Single Cell:Article Title: Nuclear microRNA-mediated transcriptional control determines adult microglial homeostasis and brain function.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Paraformaldehyde,4% Solarbio Cat#: P1110 Cole’s Hematoxylin Solution Solarbio Cat#: G1140 Eosin Y Stain Solution, For HE Solarbio Cat#: G1100 DAPI Sigma-Aldrich Cat#: D9542 Glycerol Sigma Cat#: G5516-1L Sodium chloride HUSHI Cat#: 10019318 Ni Sepharose 6 Fast Flow Cytiva Cat#:17531804 Kanamycln sulfate Aladdin Cat#: D2117220 Imidazole Sangon biotech Cat#: B528414 HEPES BIOISCO Cat#: 130420 KCl Sigma-Aldrich Cat#: 451029 DTT Sigma Cat#: 646563-10X EDTA Beyotime Cat#: ST1303 Salmon DNA Sigma Cat#: D7656 Blocking buffer Beyotime Cat#: GS009B Washing buffer Beyotime Cat#: GS009W Equilibrium buffer Beyotime Cat#: GS009A Sensor chip CM5 Cytiva Cat#: 29149604 Sensor chip SA Cytiva Cat#: BR100032 HBS-EP+ buffer,103 Cytiva Cat#: BR100826 AceQ Universal SYBR qPCR Master Mix Vazyme Cat#: Q511 Critical commercial assays Adult Brain Dissociation kit Miltenyi Biotec Cat#: 130-107-677 CD11b MicroBeads, human and mouse Miltenyi Biotec Cat#: 130-126-725 FD Rapid Golgi Stain Kit FD NeuroTechnologies, Inc. Cat#: PK401 CellTrackerTM fluorescent probes kit Invitrogen Cat#: C34552 Proteome Profiler Mouse Cytokine Array Kit R&D Systems Cat#: ARY006 Proteome Profiler Mouse Chemokine Array Kit R&D Systems Cat#: ARY020 Mouse TNF-a ELISA KIT Solarbio Cat#: SEKM-0034 Mouse IL-6 ELISA KIT Solarbio Cat#: SEKM-0007 Mouse IL-1b ELISA KIT Solarbio Cat#: SEKM-0002 Dual Luciferase Reporter Assay Kit Vazyme Cat#: DL101 Dual-Luciferase Reporter 1000 System Promega Cat#: E1980 VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina Vazyme Cat#: NR605 TruePrep DNA Library Prep Kit V2 for Illumina Vazyme Cat#: TD501 Hyperactive Universal CUT&Tag Assay Kit for Illumina Vazyme Cat#: TD903 TruePrep Index Kit V2 for Illumina Vazyme Cat#: TD202 TransScript All-in-One First-Strand cDNA Synthesis SuperMix for qPCR(One-Step gDNA Removal) TRANS Cat#: AT341 miRNA 1st Strand cDNA Synthesis Kit (by tailing A) Vazyme Cat#: MR201 Direct-zolTM RNA Miniprep Zymo Research Cat#: R2051 Cytoplasmic and Nuclear Extraction Kit for Cells Invent Biotechnologies Cat#: SC-003 (Continued on next page) Cell Reports 43, 113964, March 26, 2024 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER STEMdiff Hematopoesis Kit StemCell Technologies Cat#: 05310 STEMdiff Microglia Differentiation Kit StemCell Technologies Cat#:100-0019 STEMdiff Microglia Maturation Kit StemCell Technologies Cat#:100-0020 Chromium Next GEM Single Cell 3 Reagent Kits v3.1 10X Genomics Cat#: CG000204 Chromium Next GEM Single Cell 3 GEM, Library & Gel Bead Kit v3.1 10X Genomics Cat#: PN-1000121 Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat#: PN-1000127 Dual Index Kit TT Set A 10X Genomics Cat#: PN-1000215 Deposited data Raw and analyzed data This paper GSE222665 Experimental models: Cell lines 293T Pricella CL-0005 Experimental models: Organisms/strains Mouse: Tmem119-CreERT2 Shanghai Model Organisms Center Inc. NM-KI-200234 Mouse: Cx3cr1-CreERT2 The Jackson Laboratory JAX:021160 Mouse: Mir137loxP/loxP Cheng et al.30 