Membrane:
Derivative Assay:
Article Title: iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Amyloid Fibrils OC antibody Millipore Cat# AB2286 RRID: AB_1977024 Mouse Amyloid 1-16aa (6e10) BioLegend Cat# 803001 RRID: AB_2564653 Mouse b3Tubulin BioLegend Cat# 801201 RRID: AB_2313773 Mouse SC121 (human cytoplasm) Takara Bio Cat# AB-121-U-050, RRID: AB_2632385 Mouse ku80 (human nuclei) Abcam Cat # ab79220, RRID: AB_1603596 Chicken GFAP Abcam Cat# ab50738, RRID: AB_880201 Rabbit Iba1 Wako Cat# 27030, RRID: AB_2314667 Goat Iba1 Abcam Cat# ab5076, RRID: AB_2224402 Mouse ITGB5 Abcam Cat# ab177004 Mouse MMP9 Millipore Cat# AB19016, RRID: AB_11211211 Mouse MERTK BioLegend Cat# 367602, RRID: AB_2565898 Rabbit P2RY12 Sigma Cat# HPA014518 Rabbit PROS1 Abcam Cat# ab97387, RRID: AB_10695954 Rabbit PU1 Cell Signaling Technology Cat# 2266S, RRID: AB_10692379 Tabbit TMEM119 (human, C terminus) Abcam Cat# ab185333 Goat TREM2 (human) R&D Systems Cat# AF1828, RRID: AB_2208689 Rabbit TGFbR1 Abcam Cat# ab31013, RRID: AB_778352 Rabbit CX3CR1 Bio-Rad/AbD Serotec Cat# AHP1589, RRID: AB_2087421 LEAF Purified anti-human CD11b BioLegend Cat# 301312, RRID: AB_314164 Tau (T22), oligomeric EMD Millipore Cat# ABN454 APC-Cyanine7 CD45 (HI30) Tonbo Biosciences Cat# 25-0459-T10 PE/Cy7 CD235a (Glycophorin A) (clone HI264) BioLegend Cat# 349112, RRID: AB_2562708 APC CD43 Antibody (clone CD43-10G7) BioLegend Cat# 343206, RRID: AB_2194072 FITC CD34 Antibody (clone 561) BioLegend Cat# 343604, RRID: AB_1732005 PE CD41 Antibody (clone HIP8) BioLegend Cat# 303706, RRID: AB_314376 Zombie Violet Fixable Viability Stain BioLegend Cat# 423114 Biological Samples Human adult microglia RNA This paper N/A Human fetal microglia RNA This paper N/A Human PBMCs This paper N/A Human fetal tissue This paper N/A Chemicals, Peptides, and Recombinant Proteins Human TGFb1 Miltenyi Cat# 130-108-969 Human IL34 PeproTech Cat# 200-34 Human MCSF Thermo Fisher Scientific Cat# PHC9501 Human FGF2 Thermo Fisher Scientific Cat# PHG0261 Human BMP4 Thermo Fisher Scientific Cat# PHC9531 Human Activin A Thermo Fisher Scientific Cat# PHC9564 Human TPO Thermo Fisher Scientific Cat# PHC9514 Human IL6 Thermo Fisher Scientific Cat# PHC0061 Human IL3 Thermo Fisher Scientific Cat# PHC0031 Human VEGF Thermo Fisher Scientific Cat# PHC9391 (Continued on next page) e1 Neuron 94, 278–293.e1–e9, April 19, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human SCF Thermo Fisher Scientific Cat# PHC2111 Human Fractalkine (CX3CL1) PeproTech Cat# 300-31 Human CD200 Novoprotein Cat# C311-50ug BD Matrigel Matrix Growth Factor Reduced, Phenol Red-Free BD Biosciences Cat# 356231 TeSR-E8 STEMCELL Technologies Cat# 05940 IMDM (Iscove’s Modified Dulbecco’s Medium) Thermo Fisher Scientific Cat# 12440053 Ham’s F12 Thermo Fisher Scientific Cat# 11765054 DMEM/F-12, HEPES, no phenol red Thermo Fisher Scientific Cat# 11039021 RPMI 1640 Medium, no phenol red Thermo Fisher Scientific Cat# 11835030 BSA solution Miltenyi Cat# 130-091-376 Lithium Chloride solution Sigma Cat# L7026-100ML L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma Cat# A8960-5G 1-Thioglycerol (Monothioglycerol) Sigma Cat# M1753-100ML Poly-vinyl-Alcohol (PVA) Sigma Cat# P8136-250G B27 Supplement Thermo Fisher Scientific Cat# 17504044 N2 Supplement Thermo Fisher Scientific Cat# 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher Scientific Cat# 11140050 GlutaMax Supplement Thermo Fisher Scientific Cat# 35050061 ROCK inhibitor Y-27632 R&D Systems Cat# 1254 Human Insulin Sigma Cat# I2643-50MG Insulin-Transferrin-Selenium (ITS-G) (1003) Thermo Fisher Scientific Cat# 41400045 Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1003) Thermo Fisher Scientific Cat# 51500056 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 Adenosine 50-diphosphate Sigma Cat# 01905-250MG-F PSB 0739 Tocris Cat# 3983 Fura-2, AM, cell permeant Thermo Fisher Scientific Cat# F1201 May-Gr€unwald Stain Sigma Cat# MG1L SIGMA Giemsa Stain Sigma Cat# GS500-500ML b-Amyloid (1–42), Human AnaSpec Cat# AS-20276 b-Amyloid (1–42), HiLyte Fluor 555— labeled, Human AnaSpec Cat# AS-60480-01 Human Brain derived Tau Oligomers This paper N/A Human Brain derived Synaptosomes This paper N/A pHrodo Red Dye Thermo Fisher Scientific Cat# P36600 RNA-later Thermo Fisher Scientific Cat# AM7021 KnockOut Replacement Serum (KOSR) Thermo Fisher Scientific Cat# 10828028 Fetal Bovine Serum Thermo Fisher Scientific Cat# 10437028 Lipidure-coated 96-well V-bottom plate AMSBIO Cat# AMS.51011612 Amylo-Glo RTD Amyloid Plaque Stain Reagent Biosensis Cat# TR-300-AG TrypLE Select Enzyme (13), no phenol red Thermo Fisher Scientific 12563029 Critical Commercial Assays Human Pluripotent Stem Cell Functional Identification Kit R&D Systems Cat# SC027B V-PLEX Human Cytokine 30-Plex Meso Scale Discovery Cat# K15054D-1 (Continued on next page) Neuron 94, 278–293.e1–e9, April 19, 2017 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER nCounter Human Copy Number Variants Nanostring Cat# 115000102 nCounter Human Copy Number Variants Master Kit Nanostring Cat# 100052 Kapa Library Quantification Kit Kappa Biosystems N/A TruSeq RNA Library Prep Kit v.2 Illumina N/A QIAGEN RNA kit QIAGEN Cat# 74106 cDNA kit Thermo Fisher Scientific Cat# 11754050 EasySepTM Monocyte Enrichment Kit STEMCELL Technologies 19059 EasySep Human Pan-DC Pre-Enrichment Kit STEMCELL Technologies 19251 Deposited Data RNA-Seq Data This paper GEO: GSE89189 Experimental Models: Cell Lines Rat Hippocampal neurons This paper N/A Commercial iHPCs (Lot# 021405) Cellular Dynamics International Cat# HPC-301-020-001-PT Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 2 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 4 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 5 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 12 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC F14 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 20 Human: iPSC line from PBMC: Female UCI ADRC iPSC Core ADRC 22 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 76 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 85 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 86 Human: fetal-derived microglia: sex N/A This paper N/A Human: Monocytes—Sex inMethod Details This paper N/A Human: Monocyte-derived macrophages This paper N/A Human: Blood-borne Dendritic Cells Sex in Method Details This paper N/A Human: iPSC-derived HPCs This paper N/A Experimental Models: Organisms/Strains Rag-5xfAD; mouse: B6.Cg-Tg (APPSwFlLon,PSEN1*M146L*L286V) 6799Vas/Mmjax crossed with mouse: B10;B6-Rag2tm1Fwa Il2rgtm1Wjl From Jackson Laboratory and Taconic, respectively Blurton-Jones lab, UC Irvine, CA Marsh et al., 2016 MITRG; mouse M-CSFh;IL-3/GMCSFh;THPOh;Rag2 ;gc The Jackson Laboratory Jax: 017711 Rat: Sprague Dawley Crl:SD Charles River Charles River strain code: 400 Oligonucleotides Primers for qPCR, see Table S7 Thermo Fisher Scientific see Table S7 Software and Algorithms STAR Dobin et al., 2013 https://github.com/alexdobin/STAR RSEM Li and Dewey, 2011 https://deweylab.github.io/RSEM/ EdgeR Robinson et al., 2010 http://bioconductor.org/packages/release/ bioc/html/edgeR.html Rstudio N/A https://www.rstudio.com/ (Continued on next page) e3 Neuron 94, 278–293.e1–e9, April 19, 2017
SYBR Green Assay:
Polymerase Chain Reaction:
Reverse Transcription Polymerase Chain Reaction:
Software:
Microscopy:
other:Article Title: A short isoform of STIM1 confers frequency-dependent synaptic enhancement.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gateway BP Clonase II Enzyme mix ThermoFisher Scientific Cat #11789020 Gateway LR Clonase II Enzyme mix ThermoFisher Scientific Cat #11791020 Experimental models: cell lines HEK STIM1 / ;STIM2 / (S1/S2 DKO) kind gift by Dr. Don Gill N/A HEK Orai1 / ; Orai2 / ; Orai3 / (Orai TKO) Alansary et al., 2020 N/A MEF STIM1 / ;STIM2 / (S1/S2 DKO) Oh-Hora et al., 2008 N/A SH-SY5Y STIM1 / ;STIM2 / (S1/S2 DKO) this study N/A SH-SY5Y STIM1 / (S1 KO) this study N/A Experimental models: organisms/strains C56BI/6N Charles River Strain code 027 Oligonucleotides See Table S1 for oligonucleotide information.
