| Antibodies |
| Mouse monoclonal anti-CD11b (clone OX42) |
Bio-Rad |
Cat# MCA275R |
| Rat monoclonal anti-CD45 |
BD Pharmingen |
Cat# 550539 |
| Lectin BSL-1 |
Vector Labs |
Cat# L-1100 |
| Mouse monoclonal anti-ITGB5 |
eBioscience |
Cat# 14-0497-82 |
| Neutralizing antibodies against TGF-β (clone 1D11) |
R&D Systems |
Cat# MAB1835 |
| Anti-CD11b microbeads |
Miltenyi |
Cat# 130-049-601 |
| Rabbit monoclonal anti-TMEM119 |
(Bennett et al., 2016) |
N/A |
| Rabbit hybridoma supernatant anti-TMEM119 |
(Bennett et al., 2016) |
N/A |
| Goat anti-mouse IgG (H+L) |
Jackson ImmunoResearch |
Cat# 115-005-003 |
| Donkey anti-rabbit (H+L), 421 brilliant blue |
Biolegend |
Cat# 406410 |
| Rat monoclonal anti-mouse CD45 |
eBioscience |
Cat# 25-0451-82 |
| Rat anti-CD11b, conjugated PerCP/Cy5.5 |
Biolegend |
Cat# 101228 |
| Rat monoclonal anti-F4/80 |
Abcam |
Cat# ab6640 |
| Rabbit polyclonal anti-Iba1 |
Wako |
Cat# 019-19741 |
| Goat polyclonal anti-Iba1 |
Abcam |
Cat# AB5076 |
| Rabbit polyclonal anti-GFAP |
Dako |
Cat# Z0334 |
| O4 hybridoma supernatant mouse IgM |
(Foo et al., 2011) |
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
|
|
| Heparan sulfate |
Galen Laboratory Supplies |
Cat# GAG-HS01 |
| Heparin |
Sigma |
Cat# M3149 |
| Peptone from milk solids |
Sigma |
Cat# P6838 |
| Methyl-β-cyclodextrin |
Sigma |
Cat# C4555 |
| Human TGF-β2 |
Peprotech |
Cat# 100-35B |
| Murine IL-34 |
R&D Systems |
Cat# 5195-ML/CF |
| Ovine wool cholesterol |
Avanti Polar Lipids |
Cat# 700000P |
| Collagen IV |
Corning |
Cat#354233 |
| Oleic acid |
Cayman Chemicals |
Cat# 90260 |
| 11(Z)Eicosadienoic (Gondoic) Acid |
Cayman Chemicals |
Cat# 20606 |
| Calcein AM dye |
Invitrogen |
Cat# C3100MP |
| Ethidium homodimer-1 |
Invitrogen |
Cat# E1169 |
| Ovomucoid trypsin inhibitor |
Worthington |
Cat# LS003086
|
| Cycloheximide |
Sigma |
Cat# C7698 |
| Cytochalasin D |
Sigma |
Cat# C8273 |
| Cytosine-arabinoside |
Sigma |
Cat# C1768 |
| DNaseI |
Worthington |
Cat# DPRFS |
| Percoll PLUS |
GE Healthcare |
Cat# 17-5445-02 |
| Trypsin |
Sigma |
Cat# T9935 |
| DMEM/F12 |
Gibco |
Cat# 21041-02 |
| Penicillin/ Streptomycin |
Gibco |
Cat# 15140-122 |
| Glutamine |
Gibco |
Cat# 25030-081 |
| N-acetyl cysteine |
Sigma |
Cat# A9165 |
| Insulin |
Sigma |
Cat# I6634 |
| Apo-transferrin |
Sigma |
Cat# T1147 |
| Sodium selenite |
Sigma |
Cat# S-5261 |
| Papain |
Worthington |
Cat# LS003126
|
| DMEM (high glucose) |
Gibco |
Cat# 11960-044 |
| Neurobasal |
Gibco |
Cat# 21103-049 |
| Sodium pyruvate |
Sigma |
Cat# P5280 |
| Hydrocortisone |
Sigma |
Cat# H0888 |
| Forskolin |
Sigma |
Cat# F6886 |
| Putrescine |
Sigma |
Cat# P-5780 |
| Progesterone |
Sigma |
Cat# P-8783 |
| Dapi Fluoromount-G |
Southern Biotech |
Cat# 0100-20 |
| 30 kDa MWCO centrifugal filter unit |
Sartorius |
Cat# VS2022 |
| HiTrap Heparin HP columns |
GE Healthcare |
Cat# 17-0406-01 |
| HiTrap Q FF columns |
GE Healthcare |
Cat# 17-5053-01 |
| HiTrap Concanavalin A Sepharose 4B columns |
GE Healthcare |
Cat# 28-9520-85 |
| HiTrap Phenyl FF (High Sub) columns |
GE Healthcare |
Cat# 17-1355-01 |
| 4–20% SDS PAGE gels |
Bio-Rad |
Cat# 4561096 |
| SYPRO orange |
Invitrogen |
Cat# S6650 |