N/A Mouse: Mir137loxP/loxP;Zp3-Cre Cheng et al.30 N/A Oligonucleotides miRNA detection probe for MMU-MIR-1373P (/5DigN/ACGCGTATTCTTAAGCAAT/ 3Dig_N/) Qiagen Cat#: 339112 YD006186863-BEG Primers used in this study, see Table S5 This paper N/A Recombinant DNA psiCHECK-2-Jdp2-30UTR This paper N/A psiCHECK-2-Jdp2-mut-30UTR This paper N/A pCR2.1 TOPO-U6-miR-137 Cheng et al.30 N/A pLKO.1 mouse-shRNA-Jdp2 This paper N/A pET28a-MBP-Pu.1 This paper N/A Software and algorithms Prisim9 Graphpad https://www.graphpad.com/ scientific-software/prism/ Tree Star FlowJo X 10.0.7 R2 x64 Tree Star https://www.flowjo.com/ ZEN 3.3 ZEISS https://www.zeiss.com.cn/ Imaris 9.0.1 Win64 Imaris https://imaris.oxinst.com/support/ imaris-release-notes/9-0-0#9-0-1 Case Viewer (Version 2.4) 3DHISTECH Download caseviewer 3.3.6 for free (Windows) (freedownloadmanager.org) Skewer (Version 0.2.2) Jiang et al.60 https://www.skewers.cn/ R (Version 4.1.3) R https://www.r-project.org/ STAR (Version 2.7.9a) Dobin et al.61 https://github.com/alexdobin/STAR/tree/ 2.7.9a RSEM (Version1.3.1) Li and Dewey,62 http://deweylab.github.io/RSEM/ DAVID (Version 2021) Sherman et al.63 https://david.ncifcrf.gov/ bowtie2 (Version 2.4.4) Langmead and Salzberg,64 https://sourceforge.net/projects/ bowtie-bio/files/bowtie2/2.4.4/ GREAT (Version 4.0.4) McLean et al.65 http://great.stanford.edu/public/html/ DESeq2 (Version 1.34.0) Love et al.66 https://www.rdocumentation.org/search? q=deseq2 pheatmap (Version 1.0.12) Raivo Kolde https://CRAN.R-project.org/ package=pheatmap (Continued on next page) 20 Cell Reports 43, 113964, March 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER ggplot2 (Version 3.4.0) Hadley Wickham https://www.rdocumentation.org/ packages/ggplot2/versions/3.4.0 ggpubr (Version 0.5.0) Alboukadel Kassambara https://www.rdocumentation.org/ packages/ggpubr/versions/0.5.0 MACS2 (Version 2.2.7.1) Zhang et al.67 https://github.com/macs3-project/MACS/ tree/v2.2.7.1 chip-r (Version 1.2.0) Newell et al.68 https://github.com/rhysnewell/ChIP-R Bedtools (Version 2.30.0) Quinlan and Hall,69 https://bedtools.readthedocs.io/en/latest/ HOMER (Version 4.11) Heinz et al.70 http://homer.ucsd.edu/homer/ deepTools (Version 3.5.1) Ramı́rez et al.71 https://github.com/deeptools/deepTools Cell Ranger (Version 6.1.2) 10X Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/using/tutorial_in Seurat (Version 4.1.0) Stuart et al.72 https://www.rdocumentation.org/ packages/Seurat/versions/4.1.0 Ggcor (Version 0.9.8.1) Huang et al. https://github.com/Github-Yilei/ggcor DEsingle (Version 1.14.0) Miao et al.73 https://anaconda.org/bioconda/ bioconductor-desingle/files pyGenomeTracks (Version 3.7) Lopez-Delisle et al.74 https://github.com/deeptools/ pyGenomeTracks eisaR (Version 1.8.0) Gaidatzis et al.47 https://www.nature.com/articles/ s41586-018-0414-6 Velocyto (Version 0.17.17) La Manno et al.75 http://velocyto.org/velocyto.py/index.html QuasR (Version 1.38.0) Gaidatzis et al.76 https://bioconductor.org/packages/ release/bioc/html/QuasR.html Sylamer van Dongen et al.46 https://www.nature.com/articles/nmeth.