Modification:Article Title: iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Amyloid Fibrils OC antibody Millipore Cat# AB2286 RRID: AB_1977024 Mouse Amyloid 1-16aa (6e10) BioLegend Cat# 803001 RRID: AB_2564653 Mouse b3Tubulin BioLegend Cat# 801201 RRID: AB_2313773 Mouse SC121 (human cytoplasm) Takara Bio Cat# AB-121-U-050, RRID: AB_2632385 Mouse ku80 (human nuclei) Abcam Cat # ab79220, RRID: AB_1603596 Chicken GFAP Abcam Cat# ab50738, RRID: AB_880201 Rabbit Iba1 Wako Cat# 27030, RRID: AB_2314667 Goat Iba1 Abcam Cat# ab5076, RRID: AB_2224402 Mouse ITGB5 Abcam Cat# ab177004 Mouse MMP9 Millipore Cat# AB19016, RRID: AB_11211211 Mouse MERTK BioLegend Cat# 367602, RRID: AB_2565898 Rabbit P2RY12 Sigma Cat# HPA014518 Rabbit PROS1 Abcam Cat# ab97387, RRID: AB_10695954 Rabbit PU1 Cell Signaling Technology Cat# 2266S, RRID: AB_10692379 Tabbit TMEM119 (human, C terminus) Abcam Cat# ab185333 Goat TREM2 (human) R&D Systems Cat# AF1828, RRID: AB_2208689 Rabbit TGFbR1 Abcam Cat# ab31013, RRID: AB_778352 Rabbit CX3CR1 Bio-Rad/AbD Serotec Cat# AHP1589, RRID: AB_2087421 LEAF Purified anti-human CD11b BioLegend Cat# 301312, RRID: AB_314164 Tau (T22), oligomeric EMD Millipore Cat# ABN454 APC-Cyanine7 CD45 (HI30) Tonbo Biosciences Cat# 25-0459-T10 PE/Cy7 CD235a (Glycophorin A) (clone HI264) BioLegend Cat# 349112, RRID: AB_2562708 APC CD43 Antibody (clone CD43-10G7) BioLegend Cat# 343206, RRID: AB_2194072 FITC CD34 Antibody (clone 561) BioLegend Cat# 343604, RRID: AB_1732005 PE CD41 Antibody (clone HIP8) BioLegend Cat# 303706, RRID: AB_314376 Zombie Violet Fixable Viability Stain BioLegend Cat# 423114 Biological Samples Human adult microglia RNA This paper N/A Human fetal microglia RNA This paper N/A Human PBMCs This paper N/A Human fetal tissue This paper N/A Chemicals, Peptides, and Recombinant Proteins Human TGFb1 Miltenyi Cat# 130-108-969 Human IL34 PeproTech Cat# 200-34 Human MCSF Thermo Fisher Scientific Cat# PHC9501 Human FGF2 Thermo Fisher Scientific Cat# PHG0261 Human BMP4 Thermo Fisher Scientific Cat# PHC9531 Human Activin A Thermo Fisher Scientific Cat# PHC9564 Human TPO Thermo Fisher Scientific Cat# PHC9514 Human IL6 Thermo Fisher Scientific Cat# PHC0061 Human IL3 Thermo Fisher Scientific Cat# PHC0031 Human VEGF Thermo Fisher Scientific Cat# PHC9391 (Continued on next page) e1 Neuron 94, 278–293.e1–e9, April 19, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human SCF Thermo Fisher Scientific Cat# PHC2111 Human Fractalkine (CX3CL1) PeproTech Cat# 300-31 Human CD200 Novoprotein Cat# C311-50ug BD Matrigel Matrix Growth Factor Reduced, Phenol Red-Free BD Biosciences Cat# 356231 TeSR-E8 STEMCELL Technologies Cat# 05940 IMDM (Iscove’s Modified Dulbecco’s Medium) Thermo Fisher Scientific Cat# 12440053 Ham’s F12 Thermo Fisher Scientific Cat# 11765054 DMEM/F-12, HEPES, no phenol red Thermo Fisher Scientific Cat# 11039021 RPMI 1640 Medium, no phenol red Thermo Fisher Scientific Cat# 11835030 BSA solution Miltenyi Cat# 130-091-376 Lithium Chloride solution Sigma Cat# L7026-100ML L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma Cat# A8960-5G 1-Thioglycerol (Monothioglycerol) Sigma Cat# M1753-100ML Poly-vinyl-Alcohol (PVA) Sigma Cat# P8136-250G B27 Supplement Thermo Fisher Scientific Cat# 17504044 N2 Supplement Thermo Fisher Scientific Cat# 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher Scientific Cat# 11140050 GlutaMax Supplement Thermo Fisher Scientific Cat# 35050061 ROCK inhibitor Y-27632 R&D Systems Cat# 1254 Human Insulin Sigma Cat# I2643-50MG Insulin-Transferrin-Selenium (ITS-G) (1003) Thermo Fisher Scientific Cat# 41400045 Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1003) Thermo Fisher Scientific Cat# 51500056 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 Adenosine 50-diphosphate Sigma Cat# 01905-250MG-F PSB 0739 Tocris Cat# 3983 Fura-2, AM, cell permeant Thermo Fisher Scientific Cat# F1201 May-Gr€unwald Stain Sigma Cat# MG1L SIGMA Giemsa Stain Sigma Cat# GS500-500ML b-Amyloid (1–42), Human AnaSpec Cat# AS-20276 b-Amyloid (1–42), HiLyte Fluor 555— labeled, Human AnaSpec Cat# AS-60480-01 Human Brain derived Tau Oligomers This paper N/A Human Brain derived Synaptosomes This paper N/A pHrodo Red Dye Thermo Fisher Scientific Cat# P36600 RNA-later Thermo Fisher Scientific Cat# AM7021 KnockOut Replacement Serum (KOSR) Thermo Fisher Scientific Cat# 10828028 Fetal Bovine Serum Thermo Fisher Scientific Cat# 10437028 Lipidure-coated 96-well V-bottom plate AMSBIO Cat# AMS.51011612 Amylo-Glo RTD Amyloid Plaque Stain Reagent Biosensis Cat# TR-300-AG TrypLE Select Enzyme (13), no phenol red Thermo Fisher Scientific 12563029 Critical Commercial Assays Human Pluripotent Stem Cell Functional Identification Kit R&D Systems Cat# SC027B V-PLEX Human Cytokine 30-Plex Meso Scale Discovery Cat# K15054D-1 (Continued on next page) Neuron 94, 278–293.e1–e9, April 19, 2017 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER nCounter Human Copy Number Variants Nanostring Cat# 115000102 nCounter Human Copy Number Variants Master Kit Nanostring Cat# 100052 Kapa Library Quantification Kit Kappa Biosystems N/A TruSeq RNA Library Prep Kit v.2 Illumina N/A QIAGEN RNA kit QIAGEN Cat# 74106 cDNA kit Thermo Fisher Scientific Cat# 11754050 EasySepTM Monocyte Enrichment Kit STEMCELL Technologies 19059 EasySep Human Pan-DC Pre-Enrichment Kit STEMCELL Technologies 19251 Deposited Data RNA-Seq Data This paper GEO: GSE89189 Experimental Models: Cell Lines Rat Hippocampal neurons This paper N/A Commercial iHPCs (Lot# 021405) Cellular Dynamics International Cat# HPC-301-020-001-PT Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 2 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 4 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 5 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 12 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC F14 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 20 Human: iPSC line from PBMC: Female UCI ADRC iPSC Core ADRC 22 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 76 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 85 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 86 Human: fetal-derived microglia: sex N/A This paper N/A Human: Monocytes—Sex inMethod Details This paper N/A Human: Monocyte-derived macrophages This paper N/A Human: Blood-borne Dendritic Cells Sex in Method Details This paper N/A Human: iPSC-derived HPCs This paper N/A Experimental Models: Organisms/Strains Rag-5xfAD; mouse: B6.Cg-Tg (APPSwFlLon,PSEN1*M146L*L286V) 6799Vas/Mmjax crossed with mouse: B10;B6-Rag2tm1Fwa Il2rgtm1Wjl From Jackson Laboratory and Taconic, respectively Blurton-Jones lab, UC Irvine, CA Marsh et al., 2016 MITRG; mouse M-CSFh;IL-3/GMCSFh;THPOh;Rag2 ;gc The Jackson Laboratory Jax: 017711 Rat: Sprague Dawley Crl:SD Charles River Charles River strain code: 400 Oligonucleotides Primers for qPCR, see Table S7 Thermo Fisher Scientific see Table S7 Software and Algorithms STAR Dobin et al., 2013 https://github.com/alexdobin/STAR RSEM Li and Dewey, 2011 https://deweylab.github.io/RSEM/ EdgeR Robinson et al., 2010 http://bioconductor.org/packages/release/ bioc/html/edgeR.html Rstudio N/A https://www.rstudio.com/ (Continued on next page) e3 Neuron 94, 278–293.e1–e9, April 19, 2017
