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 |