Recombinant:Article Title: Nuclear microRNA-mediated transcriptional control determines adult microglial homeostasis and brain function.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Paraformaldehyde,4% Solarbio Cat#: P1110 Cole’s Hematoxylin Solution Solarbio Cat#: G1140 Eosin Y Stain Solution, For HE Solarbio Cat#: G1100 DAPI Sigma-Aldrich Cat#: D9542 Glycerol Sigma Cat#: G5516-1L Sodium chloride HUSHI Cat#: 10019318 Ni Sepharose 6 Fast Flow Cytiva Cat#:17531804 Kanamycln sulfate Aladdin Cat#: D2117220 Imidazole Sangon biotech Cat#: B528414 HEPES BIOISCO Cat#: 130420 KCl Sigma-Aldrich Cat#: 451029 DTT Sigma Cat#: 646563-10X EDTA Beyotime Cat#: ST1303 Salmon DNA Sigma Cat#: D7656 Blocking buffer Beyotime Cat#: GS009B Washing buffer Beyotime Cat#: GS009W Equilibrium buffer Beyotime Cat#: GS009A Sensor chip CM5 Cytiva Cat#: 29149604 Sensor chip SA Cytiva Cat#: BR100032 HBS-EP+ buffer,103 Cytiva Cat#: BR100826 AceQ Universal SYBR qPCR Master Mix Vazyme Cat#: Q511 Critical commercial assays Adult Brain Dissociation kit Miltenyi Biotec Cat#: 130-107-677 CD11b MicroBeads, human and mouse Miltenyi Biotec Cat#: 130-126-725 FD Rapid Golgi Stain Kit FD NeuroTechnologies, Inc. Cat#: PK401 CellTrackerTM fluorescent probes kit Invitrogen Cat#: C34552 Proteome Profiler Mouse Cytokine Array Kit R&D Systems Cat#: ARY006 Proteome Profiler Mouse Chemokine Array Kit R&D Systems Cat#: ARY020 Mouse TNF-a ELISA KIT Solarbio Cat#: SEKM-0034 Mouse IL-6 ELISA KIT Solarbio Cat#: SEKM-0007 Mouse IL-1b ELISA KIT Solarbio Cat#: SEKM-0002 Dual Luciferase Reporter Assay Kit Vazyme Cat#: DL101 Dual-Luciferase Reporter 1000 System Promega Cat#: E1980 VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina Vazyme Cat#: NR605 TruePrep DNA Library Prep Kit V2 for Illumina Vazyme Cat#: TD501 Hyperactive Universal CUT&Tag Assay Kit for Illumina Vazyme Cat#: TD903 TruePrep Index Kit V2 for Illumina Vazyme Cat#: TD202 TransScript All-in-One First-Strand cDNA Synthesis SuperMix for qPCR(One-Step gDNA Removal) TRANS Cat#: AT341 miRNA 1st Strand cDNA Synthesis Kit (by tailing A) Vazyme Cat#: MR201 Direct-zolTM RNA Miniprep Zymo Research Cat#: R2051 Cytoplasmic and Nuclear Extraction Kit for Cells Invent Biotechnologies Cat#: SC-003 (Continued on next page) Cell Reports 43, 113964, March 26, 2024 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER STEMdiff Hematopoesis Kit StemCell Technologies Cat#: 05310 STEMdiff Microglia Differentiation Kit StemCell Technologies Cat#:100-0019 STEMdiff Microglia Maturation Kit StemCell Technologies Cat#:100-0020 Chromium Next GEM Single Cell 3 Reagent Kits v3.1 10X Genomics Cat#: CG000204 Chromium Next GEM Single Cell 3 GEM, Library & Gel Bead Kit v3.1 10X Genomics Cat#: PN-1000121 Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat#: PN-1000127 Dual Index Kit TT Set A 10X Genomics Cat#: PN-1000215 Deposited data Raw and analyzed data This paper GSE222665 Experimental models: Cell lines 293T Pricella CL-0005 Experimental models: Organisms/strains Mouse: Tmem119-CreERT2 Shanghai Model Organisms Center Inc. NM-KI-200234 Mouse: Cx3cr1-CreERT2 The Jackson Laboratory JAX:021160 Mouse: Mir137loxP/loxP Cheng et al.30 N/A Mouse: Mir137loxP/loxP;Zp3-Cre Cheng et al.30 N/A Oligonucleotides miRNA