| Zymosan A |
Sigma |
Cat# Z4250 |
| Sheep red blood cells |
MP Biomedicals |
Cat# 55876 |
| 1.20 μm diameter amino-coated polystyrene particles |
Spherotech |
Cat# AM-10-10 |
| pHrodo Red succinimidyl ester |
ThermoFisher |
Cat# P36600
|
| Myelin Removal Beads II |
Miltenyi |
Cat# 130-096-433 |
| LS columns |
Miltenyi |
Cat# 130-042-401 |
| QuadroMACS Separator |
Miltenyi |
Cat# 130-090-976 |
| Microcapillary tube |
WPI |
Cat# 1B100f-4 |
| OCT |
ThermoFisher |
Cat# 23-730-571 |
| Vectashield with DAPI |
Vector labs |
Cat# H-1200 |
| SYBR Green PCR Master Mix |
ThermoFisher |
Cat# 4385612 |
| Vilo Master Mix |
ThermoFisher |
Cat# 11755050 |
| Powerup Sybr Green |
Thermofisher |
Cat# A25741 |
| Human serum |
Gemini |
Cat# 100-512 |
| GW2580 |
Cayman Chemicals |
Cat# 15411 |
| Critical Commercial Assays |
|
|
| LIVE/DEAD |
Life Technologies |
Cat# L23101
|
| Bradford Assay |
Bio-Rad |
Cat# 500-0006 |
| RNeasy Micro Kit |
Qiagen |
Cat# 74004 |
| High-Capacity RNA-to-cDNA Kit |
ThermoFisher Scientific |
Cat# 4387406 |
| Nextera XT DNA Sample Preparation Kit |
Illumina |
Cat# FC-131-1024 |
| Nextera XT Index Kit (24 indexes, 96 samples) |
Illumina |
Cat# FC-131-1001 |
| Deposited Data |
|
|
| SODG93A endstage versus non-transgenic day 130 for ALS |
(Chiu et al., 2013) |
|
| Mouse reference genome UCSC annotation mm10 |
UCSC Genome Browser |
|
| Rat reference genome UCSC annotation rn6 |
UCSC Genome Browser |
|
| iGenomes reference annotation gtf for rn6 |
Illumina |
|
| APP+ versus APP-for AD |
(Wang et al., 2015) |
|
| Intraperitoneal LPS (1 or 2 days post injection) versus saline for LPS 1 or LPS 2 |
(Bennett et al., 2016; Chiu et al., 2013) |
|
| E17 versus P14, P21, and P60 (average) for Dev Down 2 or Dev Up 2 |
(Bennett et al., 2016) |
|
| Brain E10.5, E11.5, and E12.5 (average) versus Adult cortex, hippocampus, and spinal cord (average) for Dev Down 1 or Dev Up 1 |
(Matcovitch-Natan et al., 2016) |
|
| Cluster 1 – microglia versus other tissue macrophages |
(Lavin et al., 2014) |
|
| Experimental Models: Organisms/Strains |
|
|
| Rat: Sprague-Dawley |
Charles River |
Cat# 400 |
| Knockout Mouse: FVB.129X1-Csf1rtm1Ers
|
(Dai et al., 2002) |
N/A |
| Mouse: FVB/NJ |
Jackson Laboratory |
Cat# 001800 |
| Oligonucleotides |
|
|
| Primers for QPCR (rat)—See Table S2
|
This Paper |
|
| Primers for QPCR (mouse) |
(Bennett et al., 2016) |
|
| Recombinant DNA |
|
|
| Software and Algorithms |
|
|
| ImageJ |
NIH |
|
| Incucyte ZOOM |
Essen Bioscience |
|
| cvMatch_Template ImageJ plugin |
https://sites.google.com/site/qingzongtseng/templatematching-ij-plugin |
|
| Primer3 |
The Whitehead Institute |
|
| Flowjo |
Treestar |
|
| HISAT version 2.0.3 |
(Kim et al., 2015) |
|
| Galaxy platform |
http://usegalaxy.org |
|
| Cufflinks version 2.2.1 |
(Trapnell et al., 2010) |
|
| DESeq2 |
(Love et al., 2014) |
|
| R (version 3.3.1) |
The R Foundation |
|
| GeneOverlap plugin for R |
https://www.bioconductor.org/packages/release/bioc/html/GeneOverlap.html |
|
| Pvclust plugin for R |
https://cran.rproject.org/web/packages/pvclust/index.html |
|
| Igor |
WaveMetrics |
|
| Other |
|
|
| Dounce homogenizer |
Wheaton |
Cat# 357424 |
