| Antibodies |
|
| Mouse anti-BRN3a |
Millipore |
Cat# MAB1585, RRID: AB_94166 |
| Rabbit anti-IBA-1 |
FUJIFILM Wako Shibayagi |
Cat# 019–19741, RRID: AB_839504 |
| Goat anti-IGFBPL1 |
R&D systems |
Cat# AF4130, RRID: AB_2279980 |
| Goat anti-IGF-1R |
R&D systems |
Cat# AF-305-NA, RRID: AB_354457 |
| Rabbit anti-COX2 |
Thermo Fisher Scientific |
Cat# MA5–14568, RRID: AB_10984436 |
| anti-pNFκB |
Cell Signaling Technology |
Cat# 3033; RRID: AB_331284 |
| anti-tNFκB |
Cell Signaling Technology |
Cat# 9460, RRID:AB_2797704 |
| anti-pIGF1r |
Cell Signaling Technology |
Cat# 3027, RRID:AB_2122378 |
| anti-IGF1r |
Millipore |
Cat# ABE332, RRID:AB_10918911 |
| Mouse anti-CD68 |
Abcam |
Cat# ab201340, RRID: AB_2920880 |
| Mouse anti-phospho-Tau (Ser202, Thr205, AT8) |
Thermo Fisher Scientific |
Cat# MN1020, RRID: AB_223647 |
| Mouse anti-phospho-Tau (Thr181, AT270) |
Thermo Fisher Scientific |
Cat# MN1050, RRID: AB_223651 |
| Rabbit anti-phosphor-Tau (Thr231, AT180) |
Thermo Fisher Scientific |
Cat# 44–746G, RRID: AB_2533742 |
| Mouse anti-Tau |
Thermo Fisher Scientific |
Cat# MN1000, RRID: AB_2314654 |
| Rabbit anti-β-amyloid1–42
|
Thermo Fisher Scientific |
Cat# 700254, RRID: AB_2532306 |
| Rabbit anti-cleaved Caspase3 |
Cell Signaling Technology |
Cat# 9661, RRID: AB_2341188 |
| Mouse anti-GFAP-CY3 |
Sigma-Aldrich |
Cat# C9205, RRID: AB_476889 |
| Mouse anti-β-actin |
Thermo Fisher Scientific |
Cat# MA5–15739, RRID: AB_10979409 |
| Rabbit anti-GFAP |
Abcam |
Cat# ab7260, RRID:AB_305808 |
| Rabbit anti-TREM2 |
Thermo Fisher Scientific |
Cat# PA5–116068, RRID: AB_2900702 |
| Rat anti-anti-mouse CD11b |
Biolegend |
Cat# 101224, RRID: AB_755986 |
| Guinea pig anti-RBPMS |
PhosphoSolutions |
Cat# 1832-RBPMS, RRID: AB_2492226 |
| Rabbit anti-PSD95 |
Abcam |
Cat# ab18258, RRID: AB_444362 |
| Mouse anti-Syn |
Millipore |
Cat# MAB5258, RRID: AB_2313839 |
| Goat Anti-Mouse IgG (H + L), Biotinylated |
Vector Laboratories |
Cat# BA-9200, RRID: AB_2336171 |
| Goat Anti-Rabbit IgG (H + L), Biotinylated |
Vector Laboratories |
Cat# BA-1000, RRID: AB_2313606 |
| Rabbit Anti-Goat IgG (H + L), Biotinylated |
Vector Laboratories |
Cat# BA-5000, RRID: AB_2336126 |
| Streptavidin, Alexa Fluor 546 conjugate |
Thermo Fisher Scientific |
Cat# S-11225, RRID: AB_2532130 |
| Streptavidin, Alexa Fluor 488 conjugate |
Thermo Fisher Scientific |
Cat# S32354, RRID: AB_2315383 |
| Cy2 Donkey Anti-rabbit |
Jackson ImmunoResearch Labs |
Cat# 711–225-152, RRID: AB_2340612 |
| Cy3 Donkey Anti-mouse |
Jackson ImmunoResearch Labs |
Cat# 715–165-150, RRID: AB_2340813 |
| Cy3 Donkey Anti-goat |
Jackson ImmunoResearch Labs |
Cat# 705–165-147, RRID: AB_2307351 |
|
| Biological samples |
|
| Human Eye: Retina (Normal) |
Florida Lions Eye Bank, Bascom Palmer Eye Institute University of Miami; Miller School of Medicine |
Case# 2021–32323; Donor #21–12-050 |
| Human Eye: Retina (Glaucoma) |
Lions Gift of Sight University of Minnesota |
Patient ID: 22–0250 |
|
| Chemicals, peptides, and recombinant proteins |
|
| Bovine Serum Albumin (BSA) |
Sigma-Aldrich |
Cat# A7030–100G |
| Triton X-100 |
Sigma-Aldrich |
Cat# T8787 |
| Tween 20 |
Sigma-Aldrich |
Cat# P5927 |
| Normal Donkey Serum |
Jackson ImmunoResearch Labs |
Cat# 017–000-121, RRID: AB_2337258 |
| Normal Goat Serum |
Jackson ImmunoResearch Labs |
Cat# 005–000-121, RRID: AB_2336990 |
| Collagenase/Dispase |
Roche |
Cat# 11097113001 |
| rmCSF1 |
PeproTech |
Cat# 315–02 |
| LPS |
Sigma Aldrich |
Cat# L6529–1MG |
| rmIGFBPL1 |
R&D systems |
Cat# 4130-BL |
| IGF1Ri H-1356 |
BACHEM |
Cat# 4018631 |
| ATP |
Thermo Fisher Scientific |
Cat# R0441 |
