KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Iba1 | Novus Biologicals | Cat#100-1028; RRID:AB_3148646 |
| Anti-CX3CR1 | Abcam | Cat#ab8020; RRID:AB_306202 |
| Alexa Fluor 488 donkey anti-goat | Thermo Fisher Scientific | Cat#A11055; RRID:AB_2534102 |
| Alexa Fluor 488 donkey anti-rabbit | Thermo Fisher Scientific | Cat#A31556; RRID:AB_221605 |
| Alexa Fluor 568 donkey anti-rabbit | Thermo Fisher Scientific | Cat#A10042; RRID:AB_2534017 |
| Anti-DGAT2 | Thermo Fisher Scientific | Cat#17100-1-AP; RRID:AB_2918049 |
| Anti-ATGL | Abcam | Cat#ab207799; RRID:AB_2888664 |
| HRP Goat anti Rabbit | AbClonal | Cat#AS014; RRID:AB_2769854 |
| Anti-NF-κB p65 | Cell Signaling Technology | Cat#8242; RRID:AB_10859369 |
| CD11b Antibody, anti-human, APC, REAfinity™ | Miltenyi Biotec | Cat#130-110-612; RRID:AB_2654666 |
|
Bacterial and virus strains | ||
| Lentivirius: DGAT1 shRNA Knockdown Vector #1 | VectorBuilder | LVS(VB240522-1447awh)-K1 |
| Lentivirius: DGAT1 shRNA Knockdown Vector #2 | VectorBuilder | LVS(VB240522-1452chc)-K1 |
| Lentivirius: DGAT1 shRNA Knockdown Vector #3 | VectorBuilder | LVS(VB240522-1455hjf)-K1 |
| Lentivirius: DGAT2 shRNA Knockdown Vector #1 | VectorBuilder | LVS(VB240522-1459hgp)-K1 |
| Lentivirius: DGAT2 shRNA Knockdown Vector #2 | VectorBuilder | LVS(VB240522-1461tqd)-K1 |
| Lentivirius: DGAT2 shRNA Knockdown Vector #3 | VectorBuilder | LVS(VB240522-1463ykr)-K1 |
| Lentivirius: Scramble_shRNA control | VectorBuilder | Made from VB010000-0009mxc |
|
Chemicals, peptides, and recombinant proteins | ||
| PF-06424439 | Sigma-Aldrich | Cat#PZ0233-5MG |
| PF-04620110 | Sigma-Aldrich | Cat#PZ0207-5MG |
| Triacsin C | Tocris, Bio-Techne | Cat#2472 |
| Atglistatin | Sigma-Aldrich | Cat # SML1075-5MG |
| KLH45 | Cayman Chemical | Cat#19889 |
| Recombinant Human GM-CSF | PeproTech | Cat#300-03 |
| Recombinant Human M-CSF | PeproTech | Cat#300-25 |
| Recombinant Human IL-34 | PeproTech | Cat#200-34 |
| Recombinant Human TGF-β1 (HEK293 derived) | PeproTech | Cat#100-21 |
| Recombinant Human Fractalkine (CX3CL1) | PeproTech | Cat#300-31 |
| Beta-Amyloid HiLyte™ Fluor 555, Human | AnaSpec | Cat#AS-60480-01 |
| Beta-Amyloid (1–42) | AnaSpec | Cat#AS-20276 |
| LPS, E. Coli O111:B4 | Sigma-Aldrich | Cat#LPS25 |
|
Critical commercial assays | ||
| LEGENDplex™ Human Inflammation Panel 1 (13-plex) with V-bottom Plate | Biolegend | Cat#740809 |
| SYBR™ GREEN FAST ADVANCED CELLS-TO-CT™ KIT | Thermo Fisher Scientific | Cat#A35380 |
| Human Apolipoprotein E ELISA Kit | Thermo Fisher Scientific | Cat#EHAPOE |
| Pierce BCA Protein Assay Kit | Thermo Fisher Scientific | Cat#23227 |
| LIVE/DEAD™ Viability/Cytotoxicity Kit, for mammalian cells | Thermo Fisher Scientific | Cat#L3224 |
| Direct-zol RNA isolation kits | Zymo Research | Cat#R2052 |
|
Deposited data | ||
| All code used to process transcriptomic data is available. | This paper | Zenodo: |
| RNA sequencing files are available. | This paper | GEO: GSE286874 |
|
Experimental models: Cell lines | ||
| Human: isogenic APOE3/APOE3 and APOE4/APOE4 iPSCs from parental line Coriell #AG09173 | Obtained via MTA from MIT21 | Coriell #AG09173; RRID: CVCL_4L66 |
| Human: isogenic APOE3/APOE3 and APOE4/APOE4 iPSCs from parental line Coriell #AG10788 | Obtained via MTA from MIT21 | Coriell #AG10788; RRID: CVCL_4M37 |