detection probe for MMU-MIR-1373P (/5DigN/ACGCGTATTCTTAAGCAAT/ 3Dig_N/) Qiagen Cat#: 339112 YD006186863-BEG Primers used in this study, see Table S5 This paper N/A Recombinant DNA psiCHECK-2-Jdp2-30UTR This paper N/A psiCHECK-2-Jdp2-mut-30UTR This paper N/A pCR2.1 TOPO-U6-miR-137 Cheng et al.30 N/A pLKO.1 mouse-shRNA-Jdp2 This paper N/A pET28a-MBP-Pu.1 This paper N/A Software and algorithms Prisim9 Graphpad https://www.graphpad.com/ scientific-software/prism/ Tree Star FlowJo X 10.0.7 R2 x64 Tree Star https://www.flowjo.com/ ZEN 3.3 ZEISS https://www.zeiss.com.cn/ Imaris 9.0.1 Win64 Imaris https://imaris.oxinst.com/support/ imaris-release-notes/9-0-0#9-0-1 Case Viewer (Version 2.4) 3DHISTECH Download caseviewer 3.3.6 for free (Windows) (freedownloadmanager.org) Skewer (Version 0.2.2) Jiang et al.60 https://www.skewers.cn/ R (Version 4.1.3) R https://www.r-project.org/ STAR (Version 2.7.9a) Dobin et al.61 https://github.com/alexdobin/STAR/tree/ 2.7.9a RSEM (Version1.3.1) Li and Dewey,62 http://deweylab.github.io/RSEM/ DAVID (Version 2021) Sherman et al.63 https://david.ncifcrf.gov/ bowtie2 (Version 2.4.4) Langmead and Salzberg,64 https://sourceforge.net/projects/ bowtie-bio/files/bowtie2/2.4.4/ GREAT (Version 4.0.4) McLean et al.65 http://great.stanford.edu/public/html/ DESeq2 (Version 1.34.0) Love et al.66 https://www.rdocumentation.org/search? q=deseq2 pheatmap (Version 1.0.12) Raivo Kolde https://CRAN.R-project.org/ package=pheatmap (Continued on next page) 20 Cell Reports 43, 113964, March 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER ggplot2 (Version 3.4.0) Hadley Wickham https://www.rdocumentation.org/ packages/ggplot2/versions/3.4.0 ggpubr (Version 0.5.0) Alboukadel Kassambara https://www.rdocumentation.org/ packages/ggpubr/versions/0.5.0 MACS2 (Version 2.2.7.1) Zhang et al.67 https://github.com/macs3-project/MACS/ tree/v2.2.7.1 chip-r (Version 1.2.0) Newell et al.68 https://github.com/rhysnewell/ChIP-R Bedtools (Version 2.30.0) Quinlan and Hall,69 https://bedtools.readthedocs.io/en/latest/ HOMER (Version 4.11) Heinz et al.70 http://homer.ucsd.edu/homer/ deepTools (Version 3.5.1) Ramı́rez et al.71 https://github.com/deeptools/deepTools Cell Ranger (Version 6.1.2) 10X Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/using/tutorial_in Seurat (Version 4.1.0) Stuart et al.72 https://www.rdocumentation.org/ packages/Seurat/versions/4.1.0 Ggcor (Version 0.9.8.1) Huang et al. https://github.com/Github-Yilei/ggcor DEsingle (Version 1.14.0) Miao et al.73 https://anaconda.org/bioconda/ bioconductor-desingle/files pyGenomeTracks (Version 3.7) Lopez-Delisle et al.74 https://github.com/deeptools/ pyGenomeTracks eisaR (Version 1.8.0) Gaidatzis et al.47 https://www.nature.com/articles/ s41586-018-0414-6 Velocyto (Version 0.17.17) La Manno et al.75 http://velocyto.org/velocyto.py/index.html QuasR (Version 1.38.0) Gaidatzis et al.76 https://bioconductor.org/packages/ release/bioc/html/QuasR.html Sylamer van Dongen et al.46 https://www.nature.com/articles/nmeth.
