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. Author manuscript; available in PMC: 2019 Jun 27.
Published in final edited form as: Neuron. 2018 May 31;98(6):1170–1183.e8. doi: 10.1016/j.neuron.2018.05.014
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Donkey anti-rabbit BV421 IgG (1:300) Biolegend Cat# 406410; RRID:AB_10897810
Rat monoclonal anti-Mouse CD45 (1:200) ebiosciences Cat# 25-0451-82; RRID:AB_469625
Anti-CD11b microbeads Miltinenyi Cat# 130-049-601
Rat anti-mouse Ly6g PercpCy5.5 (1:100) Biolegend Cat# 127615; RRID:AB_1877272
Rat anti-Mouse f4/80 APC (1:20) Biorad MCA497APC; RRID:AB_324435
PerCP/Cy5.5 anti-mouse/human CD45R/B220 (1:100) Biolegend Cat#103235; RRID:AB_893356
PE-CyTM 7 mouse anti-Human CD45 (10ul/test) BD Biosciences Cat#557748; RRID:AB_396854
Anti-Mouse Tmem119 (0.25-0.5 ug/mL) Clone [28-3] Abcam Cat# 209064 RRID:AB_2728083
Rabbit anti-human Tmem119 (1:200) Abcam Cat# 185333; RRID:AB_2687894
PerCP/Cy5.5 anti-mouse/human CD11b (1:100-200) Biolegend Cat#101228 RRID:AB_893232
PerCP/Cy5.5 anti-mouse CD3 (1:100) Biolegend Cat#100217; RRID:AB_1595597
Human BD Fc Block (20 ul/300ul cells) BD Biosciences Cat#564220 RRID:AB_2728082
Brilliant Violet 421 goat anti-mouse IgG (1:250) Biolegend Cat#405317; RRID:AB_10900419
PerCP/Cy5.5 anti-mouse CD127(IL-7Ra) (1:100) Biolegend Cat#135021; RRID:AB_1937274
BV421 Goat anti-rabbit IgG polyclonal (1:300) BD Biosciences Cat#565014; RRID:AB_2716308)
PE anti-mouse CD117(c-kit) (1:200) Biolegend Cat#105807; RRID:AB_313216
Purified rat anti-mouse CD16/CD32 (10 ul/300ul stain) BD Biosciences Cat#553142 RRID:AB_394657
PerCP/Cy5.5 anti-mouse Ly-6G (1:100) Biolegend Cat#127615; RRID:AB_1877272
PerCP/Cy5.5 anti-mouse NK-1.1 (1:100) Biolegend Cat#108727; RRID:AB_2132706
Purified mouse IgG2b, k Isotype Ctrl (concentration matched to stain) Biolegend Cat#401201 RRID:AB_326631
Purified anti-human TMEM119 clone A16075D, (0.3 ug/ml) Biolegend Forthcoming
Goat anti-mouse/human IBA1 (1:500) Abcam Cat# 5076; RRID:AB_2224402
Anti-Human cytoplasm (2ug/mL) Takara Cat# Y40410 RRID:AB_2632385
Brilliant Violet 421 anti-mouse Ly-6C (1:100) Biolegend Cat#128031; RRID:AB_2562177
Rabbit polyclonal anti-Human Ms4a7 (1:30) Atlas Cat# HPA017418; RRID:AB_1854137
PE anti-mouse/human CD11b (1:100) Biolegend Cat#101207; RRID:AB_312790
PerCP/Cy5.5 anti-mouse/human CD11b (1:100) Biolegend Cat#101228; RRID:AB_893232
Anti-mouse CD45 PE-Cyanine7 (1:200) eBioscience Cat#25-0451-82 RRID: AB_469625
Goat anti-mouse IgG Alexa 647 (1:500) Life Technologies Cat#A21236 RRID:AB_2535805
Rat anti-mouse albumin (1:750) Abcam Cat#Ab24325 RRID:AB_448009
Critical Commercial Assays
AllPrep Micro Kit Qiagen Cat#80284
RNAeasy Micro Kit Qiagen Cat# 74004
NEB Next Ultra RNAseq Kit New England Biolabs Cat# E7530S
RNAscope® Fluorescent Multiplex Detection Reagents ACDbio Cat#320851
RNAscope Multiplex Fluorescent Detection Kit v2 ACDbio Cat# 323110
RNAscope 2.5 HD Duplex Detection Reagents Kit ACDbio Cat# 322430
RNAscope® H202 & Protease Plus Reagents ACDbio Cat#322330
RNAscope® 2.5 Duplex Positive Control probe ACDbio Cat# 321641
TSA detection reagents; TSA plus Fluorescein PerkinElmer Cat# NEL741001KT
TSA detection reagents; TSA plus Cyanine 3 PerkinElmer Cat# NEL744E001KT
TSA detection reagents; TSA plus Cyanine 5 PerkinElmer Cat# NEL513001KT
Ovation-RNA-seq system V2 NuGEN Cat# 7102
Probe:Hs-Tmem119 ACDbio Cat# 478911
Probe: Mm-Ms4a7-C2 ACDbio Cat#314601-C2
Probe: Mm-Clec12a-C2 ACDbio Cat# 514351-C2
Probe: Mm-Sall1 ACDbio Cat# 469661
Probe: Mm-Tmem119-C2 ACDbio Cat# 472901-C2
Probe: Hs-Sall1 ACDbio Cat# 514331
Bone marrow monocytes isolation kit Miltenyi Biotec Cat# 130-100-629
Biological Samples
FVB Embryonic tissues Charles River Strain code: 207
Fetal brain tissue (human) Stemexpress N/A
Adult peripheral blood samples Stanford Blood Center N/A
