher Scientific Cat# 31872 TritonTM X-100 Sigma Aldrich Cat# X100-100ML DMEM-F12 Thermo Fisher Scientific Cat# 11320033 L-glutamine Thermo Fisher Scientific Cat# A2916801 Fetal Bovine Serum, heat inactivated Thermo Fisher Scientific Cat# 10100147 Deoxyribonuclease I (DNase I) Worthington Biochemical corporation Cat# LS002140 Trypsin (2.5%) Thermo Fisher Scientific Cat# 15090-046 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 HEPES Thermo Fisher Scientific Cat# 15630080 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 RNAsecureTM RNase Inactivation reagent Thermo Fisher Scientific Cat# AM7006 Critical commercial assays ReliaPrep RNA Tissue Miniprep System - Fibrous Tissue protocol Promega Cat# Z6112 High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat# 4368814 AllPrep DNA/RNA/Protein Mini kit Qiagen Cat# 80004 TapeStation D1K ScreenTape assay Agilent Cat# 5067-5363, 5067- 5361 Stranded Total RNA Prep kit with Ribo-Zero Plus Illumina Cat# 20040529 MycoAlert® Mycoplasma Detection Kit Lonza Cat# LT07-318 GenePrint® 10 System Promega Cat# B9510 TruSeq RNA Library Preparation Kit v2 Illumina Cat# RS-122-2001, RS122-2002 Deposited data RNA-seq data This paper GSE306906 Experimental models: Cell lines KM12 Camps et al.43 SW48 ATCC CCL-231 RKO ATCC CRL-2577 LIM1215 Cell Bank Australia CBA-1215 Co115 Carrel et al.44 Vaco5 McBain et al.45 Jo urn al Pr -pr oo f Experimental models: Organisms/strains Mouse: FVB BrafV637E/+ Dankort et al.46 Jackson Stock Number: 017837 Mouse: C57bl/6 VillinCreERT2 el Marjou et al.37 Jackson Stock Number: 020282 Mouse: C57bl/6 Fosl1lox/lox Eferl et al.38 N/A Mouse: C57bl/6 Col1a1tet-O-Fosl1; Rosa26LSL-rtTA Hasenfuss et al.29 N/A Oligonucleotides Primers for real-time quantitative PCR See Table S1 for full sequences N/A Recombinant DNA Software and algorithms Aperio ImageScope software v12.0.1.5027 Leica Biosystems https://www.leicabiosyste ms.com/en-au/digitalpathology/manage/aperio -imagescope/ HALO software version 3.4 Indica Labs, USA https://learn.indicalab.co m/ GraphPad Prism v8.0 GraphPad Software https://www.graphpad.co m/ STAR Dobin et al.39 https://github.com/alexdo bin/STAR. .. R R Project for Statistical Computing https://www.r-project.org/ GSEA v4.1.0 Subramanian et al.40 https://www.gseamsigdb.org Other ViiATM 7 Real Time PCR system Applied Biosystems Cat# 4453534 Leica Biosystems RM2245 Leica Biosystems https://www.leicabiosyste ms.com/en-au/histologyequipment/microtomes/lei ca-rm2245/ EprediaTM SuperFrostTM Plus Adhesion Control Microscope Slide Fisher Scientific Cat# 22-042-941 Jo urn al Pr e-p roo f MasterCycler EP Thermal Cycler Eppendorf https://www.gmiinc.com/product/eppendo rf-mastercycler-epthermal-cycler-range/ Aperio AT2 Slide Scanner Leica Biosystems N/A NovaSeq 6000 System Illumina https://sapac.illumina.com /systems/sequencingplatforms/novaseq.html Jo urn al Pr e-p roo f
Crocin Bleaching Assay:Article Title: Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis
Article Snippet: .. Hydrogen peroxide 30% Science Supply Australia Cat# HA154/500ML Sodium citrate tribasic dihydrate Sigma Aldrich Cat# S4641 Jo urn al Pr e-p roo f UltraPureTM Ethylenediaminetetraacetic Acid, Disodium Salt, Dihydrate (Na2EDTA.2H2O) Thermo Fisher Scientific Cat# 15576028 Liquid 3, 3-diaminobenzidine (DAB)+ 2-component system Agilent Technologies Australia Cat# K346811-2 Normal goat serum Thermo Fisher Scientific Cat# 31872 TritonTM X-100 Sigma Aldrich Cat# X100-100ML DMEM-F12 Thermo Fisher Scientific Cat# 11320033 L-glutamine Thermo Fisher Scientific Cat# A2916801 Fetal Bovine Serum, heat inactivated Thermo Fisher Scientific Cat# 10100147 Deoxyribonuclease I (DNase I) Worthington Biochemical corporation Cat# LS002140 Trypsin (2.5%) Thermo Fisher Scientific Cat# 15090-046 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 HEPES Thermo Fisher Scientific Cat# 15630080 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 RNAsecureTM RNase Inactivation reagent Thermo Fisher Scientific Cat# AM7006 Critical commercial assays ReliaPrep RNA Tissue Miniprep System - Fibrous Tissue protocol Promega Cat# Z6112 High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat# 4368814 AllPrep DNA/RNA/Protein Mini kit Qiagen Cat# 80004 TapeStation D1K ScreenTape assay Agilent Cat# 5067-5363, 5067- 5361 Stranded Total RNA Prep kit with Ribo-Zero Plus Illumina Cat# 20040529 MycoAlert® Mycoplasma Detection Kit Lonza Cat# LT07-318 GenePrint® 10 System Promega Cat# B9510 TruSeq RNA Library Preparation Kit v2 Illumina Cat# RS-122-2001, RS122-2002 Deposited data RNA-seq data This paper GSE306906 Experimental models: Cell lines KM12 Camps et al.43 SW48 ATCC CCL-231 RKO ATCC CRL-2577 LIM1215 Cell Bank Australia CBA-1215 Co115 Carrel et al.44 Vaco5 McBain et al.45 Jo urn al Pr -pr oo f Experimental models: Organisms/strains Mouse: FVB BrafV637E/+ Dankort et al.46 Jackson Stock Number: 017837 Mouse: C57bl/6 