| Reagent/Resource | Reference or source | Identifier or catalog number |
|---|---|---|
| Experimental models | ||
| List cell lines, model organism strains, patient samples, isolated cell types etc. Indicate the species when appropriate. | ||
| HeLa | ATCC | Cat# ATCC CCL‐2 |
| RRID: CVCL_0030 | ||
| HSML | Kudoh (Hirosaki University) | N/A |
| THP‐1 | RIKEN | Cat# RCB3686 |
| RRID: CVCL_0006 | ||
| A‐THP‐1 | Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer Tohoku University | TKG 0296 |
| RRID: CVCL_5115 | ||
| B16 | ATCC | Cat# ATCC CRL‐6322 |
| RRID: CVCL_0604 | ||
| NHDF | Lonza | Cat# CC‐2511 |
| BALL‐1 | RIKEN | Cat# RCB1882 |
| RRID: CVCL_1075 | ||
| C57BL/6 (M. musculus) | CLEA Japan Inc | C57BL/6 |
| Antibodies | ||
| Include the name of the antibody, the company (or lab) who supplied the antibody, the catalogue or clone number, the host species in which the antibody was raised and mention whether the antibody is monoclonal or polyclonal. Please indicate the concentrations used for different experimental procedures. | ||
| Anti‐mouse PECAM‐1 Hamster mAb | Sigma‐Aldrich | Cat# MAB1398Z |
| RRID: AB_94207 | ||
| Anti‐mouse CD11b Rat mAb | BD Pharmingen | Cat# 550282 |
| RRID: AB_393577 | ||
| Anti‐mouse F4/80 Rat mAb | Bio‐Rad Laboratories | Cat# MCA497GA |
| RRID: AB_323806 | ||
| Anti‐mouse Ly6G Rat mAb | BioLegend | Cat# 127602 |
| RRID: AB_1089180 | ||
| Anti‐H3K4me3 Rabbit pAb | Active Motif | Cat# 39159 |
| RRID: AB_2615077 | ||
| Anti‐H3K27ac Mouse mAb | FUJIFILM Wako | Cat# 308‐34843 |
| RRID: AB_2819244 | ||
| Anti‐SREBP2 Mouse mAb | Takao Hamakubo (University of Tokyo) | N/A |
| Anti‐Histone H3 Rabbit pAb | Abcam | Cat# ab1791 |
| RRID: AB_302613 | ||
| Anti‐GRP78 BiP Rabbit pAb | Abcam | Cat# ab21685 |
| RRID: AB_2119834 | ||
| Anti‐SREBP2 Rabbit pAb | Cayman Chemical | Cat# 10007663 |
| RRID: AB_2615896 | ||
| Anti‐TGN46 Mouse mAb | Sigma‐Aldrich | Cat# SAB4200355 |
| RRID: AB_10762671 | ||
| Anti‐KDEL Rabbit mAb | Abcam | Cat# ab176333 |
| RRID: AB_2819147 | ||
| Anti‐SREBP2 Rabbit pAb | Abcam | Cat# ab30682 |
| RRID: AB_779079 | ||
| Anti‐HMGCS1 Rabbit pAb | GeneTex | Cat# GTX112346 |
| RRID: AB_11179696 | ||
| Alexa Fluor 488–conjugated goat anti‐Rat IgG | Thermo Fisher Scientific | Cat# A‐11006 |
| RRID: AB_2534074 | ||
| Alexa Fluor 568–conjugated goat anti‐Hamster IgG | Thermo Fisher Scientific | Cat# A‐21112 |
| RRID: AB_2535761 | ||
| Alexa Fluor 568–conjugated goat anti‐Rabbit IgG | Thermo Fisher Scientific | Cat# A‐11036 |
| RRID: AB_10563566 | ||
| Peroxidase‐conjugated affinity‐purified goat anti‐mouse IgG | Sigma‐Aldrich | Cat# A4416 |
| RRID: AB_258167 | ||
| Peroxidase‐conjugated affinity‐purified goat anti‐rabbit IgG | Cell Signaling Technology | Cat# 7074 |
| RRID: AB_2099233 | ||
| PerCP‐Cy5.5 anti‐CD11b mAb (M1/70) | Biolegend | Cat# 101228 |
| PE anti‐Ly6C mAb (HK1.4) | Biolegend | Cat# 128008 |
| APC anti‐CD11c mAb (N418) | Biolegend | Cat# 117310 |
| FITC anti‐NK1.1 mAb | Biolegend | Cat# 156508 |
| FITC anti‐F4/80 mAb (BM8) | Biolegend | Cat# 123108 |
| Pacific Blue anti‐Ly6G mAb (1A8) | Biolegend | Cat# 127612 |
| APC‐Cy7 anti‐CD45 mAb (IM7) | Biolegend | Cat# 103115 |
| PE anti‐CD4 mAb (GK1.5) | Biolegend | Cat# 100408 |
| PerCP‐Cy5.5 anti‐CD8 mAb (53‐6.7) | Biolegend | Cat# 100734 |
| APC anti‐B220 mAb (RA3‐6B2) | TOMBO | 20‐0452‐U025 |
| Oligonucleotides and sequence‐based reagents | ||
| For long lists of oligos or other sequences please refer to the relevant Table(s) or EV Table(s) | ||
| qPCR primers | This study | Table EV2A |
| ChIP‐PCR primers | This study | Table EV2B |
| Sequences for siRNA | This study | Table EV2C |
| Chemicals, enzymes and other reagents | ||
| e.g., drugs, peptides, recombinant proteins, dyes etc. | ||
| Fibroblast Basal Medium | Lonza | Cat# CC‐3131 |