Staining:Article Title: iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Amyloid Fibrils OC antibody Millipore Cat# AB2286 RRID: AB_1977024 Mouse Amyloid 1-16aa (6e10) BioLegend Cat# 803001 RRID: AB_2564653 Mouse b3Tubulin BioLegend Cat# 801201 RRID: AB_2313773 Mouse SC121 (human cytoplasm) Takara Bio Cat# AB-121-U-050, RRID: AB_2632385 Mouse ku80 (human nuclei) Abcam Cat # ab79220, RRID: AB_1603596 Chicken GFAP Abcam Cat# ab50738, RRID: AB_880201 Rabbit Iba1 Wako Cat# 27030, RRID: AB_2314667 Goat Iba1 Abcam Cat# ab5076, RRID: AB_2224402 Mouse ITGB5 Abcam Cat# ab177004 Mouse MMP9 Millipore Cat# AB19016, RRID: AB_11211211 Mouse MERTK BioLegend Cat# 367602, RRID: AB_2565898 Rabbit P2RY12 Sigma Cat# HPA014518 Rabbit PROS1 Abcam Cat# ab97387, RRID: AB_10695954 Rabbit PU1 Cell Signaling Technology Cat# 2266S, RRID: AB_10692379 Tabbit TMEM119 (human, C terminus) Abcam Cat# ab185333 Goat TREM2 (human) R&D Systems Cat# AF1828, RRID: AB_2208689 Rabbit TGFbR1 Abcam Cat# ab31013, RRID: AB_778352 Rabbit CX3CR1 Bio-Rad/AbD Serotec Cat# AHP1589, RRID: AB_2087421 LEAF Purified anti-human CD11b BioLegend Cat# 301312, RRID: AB_314164 Tau (T22), oligomeric EMD Millipore Cat# ABN454 APC-Cyanine7 CD45 (HI30) Tonbo Biosciences Cat# 25-0459-T10 PE/Cy7 CD235a (Glycophorin A) (clone HI264) BioLegend Cat# 349112, RRID: AB_2562708 APC CD43 Antibody (clone CD43-10G7) BioLegend Cat# 343206, RRID: AB_2194072 FITC CD34 Antibody (clone 561) BioLegend Cat# 343604, RRID: AB_1732005 PE CD41 Antibody (clone HIP8) BioLegend Cat# 303706, RRID: AB_314376 Zombie Violet Fixable Viability Stain BioLegend Cat# 423114 Biological Samples Human adult microglia RNA This paper N/A Human fetal microglia RNA This paper N/A Human PBMCs This paper N/A Human fetal tissue This paper N/A Chemicals, Peptides, and Recombinant Proteins Human TGFb1 Miltenyi Cat# 130-108-969 Human IL34 PeproTech Cat# 200-34 Human MCSF Thermo Fisher Scientific Cat# PHC9501 Human FGF2 Thermo Fisher Scientific Cat# PHG0261 Human BMP4 Thermo Fisher Scientific Cat# PHC9531 Human Activin A Thermo Fisher Scientific Cat# PHC9564 Human TPO Thermo Fisher Scientific Cat# PHC9514 Human IL6 Thermo Fisher Scientific Cat# PHC0061 Human IL3 Thermo Fisher Scientific Cat# PHC0031 Human VEGF Thermo Fisher Scientific Cat# PHC9391 (Continued on next page) e1 Neuron 94, 278–293.e1–e9, April 19, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human SCF Thermo Fisher Scientific Cat# PHC2111 Human Fractalkine (CX3CL1) PeproTech Cat# 300-31 Human CD200 Novoprotein Cat# C311-50ug BD Matrigel Matrix Growth Factor Reduced, Phenol Red-Free BD Biosciences Cat# 356231 TeSR-E8 STEMCELL Technologies Cat# 05940 IMDM (Iscove’s Modified Dulbecco’s Medium) Thermo Fisher Scientific Cat# 12440053 Ham’s F12 Thermo Fisher Scientific Cat# 11765054 DMEM/F-12, HEPES, no phenol red Thermo Fisher Scientific Cat# 11039021 RPMI 1640 Medium, no phenol red Thermo Fisher Scientific Cat# 11835030 BSA solution Miltenyi Cat# 130-091-376 Lithium Chloride solution Sigma Cat# L7026-100ML L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma Cat# A8960-5G 1-Thioglycerol (Monothioglycerol) Sigma Cat# M1753-100ML Poly-vinyl-Alcohol (PVA) Sigma Cat# P8136-250G B27 Supplement Thermo Fisher Scientific Cat# 17504044 N2 Supplement Thermo Fisher Scientific Cat# 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher Scientific Cat# 11140050 GlutaMax Supplement Thermo Fisher Scientific Cat# 35050061 ROCK inhibitor Y-27632 R&D Systems Cat# 1254 Human Insulin Sigma Cat# I2643-50MG Insulin-Transferrin-Selenium (ITS-G) (1003) Thermo Fisher Scientific Cat# 41400045 Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1003) Thermo Fisher Scientific Cat# 51500056 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 Adenosine 50-diphosphate Sigma Cat# 01905-250MG-F PSB 0739 Tocris Cat# 3983 Fura-2, AM, cell permeant Thermo Fisher Scientific Cat# F1201 May-Gr€unwald Stain Sigma Cat# MG1L SIGMA Giemsa Stain Sigma Cat# GS500-500ML b-Amyloid (1–42), Human AnaSpec Cat# AS-20276 b-Amyloid (1–42), HiLyte Fluor 555— labeled, Human AnaSpec Cat# AS-60480-01 Human Brain derived Tau Oligomers This paper N/A Human Brain derived Synaptosomes This paper N/A pHrodo Red Dye Thermo Fisher Scientific Cat# P36600 RNA-later Thermo Fisher Scientific Cat# AM7021 KnockOut Replacement Serum (KOSR) Thermo Fisher Scientific Cat# 10828028 Fetal Bovine Serum Thermo Fisher Scientific Cat# 10437028 Lipidure-coated 96-well V-bottom plate AMSBIO Cat# AMS.51011612 Amylo-Glo RTD Amyloid Plaque Stain Reagent Biosensis Cat# TR-300-AG TrypLE Select Enzyme (13), no phenol red Thermo Fisher Scientific 12563029 Critical Commercial Assays Human Pluripotent Stem Cell Functional Identification Kit R&D Systems Cat# SC027B V-PLEX Human Cytokine 30-Plex Meso Scale Discovery Cat# K15054D-1 (Continued on next page) Neuron 94, 278–293.e1–e9, April 19, 2017 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER nCounter Human Copy Number Variants Nanostring Cat# 115000102 nCounter Human Copy Number Variants Master Kit Nanostring Cat# 100052 Kapa Library Quantification Kit Kappa Biosystems N/A TruSeq RNA Library Prep Kit v.2 Illumina N/A QIAGEN RNA kit QIAGEN Cat# 74106 cDNA kit Thermo Fisher Scientific Cat# 11754050 EasySepTM Monocyte Enrichment Kit STEMCELL Technologies 19059 EasySep Human Pan-DC Pre-Enrichment Kit STEMCELL Technologies 19251 Deposited Data RNA-Seq Data This paper GEO: GSE89189 Experimental Models: Cell Lines Rat Hippocampal neurons This paper N/A Commercial iHPCs (Lot# 021405) Cellular Dynamics International Cat# HPC-301-020-001-PT Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 2 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 4 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 5 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 12 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC F14 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 20 Human: iPSC line from PBMC: Female UCI ADRC iPSC Core ADRC 22 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 76 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 85 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 86 Human: fetal-derived microglia: sex N/A This paper N/A Human: Monocytes—Sex inMethod Details This paper N/A Human: Monocyte-derived macrophages This paper N/A Human: Blood-borne Dendritic Cells Sex in Method Details This paper N/A Human: iPSC-derived HPCs This paper N/A Experimental Models: Organisms/Strains Rag-5xfAD; mouse: B6.Cg-Tg (APPSwFlLon,PSEN1*M146L*L286V) 6799Vas/Mmjax crossed with mouse: B10;B6-Rag2tm1Fwa Il2rgtm1Wjl From Jackson Laboratory and Taconic, respectively Blurton-Jones lab, UC Irvine, CA Marsh et al., 2016 MITRG; mouse M-CSFh;IL-3/GMCSFh;THPOh;Rag2 ;gc The Jackson Laboratory Jax: 017711 Rat: Sprague Dawley Crl:SD Charles River Charles River strain code: 400 Oligonucleotides Primers for qPCR, see Table S7 Thermo Fisher Scientific see Table S7 Software and Algorithms STAR Dobin et al., 2013 https://github.com/alexdobin/STAR RSEM Li and Dewey, 2011 https://deweylab.github.io/RSEM/ EdgeR Robinson et al., 2010 http://bioconductor.org/packages/release/ bioc/html/edgeR.html Rstudio N/A https://www.rstudio.com/ (Continued on next page) e3 Neuron 94, 278–293.e1–e9, April 19, 2017