VillinCreERT2 el Marjou et al.37 Jackson Stock Number: 020282 Mouse: C57bl/6 Fosl1lox/lox Eferl et al.38 N/A Mouse: C57bl/6 Col1a1tet-O-Fosl1; Rosa26LSL-rtTA Hasenfuss et al.29 N/A Oligonucleotides Primers for real-time quantitative PCR See Table S1 for full sequences N/A Recombinant DNA Software and algorithms Aperio ImageScope software v12.0.1.5027 Leica Biosystems https://www.leicabiosyste ms.com/en-au/digitalpathology/manage/aperio -imagescope/ HALO software version 3.4 Indica Labs, USA https://learn.indicalab.co m/ GraphPad Prism v8.0 GraphPad Software https://www.graphpad.co m/ STAR Dobin et al.39 https://github.com/alexdo bin/STAR. .. R R Project for Statistical Computing https://www.r-project.org/ GSEA v4.1.0 Subramanian et al.40 https://www.gseamsigdb.org Other ViiATM 7 Real Time PCR system Applied Biosystems Cat# 4453534 Leica Biosystems RM2245 Leica Biosystems https://www.leicabiosyste ms.com/en-au/histologyequipment/microtomes/lei ca-rm2245/ EprediaTM SuperFrostTM Plus Adhesion Control Microscope Slide Fisher Scientific Cat# 22-042-941 Jo urn al Pr e-p roo f MasterCycler EP Thermal Cycler Eppendorf https://www.gmiinc.com/product/eppendo rf-mastercycler-epthermal-cycler-range/ Aperio AT2 Slide Scanner Leica Biosystems N/A NovaSeq 6000 System Illumina https://sapac.illumina.com /systems/sequencingplatforms/novaseq.html Jo urn al Pr e-p roo f
Real-time Polymerase Chain Reaction:Article Title: Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis
Article Snippet: .. Hydrogen peroxide 30% Science Supply Australia Cat# HA154/500ML Sodium citrate tribasic dihydrate Sigma Aldrich Cat# S4641 Jo urn al Pr e-p roo f UltraPureTM Ethylenediaminetetraacetic Acid, Disodium Salt, Dihydrate (Na2EDTA.2H2O) Thermo Fisher Scientific Cat# 15576028 Liquid 3, 3-diaminobenzidine (DAB)+ 2-component system Agilent Technologies Australia Cat# K346811-2 Normal goat serum Thermo Fisher Scientific Cat# 31872 TritonTM X-100 Sigma Aldrich Cat# X100-100ML DMEM-F12 Thermo Fisher Scientific Cat# 11320033 L-glutamine Thermo Fisher Scientific Cat# A2916801 Fetal Bovine Serum, heat inactivated Thermo Fisher Scientific Cat# 10100147 Deoxyribonuclease I (DNase I) Worthington Biochemical corporation Cat# LS002140 Trypsin (2.5%) Thermo Fisher Scientific Cat# 15090-046 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 HEPES Thermo Fisher Scientific Cat# 15630080 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 RNAsecureTM RNase Inactivation reagent Thermo Fisher Scientific Cat# AM7006 Critical commercial assays ReliaPrep RNA Tissue Miniprep System - Fibrous Tissue protocol Promega Cat# Z6112 High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat# 4368814 AllPrep DNA/RNA/Protein Mini kit Qiagen Cat# 80004 TapeStation D1K ScreenTape assay Agilent Cat# 5067-5363, 5067- 5361 Stranded Total RNA Prep kit with Ribo-Zero Plus Illumina Cat# 20040529 MycoAlert® Mycoplasma Detection Kit Lonza Cat# LT07-318 GenePrint® 10 System Promega Cat# B9510 TruSeq RNA Library Preparation Kit v2 Illumina Cat# RS-122-2001, RS122-2002 Deposited data RNA-seq data This paper GSE306906 Experimental models: Cell lines KM12 Camps et al.43 SW48 ATCC CCL-231 RKO ATCC CRL-2577 LIM1215 Cell Bank Australia CBA-1215 Co115 Carrel et al.44 Vaco5 McBain et al.45 Jo urn al Pr -pr oo f Experimental models: Organisms/strains Mouse: FVB BrafV637E/+ Dankort et al.46 Jackson Stock Number: 017837 Mouse: C57bl/6 VillinCreERT2 el Marjou et al.37 Jackson Stock Number: 020282 Mouse: C57bl/6 Fosl1lox/lox Eferl et al.38 N/A Mouse: C57bl/6 Col1a1tet-O-Fosl1; Rosa26LSL-rtTA Hasenfuss et al.29 N/A Oligonucleotides Primers for real-time quantitative PCR See Table S1 for full sequences N/A Recombinant DNA Software and algorithms Aperio ImageScope software v12.0.1.5027 Leica Biosystems https://www.leicabiosyste ms.com/en-au/digitalpathology/manage/aperio -imagescope/ HALO software version 3.4 Indica Labs, USA https://learn.indicalab.co m/ GraphPad Prism v8.0 GraphPad Software https://www.graphpad.co m/ STAR Dobin et al.39 https://github.com/alexdo bin/STAR. .. R R Project for Statistical Computing https://www.r-project.org/ GSEA v4.1.0 Subramanian et al.40 https://www.gseamsigdb.org Other ViiATM 7 Real Time PCR system Applied Biosystems Cat# 4453534 Leica Biosystems RM2245 Leica Biosystems https://www.leicabiosyste ms.com/en-au/histologyequipment/microtomes/lei ca-rm2245/ EprediaTM SuperFrostTM Plus Adhesion Control Microscope Slide Fisher Scientific Cat# 22-042-941 Jo urn al Pr e-p roo f MasterCycler EP Thermal Cycler Eppendorf https://www.gmiinc.com/product/eppendo rf-mastercycler-epthermal-cycler-range/ Aperio AT2 Slide Scanner Leica Biosystems N/A NovaSeq 6000 System Illumina https://sapac.illumina.com /systems/sequencingplatforms/novaseq.html Jo urn al Pr e-p roo f
other:Article Title: Chromatin-mediated anticipatory control of type I interferon production in plasmacytoid dendritic cells.