| DMEM (High Glucose) | Nacalai Tesque | Cat# 08459‐64 |
| RPMI Medium 1640 | Nacalai Tesque | Cat# 30264‐56 |
| Fetal Bovine Serum | Biosera | Cat# FB‐1285/25 |
| Newborn Calf Lipoprotein‐deficient Serum | Sigma‐Aldrich | Cat# S5394 |
| Sulforhodamine B sodium salt | Sigma‐Aldrich | Cat# S1402‐5G |
| Ribonuclease | Nippon Gene | Cat# 313‐01461 |
| Propidium Iodide | FUJIFILM Wako | Cat# 25535‐16‐4 |
| Mevastatin | Sigma‐Aldrich | Cat# 474700 |
| Mevalonolactone | Sigma‐Aldrich | Cat# M4667 |
| Cholesterol | Sigma‐Aldrich | Cat# C8667 |
| 25‐hydroxycholesterol | Sigma‐Aldrich | Cat# H1015 |
| Calpain Inhibitor I | Nacalai Tesque | Cat# 07036‐24 |
| DMSO | Nacalai Tesque | Cat# 09659‐14 |
| Methanol | FUJIFILM Wako | Cat# 134‐11821 |
| Ethanol | FUJIFILM Wako | Cat# 057‐00456 |
| Mepanipyrim | FUJIFILM Wako | Cat# 137‐12651 |
| Nocodazole | FUJIFILM Wako | Cat# 140‐08531 |
| Brefeldin A | LKT Laboratories | Cat# B6816 |
| Phorbol 12‐myristate 13‐acetate (PMA) | AdipoGen | Cat# AG‐CN2‐0010‐M010 |
| Pimonidazole Hydrochloride | Shinsuke Sando (The University of Tokyo) | N/A |
| Atorvastatin calcium salt trihydrate | Tokyo Chemical Industry | Cat# A2476 |
| Bindarit | Cayman | Cat# 11479 |
| Isogen reagent | Nippon Gene | Cat# 311‐02504 |
| 5X PrimeScript RT Master Mix | Takara | Cat# RR036A |
| Lipofectamine® RNAiMAX Reagent | Thermo Fisher Scientific | Cat# 13778‐100 |
| Opti‐MEM Reduced Serum Medium | Thermo Fisher Scientific | Cat# 31985‐070 |
| DAPI‐Fluoromount‐G | Southern Biotech | Cat# 0100‐20 |
| cOmplete™, Mini, EDTA‐free Protease Inhibitor Cocktail | Sigma‐Aldrich | Cat# 11836170001 |
| Precision Plus Protein™ Dual Color Standards | Bio‐Rad | Cat# 1610374 |
| SuperSignal™ West Dura Extended Duration Substrate | Thermo Fisher Scientific | Cat# 34075 |
| Ponceau S | Nacalai Tesque | Cat# 28322‐72 |
| Formaldehyde solution | Wako | Cat# 064‐00406 |
| 4% paraformaldehyde phosphate‐buffered solution | FUJIFILM Wako | Cat# 163‐20145 |
| Software | ||
| Include version where applicable | ||
| IMPaLa | Kamburov et al (2011) | http://impala.molgen.mpg.de/ |
| GeneChip Operating Software | Thermo Fisher Scientific | https://www.thermofisher.com/jp/en/home/life‐science/microarray‐analysis/ |
| LAS X (v. 4.2.1) | Leica | https://www.leica‐microsystems.com/ |
| Seurat 4.0.1 | Butler et al (2018) | https://satijalab.org/seurat/ |
| Scanpy 1.7.2 | Wolf et al (2018) | https://scanpy.readthedocs.io/en/stable/ |
| GSVA package 1.38.2 | Hänzelmann et al (2013) | https://www.bioconductor.org/packages/release/bioc/html/GSVA.html |
| fgsea package 1.16.0 | Korotkevich et al (preprint: Korotkevich et al, 2016) | http://bioconductor.org/packages/release/bioc/html/fgsea.html |
| glmnet package 4.0.2 | Hurvich & Tsai (1995) | https://cran.r‐project.org/web/packages/glmnet/index.html |
| GEPIA2 | Tang et al (2019) | http://gepia2.cancer‐pku.cn |
| Kaplan‐Meier Plotter | Lánczky et al (2016) | http://kmplot.com/analysis/ |
| Other | ||
| Kits, instrumentation, laboratory equipment, lab ware etc. that are critical for the experimental procedure and do not fit in any of the above categories can be listed here. | ||
| RNeasy microKit | Qiagen | Cat# 74134 |
| TruSeq RNA Library Prep | Illumina | Cat# RS‐122‐2001 or RS‐122‐2002 |
| Genechip Human Genome U133 plus 2.0 oligonucleotide arrays | Thermo Fisher Scientific | Cat# 900466 |
| THUNDERBIRD® Probe qPCR Mix | TOYOBO | Cat# QPS‐101 |
| Total Cholesterol Assay Kit (Fluorometric) | Cell Biolabs | Cat# STA‐390 |
| QIA quick PCR purification kit | QIAGEN | Cat# 28181 |
| Duolink® Proximity Ligation Assay Kit | Sigma‐Aldrich | Cat# DUO92008 |
| Hypoxyprobe™‐1 Plus Kit | Hypoxyprobe, Inc. | Cat# HP2‐100 |
| 6.5 mm Transwell® with 8.0 μm Pore Polycarbonate Membrane Insert | Corning | Cat# 3464 |
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