| Anti-CD11b Magnetic Particles |
BD Biosciences |
Cat# 558013, RRID: AB_398649 |
|
| Critical commercial assays |
|
| Chromium Single Cell A Chip Kit |
10x Genomics |
Cat# 1000269 |
| Proteome Profiler Mouse Cytokine Array Kit |
R&D Systems |
Cat# ARY006 |
|
| Deposited data |
|
| Searchable microglia gene expression website |
This paper |
www.genecards.org
|
|
| Experimented models: Cell lines |
|
| Human microglial cell line HMC3 |
ATCC |
Cat# CRL-3304, RRID: CVCL_II76 |
| Mouse microglial cell line BV2 |
ATCC |
Cat# CRL-2469, RRID: CVCL_5745 |
|
| Experimental models: Organisms/strains |
|
| C57BL/6J |
The Jackson Laboratory |
Stock No: 000664, RRID: IMSR_JAX:000664 |
|
Cx3cr1GFP/GFP
|
The Jackson Laboratory |
B6.129P-Cx3cr1tm1Litt/J, Stock No: 005582, RRID: IMSR_JAX:005582 |
| DBA/2J |
The Jackson Laboratory |
Stock No: 000671, RRID: IMSR_JAX:000671 |
|
Igf1r(flox/flox)
|
The Jackson Laboratory |
B6; 129-Igf1rtm2Arge/J, Stock No: 012251, RRID: IMSR_JAX:012251 |
|
Cx3cr1tm2.1(cre/ERT2)
|
The Jackson Laboratory |
B6.129P2(C)-Cx3cr1tm2.1(cre/ERT2)Jung/J, Stock No: 020940, RRID: IMSR_JAX:020940 |
|
Igfbpl1−/− (KO)
|
Velocigene Regeneron Pharmaceuticals |
C57BL/6N-Igfbpl1tm1(KOMP)Vlcg/Mmucd, MGI ID: MGI:1933198, Stock No: 048159- UCD, RRID: MMRRC_048159-UCD |
|
| Oligonucleotides |
|
| See Table S1
|
N/A |
N/A |
|
| Software and algorithms |
|
| Cell Ranger |
10x Genomics |
Version 3.1.0 |
| R |
https://www.r-project.org/
|
4.2.1 |
| RStudio |
https://posit.co/
|
2022.07.2 Build 576 |
| biomaRt |
https://bioconductor.org/packages/release/bioc/html/biomaRt.html
|
2.48.3 |
| cowplot |
https://cran.r-project.org/web/packages/cowplot/
|
1.1.1 |
| dittoSeq |
https://bioconductor.org/packages/release/bioc/html/dittoSeq.html
|
1.4.4 |
| dplyr |
https://dplyr.tidyverse.org/
|
1.08 |
| EnhancedVolcano |
https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html
|
1.10.0 |
| escape |
https://github.com/ncborcherding/escape
|
1.2.0 |
| ggplot2 |
https://ggplot2.tidyverse.org/
|
3.3.5 |
| GSEABase |
https://bioconductor.org/packages/release/bioc/html/GSEABase.html
|
1.54.0 |
| htmlwidgets |
https://www.htmlwidgets.org/
|
1.5.4 |
| Matrix |
https://cran.r-project.org/web/packages/Matrix/index.html
|
1.3–4 |
| patchwork |
https://patchwork.data-imaginist.com/
|
1.1.1 |
| plotly |
https://plotly.com/r/
|
4.10.0 |
| reticulate |
https://rstudio.github.io/reticulate/
|
1.24 |
| Seurat |
https://satijalab.org/seurat/
|
3.0.0/4.1.0 |
| SeuratDisk |
https://github.com/mojaveazure/seurat-disk
|
0.0.0.9019 |
| SeuratWrappers |
https://github.com/satijalab/seurat-wrappers
|
0.3.0 |
| Python |
https://www.python.org/
|
3.8 |
| Jupyter Notebook |
https://jupyter.org/
|
6.4.11 |
| scanpy |
https://scanpy.readthedocs.io/en/stable/
|
1.9.1 |
| scFates |
https://scfates.readthedocs.io/en/latest/index.html
|
0.9.0 |
| anndata |
https://anndata.readthedocs.io/en/latest/
|
0.8.0 |
| numpy |
https://numpy.org/
|
1.21.6 |
| pandas |
https://pandas.pydata.org/
|
1.1.5 |
| palantir |
https://www.palantir.com/docs/foundry/transforms-python/use-python-libraries/
|
1.0.1 |
| matplotlib |
https://matplotlib.org/
|
3.5.1 |
| seaborn |
https://seaborn.pydata.org/
|
0.11.2 |
| scvelo |
https://scvelo.readthedocs.io/en/stable/
|
0.2.4 |
| GraphPad Prism 9 |
GraphPad |
https://www.graphpad.com/
|
| ImageJ |
National Institutes of Health |
https://ImageJ.nih.gov/ij/
|
| Gene Ontology |
Webgestalt |
http://webgestalt.org/option.php
|
| Protein-protein interaction |
String |
https://www.string-db.org/
|
| Zenodo Code Repository |
Zenodo (https://zenodo.org/record/8118833) |
https://doi.org/10.5281:zenodo/8118833
|