Article Snippet: Cas9 Nuclease V3 IDT Cat# 1081058 Alt-R Cas9 Electroporation Enhancer IDT Cat# 1075915 (Z)-4-Hydroxytamoxifen Sigma-Aldrich Cat# H7904 Recombinant Mouse GM-CSF (carrier free) BioLegend Cat# 576304 Recombinant Mouse IL-4 (carrier free) BioLegend Cat# 574304 Collagenase D from Clostridium histolyticum Roche Cat# 11088858001 Pronase from Streptomyces griseus Millipore Sigma Cat# 10165921001 Amphotericin B solution Millipore Sigma Cat# A2942 Liberase TL Roche Cat# 5401020001 Bovine Serum Albumin, Powder Millipore Sigma Cat# A9647 Deoxyribonuclease I (DNase I) from bovine pancreas Roche Cat# 11284932001 RBC Lysis Buffer BioLegend Cat# 420301 Poly(I:C) high molecular weight InvivoGen Cat# tlrl-pic CpG-A/ODN 2216 InvivoGen Cat# tlrl-2216-1 DOTAP chloride MedChemExpress Cat# HY-112754A Concanavalin A from Canavalia ensiformis Millipore Sigma Cat# L7647, C2010 Paraformaldehyde Aqueous Solution, EM Grade Electron Microscopy Sciences Cat# 15710 Triton X-100 Thermo Fisher Scientific Cat# 85111 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89900 Halt Protease Inhibitor Cocktail Thermo Fisher Scientific Cat# 78429 Halt Phosphatase Inhibitor Cocktail Thermo Fisher Scientific Cat# 78420 NuPAGE LDS Sample Buffer Thermo Fisher Scientific Cat# NP0007 NuPAGE Sample Reducing Agent Thermo Fisher Scientific Cat# NP0009 TRIzol Reagent Themo Fisher Scientific Cat# 15596018 Digitonin Thermo Fisher Scientific Cat# BN2006 Trizma Hydrochloride Solution, pH 7.4 Millipore Sigma Cat# T2194 Sodium Chloride Solution, 5 M Millipore Sigma Cat# 59222C Magnesium Chloride Solution, 1M Millipore Sigma Cat# M1028 IGEPAL CA-630 Millipore Sigma Cat# I8896 Protector RNase inhibitor Millipore Sigma Cat# 3335402001 DL-Dithiothreitol (DTT) solution, 1M Millipore Sigma Cat# 646563 Bovine Serum Albumin Fraction V Solution Thermo Fisher Scientific Cat# 15260037 10% Tween 20 Bio-Rad Cat# 1662404 Critical commercial assays Venor GeM Mycoplasma PCR-Based Detection Kit Sigma-Aldrich Cat# MP0025 SF Cell Line 4D-Nucleofector X Kit L Lonza Cat# V4XC-2012 KT Streptavidin microbeads Miltenyi Biotec Cat# 130-048-101 LD columns Miltenyi Biotec Cat# 130-042-901 (Continued on next page) Immunity 59, 270–287.e1–e11, February 10, 2026 e2
Article Title: MicroRNA-19b exacerbates systemic sclerosis through promoting Th9 cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Vmac TaqMan Primer Thermo Fisher Scientific Cat# Mm01232760_m1 Mouse Hprt TaqMan Primer Thermo Fisher Scientific Cat# Mm00446968_m1 miR-19b-3p TaqMan Primer Thermo Fisher Scientific Cat# mmu478264_mir miR-467f TaqMan Primer Thermo Fisher Scientific Cat# 002886 U6 snRNA TaqMan Primer Thermo Fisher Scientific Cat# 001973 Caenorhabditis elegans miR-39-3p TaqMan Primer Thermo Fisher Scientific Cat# 478293_mir Human IL9 TaqMan Primer Thermo Fisher Scientific Cat# Hs00174125_m1 Human E2F8 TaqMan Primer Thermo Fisher Scientific Cat# Hs00226635_m1 Human GAPDH TaqMan Primer Thermo Fisher Scientific Cat# Hs99999905_m1 Recombinant DNA pMSCV-IRES-GFP-Smad3 Park et al.5 N/A pMSCV-IRES-GFP-Smad3 Mutations Park et al.5 N/A pMSCV-IRES-GFP-E2f8 Part et al.5 N/A Software and algorithms FlowJo v10.9 Software FlowJo https://www.flowjo.com/solutions/ flowjo/RRID: SCR_008520 GraphPad Prism v8 Software GraphPad Software https://www.graphpad.com/ RRID: SCR_002798 QuantStudio 3 Real-Time PCR Software Thermo Fisher Scientific https://www.thermofisher.com/order/ catalog/product/A28567#/A28567 RRID: SCR_018712 nCounter Analysis System NanoString Technologies https://www.nanostring.com/products/ ncounter-analysis-system/ncountersystems-overview/ RRID: SCR_021712 Leica Application Suite X Software Leica Biosystems https://www.leica-microsystems.com/ products/microscope-software/details/ product/leica-las-x-ls/ RRID: SCR_013673 NDP.