Giemsa Stain:Article Title: iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Amyloid Fibrils OC antibody Millipore Cat# AB2286 RRID: AB_1977024 Mouse Amyloid 1-16aa (6e10) BioLegend Cat# 803001 RRID: AB_2564653 Mouse b3Tubulin BioLegend Cat# 801201 RRID: AB_2313773 Mouse SC121 (human cytoplasm) Takara Bio Cat# AB-121-U-050, RRID: AB_2632385 Mouse ku80 (human nuclei) Abcam Cat # ab79220, RRID: AB_1603596 Chicken GFAP Abcam Cat# ab50738, RRID: AB_880201 Rabbit Iba1 Wako Cat# 27030, RRID: AB_2314667 Goat Iba1 Abcam Cat# ab5076, RRID: AB_2224402 Mouse ITGB5 Abcam Cat# ab177004 Mouse MMP9 Millipore Cat# AB19016, RRID: AB_11211211 Mouse MERTK BioLegend Cat# 367602, RRID: AB_2565898 Rabbit P2RY12 Sigma Cat# HPA014518 Rabbit PROS1 Abcam Cat# ab97387, RRID: AB_10695954 Rabbit PU1 Cell Signaling Technology Cat# 2266S, RRID: AB_10692379 Tabbit TMEM119 (human, C terminus) Abcam Cat# ab185333 Goat TREM2 (human) R&D Systems Cat# AF1828, RRID: AB_2208689 Rabbit TGFbR1 Abcam Cat# ab31013, RRID: AB_778352 Rabbit CX3CR1 Bio-Rad/AbD Serotec Cat# AHP1589, RRID: AB_2087421 LEAF Purified anti-human CD11b BioLegend Cat# 301312, RRID: AB_314164 Tau (T22), oligomeric EMD Millipore Cat# ABN454 APC-Cyanine7 CD45 (HI30) Tonbo Biosciences Cat# 25-0459-T10 PE/Cy7 CD235a (Glycophorin A) (clone HI264) BioLegend Cat# 349112, RRID: AB_2562708 APC CD43 Antibody (clone CD43-10G7) BioLegend Cat# 343206, RRID: AB_2194072 FITC CD34 Antibody (clone 561) BioLegend Cat# 343604, RRID: AB_1732005 PE CD41 Antibody (clone HIP8) BioLegend Cat# 303706, RRID: AB_314376 Zombie Violet Fixable Viability Stain BioLegend Cat# 423114 Biological Samples Human adult microglia RNA This paper N/A Human fetal microglia RNA This paper N/A Human PBMCs This paper N/A Human fetal tissue This paper N/A Chemicals, Peptides, and Recombinant Proteins Human TGFb1 Miltenyi Cat# 130-108-969 Human IL34 PeproTech Cat# 200-34 Human MCSF Thermo Fisher Scientific Cat# PHC9501 Human FGF2 Thermo Fisher Scientific Cat# PHG0261 Human BMP4 Thermo Fisher Scientific Cat# PHC9531 Human Activin A Thermo Fisher Scientific Cat# PHC9564 Human TPO Thermo Fisher Scientific Cat# PHC9514 Human IL6 Thermo Fisher Scientific Cat# PHC0061 Human IL3 Thermo Fisher Scientific Cat# PHC0031 Human VEGF Thermo Fisher Scientific Cat# PHC9391 (Continued on next page) e1 Neuron 94, 278–293.e1–e9, April 19, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human SCF Thermo Fisher Scientific Cat# PHC2111 Human Fractalkine (CX3CL1) PeproTech Cat# 300-31 Human CD200 Novoprotein Cat# C311-50ug BD Matrigel Matrix Growth Factor Reduced, Phenol Red-Free BD Biosciences Cat# 356231 TeSR-E8 STEMCELL Technologies Cat# 05940 IMDM (Iscove’s Modified Dulbecco’s Medium) Thermo Fisher Scientific Cat# 12440053 Ham’s F12 Thermo Fisher Scientific Cat# 11765054 DMEM/F-12, HEPES, no phenol red Thermo Fisher Scientific Cat# 11039021 RPMI 1640 Medium, no phenol red Thermo Fisher Scientific Cat# 11835030 BSA solution Miltenyi Cat# 130-091-376 Lithium Chloride solution Sigma Cat# L7026-100ML L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma Cat# A8960-5G 1-Thioglycerol (Monothioglycerol) Sigma Cat# M1753-100ML Poly-vinyl-Alcohol (PVA) Sigma Cat# P8136-250G B27 Supplement Thermo Fisher Scientific Cat# 17504044 N2 Supplement Thermo Fisher Scientific Cat# 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher Scientific Cat# 11140050 GlutaMax Supplement Thermo Fisher Scientific Cat# 35050061 ROCK inhibitor Y-27632 R&D Systems Cat# 1254 Human Insulin Sigma Cat# I2643-50MG Insulin-Transferrin-Selenium (ITS-G) (1003) Thermo Fisher Scientific Cat# 41400045 Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1003) Thermo Fisher Scientific Cat# 51500056 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 Adenosine 50-diphosphate Sigma Cat# 01905-250MG-F PSB 0739 Tocris Cat# 3983 Fura-2, AM, cell permeant Thermo Fisher Scientific Cat# F1201 May-Gr€unwald Stain Sigma Cat# MG1L SIGMA Giemsa Stain Sigma Cat# GS500-500ML b-Amyloid (1–42), Human AnaSpec Cat# AS-20276 b-Amyloid (1–42), HiLyte Fluor 555— labeled, Human AnaSpec Cat# AS-60480-01 Human Brain derived Tau Oligomers This paper N/A Human Brain derived Synaptosomes This paper N/A pHrodo Red Dye Thermo Fisher Scientific Cat# P36600 RNA-later Thermo Fisher Scientific Cat# AM7021 KnockOut Replacement Serum (KOSR) Thermo Fisher Scientific Cat# 10828028 Fetal Bovine Serum Thermo Fisher Scientific Cat# 10437028 Lipidure-coated 96-well V-bottom plate AMSBIO Cat# AMS.51011612 Amylo-Glo RTD Amyloid Plaque Stain Reagent Biosensis Cat# TR-300-AG TrypLE Select Enzyme (13), no phenol red Thermo Fisher Scientific 12563029 Critical Commercial Assays Human Pluripotent Stem Cell Functional Identification Kit R&D Systems Cat# SC027B V-PLEX Human Cytokine 30-Plex Meso Scale Discovery Cat# K15054D-1 (Continued on next page) Neuron 94, 278–293.e1–e9, April 19, 2017 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER nCounter Human Copy Number Variants Nanostring Cat# 115000102 nCounter Human Copy Number Variants Master Kit Nanostring Cat# 100052 Kapa Library Quantification Kit Kappa Biosystems N/A TruSeq RNA Library Prep Kit v.2 Illumina N/A QIAGEN RNA kit QIAGEN Cat# 74106 cDNA kit Thermo Fisher Scientific Cat# 11754050 EasySepTM Monocyte Enrichment Kit STEMCELL Technologies 19059 EasySep Human Pan-DC Pre-Enrichment Kit STEMCELL Technologies 19251 Deposited Data RNA-Seq Data This paper GEO: GSE89189 Experimental Models: Cell Lines Rat Hippocampal neurons This paper N/A Commercial iHPCs (Lot# 021405) Cellular Dynamics International Cat# HPC-301-020-001-PT Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 2 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 4 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 5 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 12 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC F14 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 20 Human: iPSC line from PBMC: Female UCI ADRC iPSC Core ADRC 22 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 76 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 85 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 86 Human: fetal-derived microglia: sex N/A This paper N/A Human: Monocytes—Sex inMethod Details This paper N/A Human: Monocyte-derived macrophages This paper N/A Human: Blood-borne Dendritic Cells Sex in Method Details This paper N/A Human: iPSC-derived HPCs This paper N/A Experimental Models: Organisms/Strains Rag-5xfAD; mouse: B6.Cg-Tg (APPSwFlLon,PSEN1*M146L*L286V) 6799Vas/Mmjax crossed with mouse: B10;B6-Rag2tm1Fwa Il2rgtm1Wjl From Jackson Laboratory and Taconic, respectively Blurton-Jones lab, UC Irvine, CA Marsh et al., 2016 MITRG; mouse M-CSFh;IL-3/GMCSFh;THPOh;Rag2 ;gc The Jackson Laboratory Jax: 017711 Rat: Sprague Dawley Crl:SD Charles River Charles River strain code: 400 Oligonucleotides Primers for qPCR, see Table S7 Thermo Fisher Scientific see Table S7 Software and Algorithms STAR Dobin et al., 2013 https://github.com/alexdobin/STAR RSEM Li and Dewey, 2011 https://deweylab.github.io/RSEM/ EdgeR Robinson et al., 2010 http://bioconductor.org/packages/release/ bioc/html/edgeR.html Rstudio N/A https://www.rstudio.com/ (Continued on next page) e3 Neuron 94, 278–293.e1–e9, April 19, 2017