Intraoperative brain tissue Stanford Brain Bank N/A
Post-mortem human brain samples Stanford Brain Bank N/A
Chemicals, Peptides, and Recombinant Proteins
Ms4a7 Peptide (40 molar excess) Atlas Cat# APrEST72174
TIC medium Bohlen et al., 2017 N/A
Heat inactivated FCS Gibco Cat#10437-028
ACK buffer Gibco Cat#A10492-01
RNAsin Promega Cat# N2615
DNAseI Worthington Cat# DPRFS
Trizol LS Sigma Cat# T3934
RLT buffer Qiagen Cat# 79216
RLT Plus Qiagen Cat# 1053393
DAB development Kit Thermo Scientific Cat# 34002
Z-4-Hydroxytamoxifen Sigma-Aldrich Cat# H7904
Human TGFβ2 Peprotech Cat#100-35B
Human Mcsf Peprotech Cat#300-25
Mouse Mcsf Peprotech Cat#315-02
Ovine wool cholesterol Avanti Polar Lipids Cat# 700000P
LIVE/DEAD Green (1 ul/1ml cells) Thermo Fisher Cat# L34969
Deposited Data
Microglia and MLC RNA-seq This Paper http://www.ncbi.nlm.nih.gov/bioproject/453419
Gene lists ALS UP, AD UP, LPS UP 1/2, DEV UP 1/2, CULTURE UP, and CULTURE DOWN (Bohlen et al., 2017) https://www.cell.com/action/showImagesData?pii=S0896-6273%2817%2930400-2
Gene list SALL1 UP (Buttgereit et al., 2016) https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5077/
Gene list NRROS UP (Wong et al., 2017) https://www.nature.com/articles/ni.3743#supplementary-information
Mouse reference genome UCSC annotation mm9 UCSC Genome Browser http://hgdownload.soe.ucsc.edu/downloads.html#mouse
Immune cell RNA-seq data (Lavin et al., 2014); (Zhang et al., 2014) https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63340; https://web.stanford.edu/group/barres_lab/brain_rnaseq.html
Experimental Models: Organisms/Strains
Mouse: FVB.129X1-Csf1rtmErs (also back crossed to C57BL6 in this paper) (Dai et al., 2002)/Dr. Richard Stanley RRID:MGI:3810944
Mouse: FVB/NCr Charles River RRID:MGI:2160605
Mouse: C57BL/6-Tg (CAG-EGFP)131Osb/LeySopJ- The Jackson Laboratory RRID:IMSR_JAX:006567
Mouse: Rag2tm1.1Flv CSF1tm1 (CSF1)Flv IL2rgtm1.1FLv/J The Jackson Laboratory RRID:IMSR_JAX:017708
Mouse: Rag2tm1.1Flv CSF1tm1 (CSF1)Flv IL2rgtm1.1FLv/J X Csf1rtmErs This paper N/A
Mouse: Cx3cr1CreER; B6 The Jackson Laboratory RRID:IMSR_JAX:021160
Mouse: Csf1rflox; B6 The Jackson Laboratory RRID:IMSR_JAX: 021212
Mouse: Cx3cr1CreER;Csf1rflox ; B6, CX3Cr1CreER mice were bred with Csf1rflox mice This paper N/A
Mouse: Ccr2RFP; B6 The Jackson Laboratory RRID:IMSR_JAX: 017586
Mouse: C57BL6 WT The Jackson Laboratory RRID:IMSR_JAX:000664
Oligonucleotides
Primers for Csf1r mice genotyping:
F1; 5′-AGACTCATTCCAGAACCAGAGC-3′ This Paper N/A
F2; 5′-CCGGTAGAATTCCTCGAGTCTA-3′ This Paper N/A
R1; 5′-GAATTTGGAGTCCTCACCTTTG-3′ This Paper N/A
Human Tmem119-6xhis Forward primer 5′- AAAAGTCGACGCCGCCACCAtggtttcggcggcag 3′ This Paper N/A
Human Tmem119-6xhis Reverse primer 5′ -TTTTGCGGCCGCTTAGTGGTGATGGTGATGATGACCAGAACCACCGACACTGGGGTGGACACTGC - 3′ This Paper N/A
Human Tmem119-ECD Forward primer 5′- AaaaaaggatccCgctctgtgcccctg -3′ This Paper N/A
Human Tmem119-ECD Reverse primer 5′ - TTT TTT TTG CGG CCG CCA TCA CGT ACT GGC -3′ This Paper N/A
Software and Algorithms
edgeR (Robinson et al., 2010) https://bioconductor.org/packages/release/bioc/html/edgeR.html
Tuxedo Pipeline Galaxyproject.org
ICY http://icy.bioimageanalysis.org/
Graphpad Prism (version 7.0) GraphPad https://www.graphpad.com
Clustvis http://biit.cs.ut.ee/clustvis_large/
Flowjo (version 10.4) Treestar https://www.flowjo.com
R (version 3.3.1) The R foundation https://www.r-project.org
Miseq Illumina N/A
JVenn (Bardou et al.,2014) http://jvenn.toulouse.inra.fr/app/example.html
Fiji https://imagej.net/Fiji
PVclust (Suzuki et al., 2014) www.sigmath.es.osaka-u.ac.jp/shimo-lab/prog/pvclust/
GSEA V3 http://software.broadinstitute.org/gsea/index.jsp
Other
Dounce homogenizer, 7 ml Wheaton 357542
Microcapillary tube WPI Cat#1B100f-4
DietGel Boost ClearH20 Cat#72-04-5022