MTT Assay:Article Title: Generation and characterization of a chronic in vitro model to study the early stage of metabolic dysfunction-associated steatotic liver disease (MASLD).
Article Snippet: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic and progressive liver disease with an increasing global burden that starts with an early stage of simple steatosis (MASL) which frequently progresses to liver cirrhosis and hepatocellular carcinoma (HCC).. Despite its widespread occurrence, the MASL or steatotic stage, characterized by excessive fat accumulation in the liver and considered reversible and benign, has not been extensively studied.. To study MASL effectively, it is imperative to have a clinically relevant model system that focuses solely on steatosis, in a progressive and time-dependent manner, recapitulating molecular changes associated with human disease.
Targeted Proteomics:Article Title: Generation and characterization of a chronic in vitro model to study the early stage of metabolic dysfunction-associated steatotic liver disease (MASLD).
Article Snippet: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic and progressive liver disease with an increasing global burden that starts with an early stage of simple steatosis (MASL) which frequently progresses to liver cirrhosis and hepatocellular carcinoma (HCC).. Despite its widespread occurrence, the MASL or steatotic stage, characterized by excessive fat accumulation in the liver and considered reversible and benign, has not been extensively studied.. To study MASL effectively, it is imperative to have a clinically relevant model system that focuses solely on steatosis, in a progressive and time-dependent manner, recapitulating molecular changes associated with human disease.
Laser-Scanning Microscopy:Article Title: Generation and characterization of a chronic in vitro model to study the early stage of metabolic dysfunction-associated steatotic liver disease (MASLD).
Article Snippet: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic and progressive liver disease with an increasing global burden that starts with an early stage of simple steatosis (MASL) which frequently progresses to liver cirrhosis and hepatocellular carcinoma (HCC).. Despite its widespread occurrence, the MASL or steatotic stage, characterized by excessive fat accumulation in the liver and considered reversible and benign, has not been extensively studied.. To study MASL effectively, it is imperative to have a clinically relevant model system that focuses solely on steatosis, in a progressive and time-dependent manner, recapitulating molecular changes associated with human disease.
Mass Spectrometry:Article Title: Generation and characterization of a chronic in vitro model to study the early stage of metabolic dysfunction-associated steatotic liver disease (MASLD).
Article Snippet: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic and progressive liver disease with an increasing global burden that starts with an early stage of simple steatosis (MASL) which frequently progresses to liver cirrhosis and hepatocellular carcinoma (HCC).. Despite its widespread occurrence, the MASL or steatotic stage, characterized by excessive fat accumulation in the liver and considered reversible and benign, has not been extensively studied.. To study MASL effectively, it is imperative to have a clinically relevant model system that focuses solely on steatosis, in a progressive and time-dependent manner, recapitulating molecular changes associated with human disease.
Article Title: Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chloroform Millipore Sigma Cat#1.02444; CAS: 67-66-3 Potassium Chloride Thermo Fisher Scientific Cat#BP366; CAS: 7447-40-7 Cis-10-Heptadecenoic Acid Millipore Sigma Cat#H8896; CAS: 29743-97-3 n-Hexane Millipore Sigma Cat#1.03701; CAS: 110-54-3 Methyl Acetate Millipore Sigma Cat#186325; CAS: 79-20-9 Acetonitrile, Optima LC/MS Grade Thermo Fisher Scientific Cat#A955: CAS: 75-05-8 Potassium Hydroxide Millipore Sigma Cat#484016; CAS: 1310-58-3 Formic Acid Millipore Sigma Cat#FX0440; CAS: 64-18-6 2,3,4,5,6-Pentafluorobenzyl Bromide Millipore Sigma Cat#90257; CAS: 1765-40-8 N,N-Diisopropylethylamine Millipore Sigma Cat#D125806; CAS: 7087-68-5 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Scientific Cat#78440 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34096 PowerUp SYBR Green Master Mix Thermo Fisher Scientific Cat#A25741 2,2-Diphenyl-1-picrylhydrazyl Millipore Sigma Cat#D9132; CAS: 1898-66-4 C11 BODIPY 581/591 Thermo Fisher Scientific Cat#D3861 40,6-Diamidino-2-phenylindole Invitrogen Cat#D1306 Lipofectamine 2000 Invitrogen Cat#11668027 SYTOX Green Nucleic Acid Stain Invitrogen Cat#S7020 Trypan Blue Bio-Rad Cat#1450021 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Quick-DNA Miniprep Plus Kit Zymo Research Cat#D4068 ZymoPURE II Plasmid Midiprep Kit Zymo Research Cat#D4200-A QIAprep Spin Miniprep Kit Qiagen Cat#27104 iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat#1725035 