Labeling:Article Title: iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Amyloid Fibrils OC antibody Millipore Cat# AB2286 RRID: AB_1977024 Mouse Amyloid 1-16aa (6e10) BioLegend Cat# 803001 RRID: AB_2564653 Mouse b3Tubulin BioLegend Cat# 801201 RRID: AB_2313773 Mouse SC121 (human cytoplasm) Takara Bio Cat# AB-121-U-050, RRID: AB_2632385 Mouse ku80 (human nuclei) Abcam Cat # ab79220, RRID: AB_1603596 Chicken GFAP Abcam Cat# ab50738, RRID: AB_880201 Rabbit Iba1 Wako Cat# 27030, RRID: AB_2314667 Goat Iba1 Abcam Cat# ab5076, RRID: AB_2224402 Mouse ITGB5 Abcam Cat# ab177004 Mouse MMP9 Millipore Cat# AB19016, RRID: AB_11211211 Mouse MERTK BioLegend Cat# 367602, RRID: AB_2565898 Rabbit P2RY12 Sigma Cat# HPA014518 Rabbit PROS1 Abcam Cat# ab97387, RRID: AB_10695954 Rabbit PU1 Cell Signaling Technology Cat# 2266S, RRID: AB_10692379 Tabbit TMEM119 (human, C terminus) Abcam Cat# ab185333 Goat TREM2 (human) R&D Systems Cat# AF1828, RRID: AB_2208689 Rabbit TGFbR1 Abcam Cat# ab31013, RRID: AB_778352 Rabbit CX3CR1 Bio-Rad/AbD Serotec Cat# AHP1589, RRID: AB_2087421 LEAF Purified anti-human CD11b BioLegend Cat# 301312, RRID: AB_314164 Tau (T22), oligomeric EMD Millipore Cat# ABN454 APC-Cyanine7 CD45 (HI30) Tonbo Biosciences Cat# 25-0459-T10 PE/Cy7 CD235a (Glycophorin A) (clone HI264) BioLegend Cat# 349112, RRID: AB_2562708 APC CD43 Antibody (clone CD43-10G7) BioLegend Cat# 343206, RRID: AB_2194072 FITC CD34 Antibody (clone 561) BioLegend Cat# 343604, RRID: AB_1732005 PE CD41 Antibody (clone HIP8) BioLegend Cat# 303706, RRID: AB_314376 Zombie Violet Fixable Viability Stain BioLegend Cat# 423114 Biological Samples Human adult microglia RNA This paper N/A Human fetal microglia RNA This paper N/A Human PBMCs This paper N/A Human fetal tissue This paper N/A Chemicals, Peptides, and Recombinant Proteins Human TGFb1 Miltenyi Cat# 130-108-969 Human IL34 PeproTech Cat# 200-34 Human MCSF Thermo Fisher Scientific Cat# PHC9501 Human FGF2 Thermo Fisher Scientific Cat# PHG0261 Human BMP4 Thermo Fisher Scientific Cat# PHC9531 Human Activin A Thermo Fisher Scientific Cat# PHC9564 Human TPO Thermo Fisher Scientific Cat# PHC9514 Human IL6 Thermo Fisher Scientific Cat# PHC0061 Human IL3 Thermo Fisher Scientific Cat# PHC0031 Human VEGF Thermo Fisher Scientific Cat# PHC9391 (Continued on next page) e1 Neuron 94, 278–293.e1–e9, April 19, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human SCF Thermo Fisher Scientific Cat# PHC2111 Human Fractalkine (CX3CL1) PeproTech Cat# 300-31 Human CD200 Novoprotein Cat# C311-50ug BD Matrigel Matrix Growth Factor Reduced, Phenol Red-Free BD Biosciences Cat# 356231 TeSR-E8 STEMCELL Technologies Cat# 05940 IMDM (Iscove’s Modified Dulbecco’s Medium) Thermo Fisher Scientific Cat# 12440053 Ham’s F12 Thermo Fisher Scientific Cat# 11765054 DMEM/F-12, HEPES, no phenol red Thermo Fisher Scientific Cat# 11039021 RPMI 1640 Medium, no phenol red Thermo Fisher Scientific Cat# 11835030 BSA solution Miltenyi Cat# 130-091-376 Lithium Chloride solution Sigma Cat# L7026-100ML L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma Cat# A8960-5G 1-Thioglycerol (Monothioglycerol) Sigma Cat# M1753-100ML Poly-vinyl-Alcohol (PVA) Sigma Cat# P8136-250G B27 Supplement Thermo Fisher Scientific Cat# 17504044 N2 Supplement Thermo Fisher Scientific Cat# 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher Scientific Cat# 11140050 GlutaMax Supplement Thermo Fisher Scientific Cat# 35050061 ROCK inhibitor Y-27632 R&D Systems Cat# 1254 Human Insulin Sigma Cat# I2643-50MG Insulin-Transferrin-Selenium (ITS-G) (1003) Thermo Fisher Scientific Cat# 41400045 Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1003) Thermo Fisher Scientific Cat# 51500056 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 Adenosine 50-diphosphate Sigma Cat# 01905-250MG-F PSB 0739 Tocris Cat# 3983 Fura-2, AM, cell permeant Thermo Fisher Scientific Cat# F1201 May-Gr€unwald Stain Sigma Cat# MG1L SIGMA Giemsa Stain Sigma Cat# GS500-500ML b-Amyloid (1–42), Human AnaSpec Cat# AS-20276 b-Amyloid (1–42), HiLyte Fluor 555— labeled, Human AnaSpec Cat# AS-60480-01 Human Brain derived Tau Oligomers This paper N/A Human Brain derived Synaptosomes This paper N/A pHrodo Red Dye Thermo Fisher Scientific Cat# P36600 RNA-later Thermo Fisher Scientific Cat# AM7021 KnockOut Replacement Serum (KOSR) Thermo Fisher Scientific Cat# 10828028 Fetal Bovine Serum Thermo Fisher Scientific Cat# 10437028 Lipidure-coated 96-well V-bottom plate AMSBIO Cat# AMS.51011612 Amylo-Glo RTD Amyloid Plaque Stain Reagent Biosensis Cat# TR-300-AG TrypLE Select Enzyme (13), no phenol red Thermo Fisher Scientific 12563029 Critical Commercial Assays Human Pluripotent Stem Cell Functional Identification Kit R&D Systems Cat# SC027B V-PLEX Human Cytokine 30-Plex Meso Scale Discovery Cat# K15054D-1 (Continued on next page) Neuron 94, 278–293.e1–e9, April 19, 2017 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER nCounter Human Copy Number Variants Nanostring Cat# 115000102 nCounter Human Copy Number Variants Master Kit Nanostring Cat# 100052 Kapa Library Quantification Kit Kappa Biosystems N/A TruSeq RNA Library Prep Kit v.2 Illumina N/A QIAGEN RNA kit QIAGEN Cat# 74106 cDNA kit Thermo Fisher Scientific Cat# 11754050 EasySepTM Monocyte Enrichment Kit STEMCELL Technologies 19059 EasySep Human Pan-DC Pre-Enrichment Kit STEMCELL Technologies 19251 Deposited Data RNA-Seq Data This paper GEO: GSE89189 Experimental Models: Cell Lines Rat Hippocampal neurons This paper N/A Commercial iHPCs (Lot# 021405) Cellular Dynamics International Cat# HPC-301-020-001-PT Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 2 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 4 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 5 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 12 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC F14 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 20 Human: iPSC line from PBMC: Female UCI ADRC iPSC Core ADRC 22 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 76 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 85 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 86 Human: fetal-derived microglia: sex N/A This paper N/A Human: Monocytes—Sex inMethod Details This paper N/A Human: Monocyte-derived macrophages This paper N/A Human: Blood-borne Dendritic Cells Sex in Method Details This paper N/A Human: iPSC-derived HPCs This paper N/A Experimental Models: Organisms/Strains Rag-5xfAD; mouse: B6.Cg-Tg (APPSwFlLon,PSEN1*M146L*L286V) 6799Vas/Mmjax crossed with mouse: B10;B6-Rag2tm1Fwa Il2rgtm1Wjl From Jackson Laboratory and Taconic, respectively Blurton-Jones lab, UC Irvine, CA Marsh et al., 2016 MITRG; mouse M-CSFh;IL-3/GMCSFh;THPOh;Rag2 ;gc The Jackson Laboratory Jax: 017711 Rat: Sprague Dawley Crl:SD Charles River Charles River strain code: 400 Oligonucleotides Primers for qPCR, see Table S7 Thermo Fisher Scientific see Table S7 Software and Algorithms STAR Dobin et al., 2013 https://github.com/alexdobin/STAR RSEM Li and Dewey, 2011 https://deweylab.github.io/RSEM/ EdgeR Robinson et al., 2010 http://bioconductor.org/packages/release/ bioc/html/edgeR.html Rstudio N/A https://www.rstudio.com/ (Continued on next page) e3 Neuron 94, 278–293.e1–e9, April 19, 2017
