|
Antibodies
|
| CD68 |
Abcam |
Abcam Cat# ab955, RRID:AB_307338 |
| CTIP2 |
Abcam |
Cat# ab18465, RRID:AB_2064130 |
| EOMES |
R&D Systems |
Cat# AF6166, RRID:AB_10569705 |
| FOXG1 |
Abcam |
Cat# ab196868, RRID:AB_2892604 |
| Iba1 |
Synaptic Systems |
Cat# 234 004, RRID:AB_2493179 |
| Iba1 |
Wako |
Cat# 019-19741, RRID:AB_839504 |
| IFITM3 |
Proteintech |
Cat# 11714-1-AP, RRID:AB_2295684 |
| Ki67 |
Agilent |
Cat# M724001-2, RRID:AB_2631211 |
| P2RY12 |
Sigma Aldrich |
Cat# HPA014518, RRID:AB_2669027 |
| PAX6 |
BioLegend |
Cat# 901301, RRID:AB_2565003 |
| pH2AX |
Cell Signaling Technologies |
Cat# 9718, RRID:AB_2118009 |
| psd95 |
Thermo Fisher |
Cat# 51-6900, RRID:AB_2533914 |
| SATB2 |
Santa Cruz Biotechnology |
Cat# sc-81376, RRID:AB_1129287 |
| SOX2 |
Santa Cruz Biotechnology |
Cat# sc-17320, RRID:AB_2286684 |
| Tuj1 |
Biolegend |
Cat# 80120, RRID:AB_2313773 |
| VGLUT1 |
Millipore Sigma |
Cat# MAB5502, RRID:AB_262185 |
|
Bacterial and Viral Strains
|
| AV-CMV-GFP |
Vector Biolabs |
1060 |
|
Chemicals, Peptides, and Recombinant Proteins
|
| Antibiotic-Antimycotic |
Gibco |
15240-062 |
| B27 supplement w/o Vitamin A |
Gibco |
12587-001 |
| B27 w/ Vitamin A |
Gibco |
17504-001 |
| BDNF |
Alomone |
b250 |
| CD lipid concentrate |
Thermo Fisher |
11905031 |
| CellTracker CM-DiI |
Thermo Fisher |
C7000 |
| DAPI Fluoromount |
Southern Biotech |
0100-20 |
| DMEM/F12 with Glutamax |
Gibco |
10565042 |
| Dnase |
Sigma Aldrich |
DN25 |
| Donkey Serum |
Jackson Immuno |
017-000-121 |
| Dorsomorphin |
Sigma-Aldrich |
P5499 |
| DPBS |
Gibco |
14190250 |
| Eagle’s basal medium |
UCSF Media Production Core |
N/A |
| EGF |
Peprotech |
100-47 |
| FBS |
HyClone |
SH30071.03 |
| Fibronectin |
Corning |
354008 |
| FGFb |
Peprotech |
100-18B |
| GlutaMax Supplement |
Thermo Fisher Scientific |
35050061 |
| HBSS |
UCSF Media Production Core |
N/A |
| Human Insulin |
Sigma |
I2643-50MG |
| IL34 |
Peprotech |
200-34 |
| Insulin-Transferrin-Selenium (ITS-G) (100×) |
Thermo Fisher Scientific |
41400045 |
| IWR1 -ε |
Cayman Chemical |
13659 |
| Laminin |
Thermo Fisher |
23017015 |
| Matrigel |
Fisher Scientific |
354234 |
| N2 supplement |
Gibco |
17502-048 |
| Neurobasal |
Gibco |
21103049 |
| Non-essential Amino Acids (NEAA) |
Thermo Fisher Scientific |
11140050 |
| PBS-EDTA, pH 7.5 |
Lonza |
BE02-017F |
| Trypsin, 2.5% |
Gibco |
15090046 |
| Trypsin, 0.25% |
Thermo Fisher |
25200056 |
|
Critical Commercial Assays
|
| 10X Chromium V2 |
10X Genomics |
PN-120237 |
| 10X Chromium V3 |
10X Genomics |
PN-1000092 |
| Cd11b magnetic beads |
Miltenyi Biotec |
130-049-601 |
|
Experimental Models: Cell Lines
|
| Human iPS cell line 28126 (male) |
Gilad Lab (Gallego Romero et al., 2015) |
|
| Human iPS cell line “WTC-11” (male) |
Conklin Lab (Bershteyn et al., 2017; Kreitzer et al., 2013) |
CVCL_Y803 |
| Human iPS cell line “1323-4” (female) |
Conklin Lab (Matsumoto et al., 2013) |
CVCL_0G84 |
| Human iPS cell line “WTC-10” (male) |
Conklin Lab (Bershteyn et al., 2017; Kreitzer et al., 2013) |
|
| Human iMG |
Fujifilm Cellular Dynamics |
01279 |
|
Software and Algorithms
|
| ImageJ (Fiji) |
Schindelin et al., 2012 |
https://imagej.net/Fiji
|
| CellRanger v3.0 |
10X Genomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
| Seurat v3.0 |
Satija Lab (Butler et al., 2018a) |
https://satijalab.org/seurat/
|
| deMULTIplex |
Gartner Lab (McGinnis et al., 2019) |
https://github.com/chris-mcginnis-ucsf/MULTI-seq
|
| CellProfiler 3.0 |
McQuin, Goodman et al. 2018
|
https://cellprofiler.org/
|
| CellBender |
(Fleming, Marioni et al. 2019) |
https://github.com/broadinstitute/CellBender
|
| UCell |
(Andreatta and Carmona 2021) |
https://github.com/carmonalab/UCell
|
|
Deposited data
|
| Primary microglia BICCN scRNAseq |
Brain Initiative Cell Census Network |
NeMO archive: RRID:SCR_015820 |
| Primary microglia in vitro culture scRNAseq |
This study |
Synapse: syn26009957 |
| Primary microglia in organoids scRNAseq |
This study |
Synapse: syn26009957 |
| Induced microglia scRNAseq |
This study |
GEO: GSE180945
|
| Organoids scRNAseq |
This study |
GEO: GSE180945
|
| Microglia in mouse brain scRNAseq |
(Svoboda, Barrasa et al. 2019) |
GEO: GSE139194
|
|
Other
|
| 6-well Ultralow Attachment Plates |
Corning |
3471 |
| 40 μm cell strainer |
Corning |
352340 |
| LS columns |
Miltenyi Biotec |
130-042-401 |
| glass-bottom 24 well plates |
Cellvis |
P24-1.5H-N |
| glass-bottom six-well plate |
Mattek |
P06G-1.5-10-F |