Deposited data Raw unprocessed fatty acid and lipidomics mass spectrometry data This paper MassIVE: MSV000095863; https://massive. ucsd.edu/ProteoSAFe/dataset.jsp? accession=MSV000095863 Uncropped Western blot images This paper Mendeley Data: https://doi.org/10.17632/ 95wwrptr59.1 Experimental models: Cell lines Human: A549 ATCC Cat#CCL-185 Human: HeLa ATCC Cat#CCL-2 Human: Panc1 ATCC Cat#CRL-1469 Human: H2199 ATCC Cat#CRL-5803 Human: MIA PaCa-2 ATCC Cat#CRL-1420 Human: 293T ATCC Cat#CRL-3216 Human: A549 sgNTC This paper N/A Human: A549 sgATGL #3.1 This paper N/A Human: A549 sgATGL #5.1 This paper N/A Human: A549 sgFADS2 #1.1 This paper N/A Human: A549 sgAGPS #1.1 This paper N/A Human: A549 sgAGPS #4.1 This paper N/A Oligonucleotides See Table S1 N/A N/A (Continued on next page) Cell Chemical Biology 32, 1–15.e1–e6, February 20, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Ran et al.52 Addgene Plasmid #48138 Software and algorithms Microsoft Excel 16.87 Microsoft Corporation https://www.microsoft.com/en-us/ microsoft-365/excel R 4.3.1 The R Project https://www.r-project.org/ Prism 10.2.3 GraphPad https://www.graphpad.com/features FlowJo 10.10.0 Becton Dickinson https://www.flowjo.com/ LipidSearch 5.0 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/multi-omics-dataanalysis/lipid-search-software.html El-Maven 0.12 Agrawal et al.46 https://github.com/ElucidataInc/ElMaven Skyline 23.1.0.455 Adams et al.48 https://skyline.ms/project/home/software/ Skyline/begin.view IsoCorrectoR Heinrich et al.49 https://www.bioconductor.org/packages/ release/bioc/html/IsoCorrectoR.html CRISPResso2 Clement et al.53 http://crispresso2.pinellolab.org/ submission
DNA Synthesis:Article Title: Generation and characterization of a chronic in vitro model to study the early stage of metabolic dysfunction-associated steatotic liver disease (MASLD).
Article Snippet: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic and progressive liver disease with an increasing global burden that starts with an early stage of simple steatosis (MASL) which frequently progresses to liver cirrhosis and hepatocellular carcinoma (HCC).. Despite its widespread occurrence, the MASL or steatotic stage, characterized by excessive fat accumulation in the liver and considered reversible and benign, has not been extensively studied.. To study MASL effectively, it is imperative to have a clinically relevant model system that focuses solely on steatosis, in a progressive and time-dependent manner, recapitulating molecular changes associated with human disease.
Polymer:Article Title: Single extracellular vesicle detection assay identifies membrane-associated α-synuclein as an early-stage biomarker in Parkinson's disease.
Article Snippet: Software and algorithms AutoCAD Autodesk https://www.autodesk.com/products/ autocad/overview?term=1-YEAR; RRID:SCR_021072 NIS-Elements Nikon https://www.nikoninstruments.com/ Products/Software; RRID:SCR_014329 Fiji ImageJ GNU General Public License https://ImageJ.net/software/fiji; RRID: SCR_002285 CODI ONI https://alto.codi.bio/ GraphPad Prism GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 Biorender Biorender www.biorender.com; RRID:SCR_018361 Other mTeSRTM1 Stem Cell Technologies Cat# 85857 Versene solution Thermo Fisher Scientific Cat# 15040066 GeltrexTM LDEV-free reduced growth factor basement membrane matrix Thermo Fisher Scientific Cat# A1413202 DMEM - high glucose Sigma Cat# D5671 Fetal Bovine Serum (FBS) Sigma Cat# F7524 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 (Continued on next page) e2 Cell Reports Medicine 6, 101999, March 18, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER GlutaMAXTM Supplement Thermo Fisher Scientific Cat# 35050061 Antibiotic-Antimycotic (100X) Thermo Fisher Scientific Cat# 15240062 TrypLETM Express Enzyme (1X), phenol red Thermo Fisher Scientific Cat# 12605036 HaltTM protease and phosphatase inhibitor cocktail Thermo Fisher Scientific Cat# 78444 Encapsulated superparamagnetic microspheres polymer-COOH (Glacial Blue) Bangs Laboratories Cat# MEGB002 Encapsulated superparamagnetic microspheres polymer-COOH (Flash Red) Bangs Laboratories Cat# MEFR002 Bovine serum albumin (BSA) Sigma Cat# A7030 EZ-LinkTM Micro Sulfo-NHS-LC-Biotinylation Kit Thermo Fisher Scientific Cat# 21935 SU-8 3025 Permanent negative epoxy photoresist Kayaku Cat# SU-8 3025 SYLGARDTM 184 Silicone Elastomer Kit Dow-Corning Cat# PDMS184 RIPA lysis and extraction buffer Thermo Fisher Scientific Cat# 89901 Amersham ECL prime western blotting detection reagent Cytiva Cat# RPN2232 HBSS Thermo Fisher Scientific Cat# 88284 Alexa Fluor 647Conjugation Kit (Fast) - Lightning-Link Abcam Cat# 269823 Alexa Fluor 488 Conjugation Kit (Fast) - Lightning-Link Abcam Cat# 236553 NEBuilder HiFi DNA Assembly Master Mix New England Biolabs Cat# E2621S OPEN ACCESS ..
Western Blot:Article Title: Single extracellular vesicle detection assay identifies membrane-associated α-synuclein as an early-stage biomarker in Parkinson's disease.