Knock-Out:Article Title: iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Amyloid Fibrils OC antibody Millipore Cat# AB2286 RRID: AB_1977024 Mouse Amyloid 1-16aa (6e10) BioLegend Cat# 803001 RRID: AB_2564653 Mouse b3Tubulin BioLegend Cat# 801201 RRID: AB_2313773 Mouse SC121 (human cytoplasm) Takara Bio Cat# AB-121-U-050, RRID: AB_2632385 Mouse ku80 (human nuclei) Abcam Cat # ab79220, RRID: AB_1603596 Chicken GFAP Abcam Cat# ab50738, RRID: AB_880201 Rabbit Iba1 Wako Cat# 27030, RRID: AB_2314667 Goat Iba1 Abcam Cat# ab5076, RRID: AB_2224402 Mouse ITGB5 Abcam Cat# ab177004 Mouse MMP9 Millipore Cat# AB19016, RRID: AB_11211211 Mouse MERTK BioLegend Cat# 367602, RRID: AB_2565898 Rabbit P2RY12 Sigma Cat# HPA014518 Rabbit PROS1 Abcam Cat# ab97387, RRID: AB_10695954 Rabbit PU1 Cell Signaling Technology Cat# 2266S, RRID: AB_10692379 Tabbit TMEM119 (human, C terminus) Abcam Cat# ab185333 Goat TREM2 (human) R&D Systems Cat# AF1828, RRID: AB_2208689 Rabbit TGFbR1 Abcam Cat# ab31013, RRID: AB_778352 Rabbit CX3CR1 Bio-Rad/AbD Serotec Cat# AHP1589, RRID: AB_2087421 LEAF Purified anti-human CD11b BioLegend Cat# 301312, RRID: AB_314164 Tau (T22), oligomeric EMD Millipore Cat# ABN454 APC-Cyanine7 CD45 (HI30) Tonbo Biosciences Cat# 25-0459-T10 PE/Cy7 CD235a (Glycophorin A) (clone HI264) BioLegend Cat# 349112, RRID: AB_2562708 APC CD43 Antibody (clone CD43-10G7) BioLegend Cat# 343206, RRID: AB_2194072 FITC CD34 Antibody (clone 561) BioLegend Cat# 343604, RRID: AB_1732005 PE CD41 Antibody (clone HIP8) BioLegend Cat# 303706, RRID: AB_314376 Zombie Violet Fixable Viability Stain BioLegend Cat# 423114 Biological Samples Human adult microglia RNA This paper N/A Human fetal microglia RNA This paper N/A Human PBMCs This paper N/A Human fetal tissue This paper N/A Chemicals, Peptides, and Recombinant Proteins Human TGFb1 Miltenyi Cat# 130-108-969 Human IL34 PeproTech Cat# 200-34 Human MCSF Thermo Fisher Scientific Cat# PHC9501 Human FGF2 Thermo Fisher Scientific Cat# PHG0261 Human BMP4 Thermo Fisher Scientific Cat# PHC9531 Human Activin A Thermo Fisher Scientific Cat# PHC9564 Human TPO Thermo Fisher Scientific Cat# PHC9514 Human IL6 Thermo Fisher Scientific Cat# PHC0061 Human IL3 Thermo Fisher Scientific Cat# PHC0031 Human VEGF Thermo Fisher Scientific Cat# PHC9391 (Continued on next page) e1 Neuron 94, 278–293.e1–e9, April 19, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human SCF Thermo Fisher Scientific Cat# PHC2111 Human Fractalkine (CX3CL1) PeproTech Cat# 300-31 Human CD200 Novoprotein Cat# C311-50ug BD Matrigel Matrix Growth Factor Reduced, Phenol Red-Free BD Biosciences Cat# 356231 TeSR-E8 STEMCELL Technologies Cat# 05940 IMDM (Iscove’s Modified Dulbecco’s Medium) Thermo Fisher Scientific Cat# 12440053 Ham’s F12 Thermo Fisher Scientific Cat# 11765054 DMEM/F-12, HEPES, no phenol red Thermo Fisher Scientific Cat# 11039021 RPMI 1640 Medium, no phenol red Thermo Fisher Scientific Cat# 11835030 BSA solution Miltenyi Cat# 130-091-376 Lithium Chloride solution Sigma Cat# L7026-100ML L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma Cat# A8960-5G 1-Thioglycerol (Monothioglycerol) Sigma Cat# M1753-100ML Poly-vinyl-Alcohol (PVA) Sigma Cat# P8136-250G B27 Supplement Thermo Fisher Scientific Cat# 17504044 N2 Supplement Thermo Fisher Scientific Cat# 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher Scientific Cat# 11140050 GlutaMax Supplement Thermo Fisher Scientific Cat# 35050061 ROCK inhibitor Y-27632 R&D Systems Cat# 1254 Human Insulin Sigma Cat# I2643-50MG Insulin-Transferrin-Selenium (ITS-G) (1003) Thermo Fisher Scientific Cat# 41400045 Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1003) Thermo Fisher Scientific Cat# 51500056 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 Adenosine 50-diphosphate Sigma Cat# 01905-250MG-F PSB 0739 Tocris Cat# 3983 Fura-2, AM, cell permeant Thermo Fisher Scientific Cat# F1201 May-Gr€unwald Stain Sigma Cat# MG1L SIGMA Giemsa Stain Sigma Cat# GS500-500ML b-Amyloid (1–42), Human AnaSpec Cat# AS-20276 b-Amyloid (1–42), HiLyte Fluor 555— labeled, Human AnaSpec Cat# AS-60480-01 Human Brain derived Tau Oligomers This paper N/A Human Brain derived Synaptosomes This paper N/A pHrodo Red Dye Thermo Fisher Scientific Cat# P36600 RNA-later Thermo Fisher Scientific Cat# AM7021 KnockOut Replacement Serum (KOSR) Thermo Fisher Scientific Cat# 10828028 Fetal Bovine Serum Thermo Fisher Scientific Cat# 10437028 Lipidure-coated 96-well V-bottom plate AMSBIO Cat# AMS.51011612 Amylo-Glo RTD Amyloid Plaque Stain Reagent Biosensis Cat# TR-300-AG TrypLE Select Enzyme (13), no phenol red Thermo Fisher Scientific 12563029 Critical Commercial Assays Human Pluripotent Stem Cell Functional Identification Kit R&D Systems Cat# SC027B V-PLEX Human Cytokine 30-Plex Meso Scale Discovery Cat# K15054D-1 (Continued on next page) Neuron 94, 278–293.e1–e9, April 19, 2017 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER nCounter Human Copy Number Variants Nanostring Cat# 115000102 nCounter Human Copy Number Variants Master Kit Nanostring Cat# 100052 Kapa Library Quantification Kit Kappa Biosystems N/A TruSeq RNA Library Prep Kit v.2 Illumina N/A QIAGEN RNA kit QIAGEN Cat# 74106 cDNA kit Thermo Fisher Scientific Cat# 11754050 EasySepTM Monocyte Enrichment Kit STEMCELL Technologies 19059 EasySep Human Pan-DC Pre-Enrichment Kit STEMCELL Technologies 19251 Deposited Data RNA-Seq Data This paper GEO: GSE89189 Experimental Models: Cell Lines Rat Hippocampal neurons This paper N/A Commercial iHPCs (Lot# 021405) Cellular Dynamics International Cat# HPC-301-020-001-PT Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 2 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 4 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 5 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 12 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC F14 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 20 Human: iPSC line from PBMC: Female UCI ADRC iPSC Core ADRC 22 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 76 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 85 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 86 Human: fetal-derived microglia: sex N/A This paper N/A Human: Monocytes—Sex inMethod Details This paper N/A Human: Monocyte-derived macrophages This paper N/A Human: Blood-borne Dendritic Cells Sex in Method Details This paper N/A Human: iPSC-derived HPCs This paper N/A Experimental Models: Organisms/Strains Rag-5xfAD; mouse: B6.Cg-Tg (APPSwFlLon,PSEN1*M146L*L286V) 6799Vas/Mmjax crossed with mouse: B10;B6-Rag2tm1Fwa Il2rgtm1Wjl From Jackson Laboratory and Taconic, respectively Blurton-Jones lab, UC Irvine, CA Marsh et al., 2016 MITRG; mouse M-CSFh;IL-3/GMCSFh;THPOh;Rag2 ;gc The Jackson Laboratory Jax: 017711 Rat: Sprague Dawley Crl:SD Charles River Charles River strain code: 400 Oligonucleotides Primers for qPCR, see Table S7 Thermo Fisher Scientific see Table S7 Software and Algorithms STAR Dobin et al., 2013 https://github.com/alexdobin/STAR RSEM Li and Dewey, 2011 https://deweylab.github.io/RSEM/ EdgeR Robinson et al., 2010 http://bioconductor.org/packages/release/ bioc/html/edgeR.html Rstudio N/A https://www.rstudio.com/ (Continued on next page) e3 Neuron 94, 278–293.e1–e9, April 19, 2017