| Human: WTC-11 iPSCs | Obtained via MTA from UCSF32 | Derivative of RRID: CVCL_Y803 |
| Human: KOLF2.1J iPSCs | Gift from William Skarnes, The Jackson Laboratory | Derivative of RRID: CVCL_B5P3 |
| Lenti-XTM 293T cells | Clontech Laboratories | Cat#632180; RRID: CVCL_4401 |
|
Experimental models: Organisms/strains | ||
| Mouse: B6.129P2(Cg)-Cx3cr1tm1Litt/J | The Jackson Laboratory | RRID:IMSR_JAX:005582 |
| MOUSE: B6.CG-APOEEM2(APOE*)ADIUJ/J | The Jackson Laboratory | RRID:IMSR_JAX:029018 |
| Mouse: B6(SJL)-Apoetm1.1(APOE*4)Adiuj/J | The Jackson Laboratory | RRID:IMSR_JAX:027894 |
|
Oligonucleotides | ||
| DGAT1 Taqman Assay | Thermo Fisher Scientific | HS00201385_M1 DGAT1 |
| DGAT2 Taqman Assay | Thermo Fisher Scientific | HS01045913_M1 DGAT2 |
| PPID Taqman Assay | Thermo Fisher Scientific | Hs00234593_m1 PPID |
|
Recombinant DNA | ||
| pMD2.G | Addgene | Plasmid #12259 |
| pSIV-D3psi/delta env/delta Vif/delta Vpr | Addgene66 | Plasmid #132928 |
|
Software and algorithms | ||
| Live-Cell Imaging Analysis software | Sartorius | Version2021C https://www.sartorius.com/en/products/live-cell-imaging-analysis/live-cell-analysis-software |
| Fiji | ImageJ | Schindelin et al. 201267 |
| Nikon NIS-Elements AR software | Nikon | version 6.10.01 https://www.microscope.healthcare.nikon.com/products/software/nis-elements/nis-elements-advanced-research |
| Leica Application Suite X software | Leica | version 3.5.7.2 https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/ |
| R software | R project | https://cran.r-project.org/ |
| GraphPad Prism software | GraphPad Prism | https://www.graphpad.com/ |
| FlowJo™ | BD Life Sciences | version 10.9.0 https://www.flowjo.com/flowjo/overview |
| ShinyGO | Ge 202035 | https://bioinformatics.sdstate.edu/go/ |
| Metascape | Zhou et al.201939 | https://metascape.org/gp/index.html#/main/step1 |
| FastQC | Babraham Institute | https://www.bioinformatics.babraham.ac.uk |
| MultiQC | Seqera | https://multiqc.info |
| Qognit Software | BioLegend | https://legendplex.qognit.com |
| Eulerr.co | Eulerr | https://eulerr.co/ |
| Hypergeometric test software | Graeber Lab website, UCLA | https://systems.crump.ucla.edu/hypergeometric/ |
| OMNICxi software | Thermo Fisher Scientific | https://www.thermofisher.com/order/catalog/product/INQSOF018 |
|
Other | ||
| ViaFluor® 488 | Biotium | Cat#30086 |
| Alexa Fluor™ Plus 647 Phalloidin | Thermo Fisher Scientific | Cat#A30107 |
| Dextran, Texas Red™, 70,000 MW, Lysine Fixable | Thermo Fisher Scientific | Cat#D1864 |
| pHrodo™ Red Zymosan BioParticles™ Conjugate for Phagocytosis | Thermo Fisher Scientific | Cat#P35364 |
| Biotium LipidSpot™ 488 Lipid Droplet Stain | Biotium | Cat#70065 |
| STEMDIFF™ HEMATOPOIETIC KIT | Stem Cell Technologies | Cat#05310 |
| STEMDIFF™ MICROGLIA DIFFERENTIATION KIT | Stem Cell Technologies | Cat#100-0019 |
| STEMDIFF™ MICROGLIA MATURATION KIT | Stem Cell Technologies | Cat#100-0020 |
| SNCY 5.5 | Tocris, Bio-Techne | Cat#7295 |
| HCS LIPIDTOX™ DEEP RED NEUTRAL LIPID STAIN | Thermo Fisher Scientific | Cat# H34477 |
| REVERT™700 TOTAL PROTEIN STAIN | LI-COR Biotech | Cat#926-11016 |
| Hoechst 33258 | Sigma-Aldrich | Cat#94403 |