Article Snippet: Software and algorithms AutoCAD Autodesk https://www.autodesk.com/products/ autocad/overview?term=1-YEAR; RRID:SCR_021072 NIS-Elements Nikon https://www.nikoninstruments.com/ Products/Software; RRID:SCR_014329 Fiji ImageJ GNU General Public License https://ImageJ.net/software/fiji; RRID: SCR_002285 CODI ONI https://alto.codi.bio/ GraphPad Prism GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 Biorender Biorender www.biorender.com; RRID:SCR_018361 Other mTeSRTM1 Stem Cell Technologies Cat# 85857 Versene solution Thermo Fisher Scientific Cat# 15040066 GeltrexTM LDEV-free reduced growth factor basement membrane matrix Thermo Fisher Scientific Cat# A1413202 DMEM - high glucose Sigma Cat# D5671 Fetal Bovine Serum (FBS) Sigma Cat# F7524 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 (Continued on next page) e2 Cell Reports Medicine 6, 101999, March 18, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER GlutaMAXTM Supplement Thermo Fisher Scientific Cat# 35050061 Antibiotic-Antimycotic (100X) Thermo Fisher Scientific Cat# 15240062 TrypLETM Express Enzyme (1X), phenol red Thermo Fisher Scientific Cat# 12605036 HaltTM protease and phosphatase inhibitor cocktail Thermo Fisher Scientific Cat# 78444 Encapsulated superparamagnetic microspheres polymer-COOH (Glacial Blue) Bangs Laboratories Cat# MEGB002 Encapsulated superparamagnetic microspheres polymer-COOH (Flash Red) Bangs Laboratories Cat# MEFR002 Bovine serum albumin (BSA) Sigma Cat# A7030 EZ-LinkTM Micro Sulfo-NHS-LC-Biotinylation Kit Thermo Fisher Scientific Cat# 21935 SU-8 3025 Permanent negative epoxy photoresist Kayaku Cat# SU-8 3025 SYLGARDTM 184 Silicone Elastomer Kit Dow-Corning Cat# PDMS184 RIPA lysis and extraction buffer Thermo Fisher Scientific Cat# 89901 Amersham ECL prime western blotting detection reagent Cytiva Cat# RPN2232 HBSS Thermo Fisher Scientific Cat# 88284 Alexa Fluor 647Conjugation Kit (Fast) - Lightning-Link Abcam Cat# 269823 Alexa Fluor 488 Conjugation Kit (Fast) - Lightning-Link Abcam Cat# 236553 NEBuilder HiFi DNA Assembly Master Mix New England Biolabs Cat# E2621S OPEN ACCESS ..
Article Title: Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chloroform Millipore Sigma Cat#1.02444; CAS: 67-66-3 Potassium Chloride Thermo Fisher Scientific Cat#BP366; CAS: 7447-40-7 Cis-10-Heptadecenoic Acid Millipore Sigma Cat#H8896; CAS: 29743-97-3 n-Hexane Millipore Sigma Cat#1.03701; CAS: 110-54-3 Methyl Acetate Millipore Sigma Cat#186325; CAS: 79-20-9 Acetonitrile, Optima LC/MS Grade Thermo Fisher Scientific Cat#A955: CAS: 75-05-8 Potassium Hydroxide Millipore Sigma Cat#484016; CAS: 1310-58-3 Formic Acid Millipore Sigma Cat#FX0440; CAS: 64-18-6 2,3,4,5,6-Pentafluorobenzyl Bromide Millipore Sigma Cat#90257; CAS: 1765-40-8 N,N-Diisopropylethylamine Millipore Sigma Cat#D125806; CAS: 7087-68-5 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Scientific Cat#78440 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34096 PowerUp SYBR Green Master Mix Thermo Fisher Scientific Cat#A25741 2,2-Diphenyl-1-picrylhydrazyl Millipore Sigma Cat#D9132; CAS: 1898-66-4 C11 BODIPY 581/591 Thermo Fisher Scientific Cat#D3861 40,6-Diamidino-2-phenylindole Invitrogen Cat#D1306 Lipofectamine 2000 Invitrogen Cat#11668027 SYTOX Green Nucleic Acid Stain Invitrogen Cat#S7020 Trypan Blue Bio-Rad Cat#1450021 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Quick-DNA Miniprep Plus Kit Zymo Research Cat#D4068 ZymoPURE II Plasmid Midiprep Kit Zymo Research Cat#D4200-A QIAprep Spin Miniprep Kit Qiagen Cat#27104 iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat#1725035 Deposited data Raw unprocessed fatty acid and lipidomics mass spectrometry data This paper MassIVE: MSV000095863; https://massive. ucsd.edu/ProteoSAFe/dataset.jsp? accession=MSV000095863 Uncropped Western blot images This paper Mendeley Data: https://doi.org/10.17632/ 95wwrptr59.1 Experimental models: Cell lines Human: A549 ATCC Cat#CCL-185 Human: HeLa ATCC Cat#CCL-2 Human: Panc1 ATCC Cat#CRL-1469 Human: H2199 ATCC Cat#CRL-5803 Human: MIA PaCa-2 ATCC Cat#CRL-1420 Human: 293T ATCC Cat#CRL-3216 Human: A549 sgNTC This paper N/A Human: A549 sgATGL #3.1 This paper N/A Human: A549 sgATGL #5.1 This paper N/A Human: A549 sgFADS2 #1.1 This paper N/A Human: A549 sgAGPS #1.1 This paper N/A Human: A549 sgAGPS #4.1 This paper N/A Oligonucleotides See Table S1 N/A N/A (Continued on next page) Cell Chemical Biology 32, 1–15.e1–e6, February 20, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Ran et al.52 Addgene Plasmid #48138 Software and algorithms Microsoft Excel 16.87 Microsoft Corporation https://www.microsoft.com/en-us/ microsoft-365/excel R 4.3.1 The R Project https://www.r-project.org/ Prism 10.2.3 GraphPad https://www.graphpad.com/features FlowJo 10.10.0 Becton Dickinson https://www.flowjo.com/ LipidSearch 5.0 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/multi-omics-dataanalysis/lipid-search-software.html El-Maven 0.12 Agrawal et al.46 https://github.com/ElucidataInc/ElMaven Skyline 23.1.0.455 Adams et al.48 https://skyline.ms/project/home/software/ Skyline/begin.view IsoCorrectoR Heinrich et al.49 https://www.bioconductor.org/packages/ release/bioc/html/IsoCorrectoR.html CRISPResso2 Clement et al.53 http://crispresso2.pinellolab.org/ submission
Conjugation Assay:Article Title: Single extracellular vesicle detection assay identifies membrane-associated α-synuclein as an early-stage biomarker in Parkinson's disease.