Affinity Magnetic Separation:Article Title: iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Amyloid Fibrils OC antibody Millipore Cat# AB2286 RRID: AB_1977024 Mouse Amyloid 1-16aa (6e10) BioLegend Cat# 803001 RRID: AB_2564653 Mouse b3Tubulin BioLegend Cat# 801201 RRID: AB_2313773 Mouse SC121 (human cytoplasm) Takara Bio Cat# AB-121-U-050, RRID: AB_2632385 Mouse ku80 (human nuclei) Abcam Cat # ab79220, RRID: AB_1603596 Chicken GFAP Abcam Cat# ab50738, RRID: AB_880201 Rabbit Iba1 Wako Cat# 27030, RRID: AB_2314667 Goat Iba1 Abcam Cat# ab5076, RRID: AB_2224402 Mouse ITGB5 Abcam Cat# ab177004 Mouse MMP9 Millipore Cat# AB19016, RRID: AB_11211211 Mouse MERTK BioLegend Cat# 367602, RRID: AB_2565898 Rabbit P2RY12 Sigma Cat# HPA014518 Rabbit PROS1 Abcam Cat# ab97387, RRID: AB_10695954 Rabbit PU1 Cell Signaling Technology Cat# 2266S, RRID: AB_10692379 Tabbit TMEM119 (human, C terminus) Abcam Cat# ab185333 Goat TREM2 (human) R&D Systems Cat# AF1828, RRID: AB_2208689 Rabbit TGFbR1 Abcam Cat# ab31013, RRID: AB_778352 Rabbit CX3CR1 Bio-Rad/AbD Serotec Cat# AHP1589, RRID: AB_2087421 LEAF Purified anti-human CD11b BioLegend Cat# 301312, RRID: AB_314164 Tau (T22), oligomeric EMD Millipore Cat# ABN454 APC-Cyanine7 CD45 (HI30) Tonbo Biosciences Cat# 25-0459-T10 PE/Cy7 CD235a (Glycophorin A) (clone HI264) BioLegend Cat# 349112, RRID: AB_2562708 APC CD43 Antibody (clone CD43-10G7) BioLegend Cat# 343206, RRID: AB_2194072 FITC CD34 Antibody (clone 561) BioLegend Cat# 343604, RRID: AB_1732005 PE CD41 Antibody (clone HIP8) BioLegend Cat# 303706, RRID: AB_314376 Zombie Violet Fixable Viability Stain BioLegend Cat# 423114 Biological Samples Human adult microglia RNA This paper N/A Human fetal microglia RNA This paper N/A Human PBMCs This paper N/A Human fetal tissue This paper N/A Chemicals, Peptides, and Recombinant Proteins Human TGFb1 Miltenyi Cat# 130-108-969 Human IL34 PeproTech Cat# 200-34 Human MCSF Thermo Fisher Scientific Cat# PHC9501 Human FGF2 Thermo Fisher Scientific Cat# PHG0261 Human BMP4 Thermo Fisher Scientific Cat# PHC9531 Human Activin A Thermo Fisher Scientific Cat# PHC9564 Human TPO Thermo Fisher Scientific Cat# PHC9514 Human IL6 Thermo Fisher Scientific Cat# PHC0061 Human IL3 Thermo Fisher Scientific Cat# PHC0031 Human VEGF Thermo Fisher Scientific Cat# PHC9391 (Continued on next page) e1 Neuron 94, 278–293.e1–e9, April 19, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human SCF Thermo Fisher Scientific Cat# PHC2111 Human Fractalkine (CX3CL1) PeproTech Cat# 300-31 Human CD200 Novoprotein Cat# C311-50ug BD Matrigel Matrix Growth Factor Reduced, Phenol Red-Free BD Biosciences Cat# 356231 TeSR-E8 STEMCELL Technologies Cat# 05940 IMDM (Iscove’s Modified Dulbecco’s Medium) Thermo Fisher Scientific Cat# 12440053 Ham’s F12 Thermo Fisher Scientific Cat# 11765054 DMEM/F-12, HEPES, no phenol red Thermo Fisher Scientific Cat# 11039021 RPMI 1640 Medium, no phenol red Thermo Fisher Scientific Cat# 11835030 BSA solution Miltenyi Cat# 130-091-376 Lithium Chloride solution Sigma Cat# L7026-100ML L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma Cat# A8960-5G 1-Thioglycerol (Monothioglycerol) Sigma Cat# M1753-100ML Poly-vinyl-Alcohol (PVA) Sigma Cat# P8136-250G B27 Supplement Thermo Fisher Scientific Cat# 17504044 N2 Supplement Thermo Fisher Scientific Cat# 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher Scientific Cat# 11140050 GlutaMax Supplement Thermo Fisher Scientific Cat# 35050061 ROCK inhibitor Y-27632 R&D Systems Cat# 1254 Human Insulin Sigma Cat# I2643-50MG Insulin-Transferrin-Selenium (ITS-G) (1003) Thermo Fisher Scientific Cat# 41400045 Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1003) Thermo Fisher Scientific Cat# 51500056 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 Adenosine 50-diphosphate Sigma Cat# 01905-250MG-F PSB 0739 Tocris Cat# 3983 Fura-2, AM, cell permeant Thermo Fisher Scientific Cat# F1201 May-Gr€unwald Stain Sigma Cat# MG1L SIGMA Giemsa Stain Sigma Cat# GS500-500ML b-Amyloid (1–42), Human AnaSpec Cat# AS-20276 b-Amyloid (1–42), HiLyte Fluor 555— labeled, Human AnaSpec Cat# AS-60480-01 Human Brain derived Tau Oligomers This paper N/A Human Brain derived Synaptosomes This paper N/A pHrodo Red Dye Thermo Fisher Scientific Cat# P36600 RNA-later Thermo Fisher Scientific Cat# AM7021 KnockOut Replacement Serum (KOSR) Thermo Fisher Scientific Cat# 10828028 Fetal Bovine Serum Thermo Fisher Scientific Cat# 10437028 Lipidure-coated 96-well V-bottom plate AMSBIO Cat# AMS.51011612 Amylo-Glo RTD Amyloid Plaque Stain Reagent Biosensis Cat# TR-300-AG TrypLE Select Enzyme (13), no phenol red Thermo Fisher Scientific 12563029 Critical Commercial Assays Human Pluripotent Stem Cell Functional Identification Kit R&D Systems Cat# SC027B V-PLEX Human Cytokine 30-Plex Meso Scale Discovery Cat# K15054D-1 (Continued on next page) Neuron 94, 278–293.e1–e9, April 19, 2017 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER nCounter Human Copy Number Variants Nanostring Cat# 115000102 nCounter Human Copy Number Variants Master Kit Nanostring Cat# 100052 Kapa Library Quantification Kit Kappa Biosystems N/A TruSeq RNA Library Prep Kit v.2 Illumina N/A QIAGEN RNA kit QIAGEN Cat# 74106 cDNA kit Thermo Fisher Scientific Cat# 11754050 EasySepTM Monocyte Enrichment Kit STEMCELL Technologies 19059 EasySep Human Pan-DC Pre-Enrichment Kit STEMCELL Technologies 19251 Deposited Data RNA-Seq Data This paper GEO: GSE89189 Experimental Models: Cell Lines Rat Hippocampal neurons This paper N/A Commercial iHPCs (Lot# 021405) Cellular Dynamics International Cat# HPC-301-020-001-PT Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 2 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 4 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 5 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 12 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC F14 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 20 Human: iPSC line from PBMC: Female UCI ADRC iPSC Core ADRC 22 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 76 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 85 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 86 Human: fetal-derived microglia: sex N/A This paper N/A Human: Monocytes—Sex inMethod Details This paper N/A Human: Monocyte-derived macrophages This paper N/A Human: Blood-borne Dendritic Cells Sex in Method Details This paper N/A Human: iPSC-derived HPCs This paper N/A Experimental Models: Organisms/Strains Rag-5xfAD; mouse: B6.Cg-Tg (APPSwFlLon,PSEN1*M146L*L286V) 6799Vas/Mmjax crossed with mouse: B10;B6-Rag2tm1Fwa Il2rgtm1Wjl From Jackson Laboratory and Taconic, respectively Blurton-Jones lab, UC Irvine, CA Marsh et al., 2016 MITRG; mouse M-CSFh;IL-3/GMCSFh;THPOh;Rag2 ;gc The Jackson Laboratory Jax: 017711 Rat: Sprague Dawley Crl:SD Charles River Charles River strain code: 400 Oligonucleotides Primers for qPCR, see Table S7 Thermo Fisher Scientific see Table S7 Software and Algorithms STAR Dobin et al., 2013 https://github.com/alexdobin/STAR RSEM Li and Dewey, 2011 https://deweylab.github.io/RSEM/ EdgeR Robinson et al., 2010 http://bioconductor.org/packages/release/ bioc/html/edgeR.html Rstudio N/A https://www.rstudio.com/ (Continued on next page) e3 Neuron 94, 278–293.e1–e9, April 19, 2017