Article Snippet: Software and algorithms AutoCAD Autodesk https://www.autodesk.com/products/ autocad/overview?term=1-YEAR; RRID:SCR_021072 NIS-Elements Nikon https://www.nikoninstruments.com/ Products/Software; RRID:SCR_014329 Fiji ImageJ GNU General Public License https://ImageJ.net/software/fiji; RRID: SCR_002285 CODI ONI https://alto.codi.bio/ GraphPad Prism GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 Biorender Biorender www.biorender.com; RRID:SCR_018361 Other mTeSRTM1 Stem Cell Technologies Cat# 85857 Versene solution Thermo Fisher Scientific Cat# 15040066 GeltrexTM LDEV-free reduced growth factor basement membrane matrix Thermo Fisher Scientific Cat# A1413202 DMEM - high glucose Sigma Cat# D5671 Fetal Bovine Serum (FBS) Sigma Cat# F7524 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 (Continued on next page) e2 Cell Reports Medicine 6, 101999, March 18, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER GlutaMAXTM Supplement Thermo Fisher Scientific Cat# 35050061 Antibiotic-Antimycotic (100X) Thermo Fisher Scientific Cat# 15240062 TrypLETM Express Enzyme (1X), phenol red Thermo Fisher Scientific Cat# 12605036 HaltTM protease and phosphatase inhibitor cocktail Thermo Fisher Scientific Cat# 78444 Encapsulated superparamagnetic microspheres polymer-COOH (Glacial Blue) Bangs Laboratories Cat# MEGB002 Encapsulated superparamagnetic microspheres polymer-COOH (Flash Red) Bangs Laboratories Cat# MEFR002 Bovine serum albumin (BSA) Sigma Cat# A7030 EZ-LinkTM Micro Sulfo-NHS-LC-Biotinylation Kit Thermo Fisher Scientific Cat# 21935 SU-8 3025 Permanent negative epoxy photoresist Kayaku Cat# SU-8 3025 SYLGARDTM 184 Silicone Elastomer Kit Dow-Corning Cat# PDMS184 RIPA lysis and extraction buffer Thermo Fisher Scientific Cat# 89901 Amersham ECL prime western blotting detection reagent Cytiva Cat# RPN2232 HBSS Thermo Fisher Scientific Cat# 88284 Alexa Fluor 647Conjugation Kit (Fast) - Lightning-Link Abcam Cat# 269823 Alexa Fluor 488 Conjugation Kit (Fast) - Lightning-Link Abcam Cat# 236553 NEBuilder HiFi DNA Assembly Master Mix New England Biolabs Cat# E2621S OPEN ACCESS ..
SYBR Green Assay:Article Title: Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chloroform Millipore Sigma Cat#1.02444; CAS: 67-66-3 Potassium Chloride Thermo Fisher Scientific Cat#BP366; CAS: 7447-40-7 Cis-10-Heptadecenoic Acid Millipore Sigma Cat#H8896; CAS: 29743-97-3 n-Hexane Millipore Sigma Cat#1.03701; CAS: 110-54-3 Methyl Acetate Millipore Sigma Cat#186325; CAS: 79-20-9 Acetonitrile, Optima LC/MS Grade Thermo Fisher Scientific Cat#A955: CAS: 75-05-8 Potassium Hydroxide Millipore Sigma Cat#484016; CAS: 1310-58-3 Formic Acid Millipore Sigma Cat#FX0440; CAS: 64-18-6 2,3,4,5,6-Pentafluorobenzyl Bromide Millipore Sigma Cat#90257; CAS: 1765-40-8 N,N-Diisopropylethylamine Millipore Sigma Cat#D125806; CAS: 7087-68-5 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Scientific Cat#78440 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34096 PowerUp SYBR Green Master Mix Thermo Fisher Scientific Cat#A25741 2,2-Diphenyl-1-picrylhydrazyl Millipore Sigma Cat#D9132; CAS: 1898-66-4 C11 BODIPY 581/591 Thermo Fisher Scientific Cat#D3861 40,6-Diamidino-2-phenylindole Invitrogen Cat#D1306 Lipofectamine 2000 Invitrogen Cat#11668027 SYTOX Green Nucleic Acid Stain Invitrogen Cat#S7020 Trypan Blue Bio-Rad Cat#1450021 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Quick-DNA Miniprep Plus Kit Zymo Research Cat#D4068 ZymoPURE II Plasmid Midiprep Kit Zymo Research Cat#D4200-A QIAprep Spin Miniprep Kit Qiagen Cat#27104 iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat#1725035 Deposited data Raw unprocessed fatty acid and lipidomics mass spectrometry data This paper MassIVE: MSV000095863; https://massive. ucsd.edu/ProteoSAFe/dataset.jsp? accession=MSV000095863 Uncropped Western blot images This paper Mendeley Data: https://doi.org/10.17632/ 95wwrptr59.1 Experimental models: Cell lines Human: A549 ATCC Cat#CCL-185 Human: HeLa ATCC Cat#CCL-2 Human: Panc1 ATCC Cat#CRL-1469 Human: H2199 ATCC Cat#CRL-5803 Human: MIA PaCa-2 ATCC Cat#CRL-1420 Human: 293T ATCC Cat#CRL-3216 Human: A549 sgNTC This paper N/A Human: A549 sgATGL #3.1 This paper N/A Human: A549 sgATGL #5.1 This paper N/A Human: A549 sgFADS2 #1.1 This paper N/A Human: A549 sgAGPS #1.1 This paper N/A Human: A549 sgAGPS #4.1 This paper N/A Oligonucleotides See Table S1 N/A N/A (Continued on next page) Cell Chemical Biology 32, 1–15.e1–e6, February 20, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Ran et al.52 Addgene Plasmid #48138 Software and algorithms Microsoft Excel 16.87 Microsoft Corporation https://www.microsoft.com/en-us/ microsoft-365/excel R 4.3.1 The R Project https://www.r-project.org/ Prism 10.2.3 GraphPad https://www.graphpad.com/features FlowJo 10.10.0 Becton Dickinson https://www.flowjo.com/ LipidSearch 5.0 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/multi-omics-dataanalysis/lipid-search-software.html El-Maven 0.12 Agrawal et al.46 https://github.com/ElucidataInc/ElMaven Skyline 23.1.0.455 Adams et al.48 https://skyline.ms/project/home/software/ Skyline/begin.view IsoCorrectoR Heinrich et al.49 https://www.bioconductor.org/packages/ release/bioc/html/IsoCorrectoR.html CRISPResso2 Clement et al.53 http://crispresso2.pinellolab.org/ submission
cDNA Synthesis:Article Title: Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chloroform Millipore Sigma Cat#1.02444; CAS: 67-66-3 Potassium Chloride Thermo Fisher Scientific Cat#BP366; CAS: 7447-40-7 Cis-10-Heptadecenoic Acid Millipore Sigma Cat#H8896; CAS: 29743-97-3 n-Hexane Millipore Sigma Cat#1.03701; CAS: 110-54-3 Methyl Acetate Millipore Sigma Cat#186325; CAS: 79-20-9 Acetonitrile, Optima LC/MS Grade Thermo Fisher Scientific Cat#A955: CAS: 75-05-8 Potassium Hydroxide Millipore Sigma Cat#484016; CAS: 1310-58-3 Formic Acid Millipore Sigma Cat#FX0440; CAS: 64-18-6 2,3,4,5,6-Pentafluorobenzyl Bromide Millipore Sigma Cat#90257; CAS: 1765-40-8 N,N-Diisopropylethylamine Millipore Sigma Cat#D125806; CAS: 7087-68-5 RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Scientific Cat#78440 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34096 PowerUp SYBR Green Master Mix Thermo Fisher Scientific Cat#A25741 2,2-Diphenyl-1-picrylhydrazyl Millipore Sigma Cat#D9132; CAS: 1898-66-4 C11 BODIPY 581/591 Thermo Fisher Scientific Cat#D3861 40,6-Diamidino-2-phenylindole Invitrogen Cat#D1306 Lipofectamine 2000 Invitrogen Cat#11668027 SYTOX Green Nucleic Acid Stain Invitrogen Cat#S7020 Trypan Blue Bio-Rad Cat#1450021 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Quick-DNA Miniprep Plus Kit Zymo Research Cat#D4068 ZymoPURE II Plasmid Midiprep Kit Zymo Research Cat#D4200-A QIAprep Spin Miniprep Kit Qiagen Cat#27104 iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat#1725035 Deposited data Raw unprocessed fatty acid and lipidomics mass spectrometry data This paper MassIVE: MSV000095863; https://massive. ucsd.edu/ProteoSAFe/dataset.jsp? accession=MSV000095863 Uncropped Western blot images This paper Mendeley Data: https://doi.org/10.17632/ 95wwrptr59.1 Experimental models: Cell lines Human: A549 ATCC Cat#CCL-185 Human: HeLa ATCC Cat#CCL-2 Human: Panc1 ATCC Cat#CRL-1469 Human: H2199 ATCC Cat#CRL-5803 Human: MIA PaCa-2 ATCC Cat#CRL-1420 Human: 293T ATCC Cat#CRL-3216 Human: A549 sgNTC This paper N/A Human: A549 sgATGL #3.1 This paper N/A Human: A549 sgATGL #5.1 This paper N/A Human: A549 sgFADS2 #1.1 This paper N/A Human: A549 sgAGPS #1.1 This paper N/A Human: A549 sgAGPS #4.1 This paper N/A Oligonucleotides See Table S1 N/A N/A (Continued on next page) Cell Chemical Biology 32, 1–15.e1–e6, February 20, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Ran et al.52 Addgene Plasmid #48138 Software and algorithms Microsoft Excel 16.87 Microsoft Corporation https://www.microsoft.com/en-us/ microsoft-365/excel R 4.3.1 The R Project https://www.r-project.org/ Prism 10.2.3 GraphPad https://www.graphpad.com/features FlowJo 10.10.0 Becton Dickinson https://www.flowjo.com/ LipidSearch 5.0 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/multi-omics-dataanalysis/lipid-search-software.html El-Maven 0.12 Agrawal et al.46 https://github.com/ElucidataInc/ElMaven Skyline 23.1.0.455 Adams et al.48 https://skyline.ms/project/home/software/ Skyline/begin.view IsoCorrectoR Heinrich et al.49 https://www.bioconductor.org/packages/ release/bioc/html/IsoCorrectoR.html CRISPResso2 Clement et al.53 http://crispresso2.pinellolab.org/ submission
|
Thermo Fisher is a verified supplier 
Thermo Fisher manufactures this product 