Functional Assay:Article Title: iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Amyloid Fibrils OC antibody Millipore Cat# AB2286 RRID: AB_1977024 Mouse Amyloid 1-16aa (6e10) BioLegend Cat# 803001 RRID: AB_2564653 Mouse b3Tubulin BioLegend Cat# 801201 RRID: AB_2313773 Mouse SC121 (human cytoplasm) Takara Bio Cat# AB-121-U-050, RRID: AB_2632385 Mouse ku80 (human nuclei) Abcam Cat # ab79220, RRID: AB_1603596 Chicken GFAP Abcam Cat# ab50738, RRID: AB_880201 Rabbit Iba1 Wako Cat# 27030, RRID: AB_2314667 Goat Iba1 Abcam Cat# ab5076, RRID: AB_2224402 Mouse ITGB5 Abcam Cat# ab177004 Mouse MMP9 Millipore Cat# AB19016, RRID: AB_11211211 Mouse MERTK BioLegend Cat# 367602, RRID: AB_2565898 Rabbit P2RY12 Sigma Cat# HPA014518 Rabbit PROS1 Abcam Cat# ab97387, RRID: AB_10695954 Rabbit PU1 Cell Signaling Technology Cat# 2266S, RRID: AB_10692379 Tabbit TMEM119 (human, C terminus) Abcam Cat# ab185333 Goat TREM2 (human) R&D Systems Cat# AF1828, RRID: AB_2208689 Rabbit TGFbR1 Abcam Cat# ab31013, RRID: AB_778352 Rabbit CX3CR1 Bio-Rad/AbD Serotec Cat# AHP1589, RRID: AB_2087421 LEAF Purified anti-human CD11b BioLegend Cat# 301312, RRID: AB_314164 Tau (T22), oligomeric EMD Millipore Cat# ABN454 APC-Cyanine7 CD45 (HI30) Tonbo Biosciences Cat# 25-0459-T10 PE/Cy7 CD235a (Glycophorin A) (clone HI264) BioLegend Cat# 349112, RRID: AB_2562708 APC CD43 Antibody (clone CD43-10G7) BioLegend Cat# 343206, RRID: AB_2194072 FITC CD34 Antibody (clone 561) BioLegend Cat# 343604, RRID: AB_1732005 PE CD41 Antibody (clone HIP8) BioLegend Cat# 303706, RRID: AB_314376 Zombie Violet Fixable Viability Stain BioLegend Cat# 423114 Biological Samples Human adult microglia RNA This paper N/A Human fetal microglia RNA This paper N/A Human PBMCs This paper N/A Human fetal tissue This paper N/A Chemicals, Peptides, and Recombinant Proteins Human TGFb1 Miltenyi Cat# 130-108-969 Human IL34 PeproTech Cat# 200-34 Human MCSF Thermo Fisher Scientific Cat# PHC9501 Human FGF2 Thermo Fisher Scientific Cat# PHG0261 Human BMP4 Thermo Fisher Scientific Cat# PHC9531 Human Activin A Thermo Fisher Scientific Cat# PHC9564 Human TPO Thermo Fisher Scientific Cat# PHC9514 Human IL6 Thermo Fisher Scientific Cat# PHC0061 Human IL3 Thermo Fisher Scientific Cat# PHC0031 Human VEGF Thermo Fisher Scientific Cat# PHC9391 (Continued on next page) e1 Neuron 94, 278–293.e1–e9, April 19, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human SCF Thermo Fisher Scientific Cat# PHC2111 Human Fractalkine (CX3CL1) PeproTech Cat# 300-31 Human CD200 Novoprotein Cat# C311-50ug BD Matrigel Matrix Growth Factor Reduced, Phenol Red-Free BD Biosciences Cat# 356231 TeSR-E8 STEMCELL Technologies Cat# 05940 IMDM (Iscove’s Modified Dulbecco’s Medium) Thermo Fisher Scientific Cat# 12440053 Ham’s F12 Thermo Fisher Scientific Cat# 11765054 DMEM/F-12, HEPES, no phenol red Thermo Fisher Scientific Cat# 11039021 RPMI 1640 Medium, no phenol red Thermo Fisher Scientific Cat# 11835030 BSA solution Miltenyi Cat# 130-091-376 Lithium Chloride solution Sigma Cat# L7026-100ML L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma Cat# A8960-5G 1-Thioglycerol (Monothioglycerol) Sigma Cat# M1753-100ML Poly-vinyl-Alcohol (PVA) Sigma Cat# P8136-250G B27 Supplement Thermo Fisher Scientific Cat# 17504044 N2 Supplement Thermo Fisher Scientific Cat# 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher Scientific Cat# 11140050 GlutaMax Supplement Thermo Fisher Scientific Cat# 35050061 ROCK inhibitor Y-27632 R&D Systems Cat# 1254 Human Insulin Sigma Cat# I2643-50MG Insulin-Transferrin-Selenium (ITS-G) (1003) Thermo Fisher Scientific Cat# 41400045 Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1003) Thermo Fisher Scientific Cat# 51500056 Penicillin-Streptomycin Thermo Fisher Scientific Cat# 15140122 Adenosine 50-diphosphate Sigma Cat# 01905-250MG-F PSB 0739 Tocris Cat# 3983 Fura-2, AM, cell permeant Thermo Fisher Scientific Cat# F1201 May-Gr€unwald Stain Sigma Cat# MG1L SIGMA Giemsa Stain Sigma Cat# GS500-500ML b-Amyloid (1–42), Human AnaSpec Cat# AS-20276 b-Amyloid (1–42), HiLyte Fluor 555— labeled, Human AnaSpec Cat# AS-60480-01 Human Brain derived Tau Oligomers This paper N/A Human Brain derived Synaptosomes This paper N/A pHrodo Red Dye Thermo Fisher Scientific Cat# P36600 RNA-later Thermo Fisher Scientific Cat# AM7021 KnockOut Replacement Serum (KOSR) Thermo Fisher Scientific Cat# 10828028 Fetal Bovine Serum Thermo Fisher Scientific Cat# 10437028 Lipidure-coated 96-well V-bottom plate AMSBIO Cat# AMS.51011612 Amylo-Glo RTD Amyloid Plaque Stain Reagent Biosensis Cat# TR-300-AG TrypLE Select Enzyme (13), no phenol red Thermo Fisher Scientific 12563029 Critical Commercial Assays Human Pluripotent Stem Cell Functional Identification Kit R&D Systems Cat# SC027B V-PLEX Human Cytokine 30-Plex Meso Scale Discovery Cat# K15054D-1 (Continued on next page) Neuron 94, 278–293.e1–e9, April 19, 2017 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER nCounter Human Copy Number Variants Nanostring Cat# 115000102 nCounter Human Copy Number Variants Master Kit Nanostring Cat# 100052 Kapa Library Quantification Kit Kappa Biosystems N/A TruSeq RNA Library Prep Kit v.2 Illumina N/A QIAGEN RNA kit QIAGEN Cat# 74106 cDNA kit Thermo Fisher Scientific Cat# 11754050 EasySepTM Monocyte Enrichment Kit STEMCELL Technologies 19059 EasySep Human Pan-DC Pre-Enrichment Kit STEMCELL Technologies 19251 Deposited Data RNA-Seq Data This paper GEO: GSE89189 Experimental Models: Cell Lines Rat Hippocampal neurons This paper N/A Commercial iHPCs (Lot# 021405) Cellular Dynamics International Cat# HPC-301-020-001-PT Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 2 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 4 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 5 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 12 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC F14 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 20 Human: iPSC line from PBMC: Female UCI ADRC iPSC Core ADRC 22 Human: iPSC line from PBMC: Male UCI ADRC iPSC Core ADRC 76 Human: iPSC line from Fibroblast: Male UCI ADRC iPSC Core ADRC 85 Human: iPSC line from Fibroblast: Female UCI ADRC iPSC Core ADRC 86 Human: fetal-derived microglia: sex N/A This paper N/A Human: Monocytes—Sex inMethod Details This paper N/A Human: Monocyte-derived macrophages This paper N/A Human: Blood-borne Dendritic Cells Sex in Method Details This paper N/A Human: iPSC-derived HPCs This paper N/A Experimental Models: Organisms/Strains Rag-5xfAD; mouse: B6.Cg-Tg (APPSwFlLon,PSEN1*M146L*L286V) 6799Vas/Mmjax crossed with mouse: B10;B6-Rag2tm1Fwa Il2rgtm1Wjl From Jackson Laboratory and Taconic, respectively Blurton-Jones lab, UC Irvine, CA Marsh et al., 2016 MITRG; mouse M-CSFh;IL-3/GMCSFh;THPOh;Rag2 ;gc The Jackson Laboratory Jax: 017711 Rat: Sprague Dawley Crl:SD Charles River Charles River strain code: 400 Oligonucleotides Primers for qPCR, see Table S7 Thermo Fisher Scientific see Table S7 Software and Algorithms STAR Dobin et al., 2013 https://github.com/alexdobin/STAR RSEM Li and Dewey, 2011 https://deweylab.github.io/RSEM/ EdgeR Robinson et al., 2010 http://bioconductor.org/packages/release/ bioc/html/edgeR.html Rstudio N/A https://www.rstudio.com/ (Continued on next page) e3 Neuron 94, 278–293.e1–e9, April 19, 2017
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