Software:Article Title: Nuclear microRNA-mediated transcriptional control determines adult microglial homeostasis and brain function.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Paraformaldehyde,4% Solarbio Cat#: P1110 Cole’s Hematoxylin Solution Solarbio Cat#: G1140 Eosin Y Stain Solution, For HE Solarbio Cat#: G1100 DAPI Sigma-Aldrich Cat#: D9542 Glycerol Sigma Cat#: G5516-1L Sodium chloride HUSHI Cat#: 10019318 Ni Sepharose 6 Fast Flow Cytiva Cat#:17531804 Kanamycln sulfate Aladdin Cat#: D2117220 Imidazole Sangon biotech Cat#: B528414 HEPES BIOISCO Cat#: 130420 KCl Sigma-Aldrich Cat#: 451029 DTT Sigma Cat#: 646563-10X EDTA Beyotime Cat#: ST1303 Salmon DNA Sigma Cat#: D7656 Blocking buffer Beyotime Cat#: GS009B Washing buffer Beyotime Cat#: GS009W Equilibrium buffer Beyotime Cat#: GS009A Sensor chip CM5 Cytiva Cat#: 29149604 Sensor chip SA Cytiva Cat#: BR100032 HBS-EP+ buffer,103 Cytiva Cat#: BR100826 AceQ Universal SYBR qPCR Master Mix Vazyme Cat#: Q511 Critical commercial assays Adult Brain Dissociation kit Miltenyi Biotec Cat#: 130-107-677 CD11b MicroBeads, human and mouse Miltenyi Biotec Cat#: 130-126-725 FD Rapid Golgi Stain Kit FD NeuroTechnologies, Inc. Cat#: PK401 CellTrackerTM fluorescent probes kit Invitrogen Cat#: C34552 Proteome Profiler Mouse Cytokine Array Kit R&D Systems Cat#: ARY006 Proteome Profiler Mouse Chemokine Array Kit R&D Systems Cat#: ARY020 Mouse TNF-a ELISA KIT Solarbio Cat#: SEKM-0034 Mouse IL-6 ELISA KIT Solarbio Cat#: SEKM-0007 Mouse IL-1b ELISA KIT Solarbio Cat#: SEKM-0002 Dual Luciferase Reporter Assay Kit Vazyme Cat#: DL101 Dual-Luciferase Reporter 1000 System Promega Cat#: E1980 VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina Vazyme Cat#: NR605 TruePrep DNA Library Prep Kit V2 for Illumina Vazyme Cat#: TD501 Hyperactive Universal CUT&Tag Assay Kit for Illumina Vazyme Cat#: TD903 TruePrep Index Kit V2 for Illumina Vazyme Cat#: TD202 TransScript All-in-One First-Strand cDNA Synthesis SuperMix for qPCR(One-Step gDNA Removal) TRANS Cat#: AT341 miRNA 1st Strand cDNA Synthesis Kit (by tailing A) Vazyme Cat#: MR201 Direct-zolTM RNA Miniprep Zymo Research Cat#: R2051 Cytoplasmic and Nuclear Extraction Kit for Cells Invent Biotechnologies Cat#: SC-003 (Continued on next page) Cell Reports 43, 113964, March 26, 2024 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER STEMdiff Hematopoesis Kit StemCell Technologies Cat#: 05310 STEMdiff Microglia Differentiation Kit StemCell Technologies Cat#:100-0019 STEMdiff Microglia Maturation Kit StemCell Technologies Cat#:100-0020 Chromium Next GEM Single Cell 3 Reagent Kits v3.1 10X Genomics Cat#: CG000204 Chromium Next GEM Single Cell 3 GEM, Library & Gel Bead Kit v3.1 10X Genomics Cat#: PN-1000121 Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat#: PN-1000127 Dual Index Kit TT Set A 10X Genomics Cat#: PN-1000215 Deposited data Raw and analyzed data This paper GSE222665 Experimental models: Cell lines 293T Pricella CL-0005 Experimental models: Organisms/strains Mouse: Tmem119-CreERT2 Shanghai Model Organisms Center Inc. NM-KI-200234 Mouse: Cx3cr1-CreERT2 The Jackson Laboratory JAX:021160 Mouse: Mir137loxP/loxP Cheng et al.30 N/A Mouse: Mir137loxP/loxP;Zp3-Cre Cheng et al.30 N/A Oligonucleotides miRNA detection probe for MMU-MIR-1373P (/5DigN/ACGCGTATTCTTAAGCAAT/ 3Dig_N/) Qiagen Cat#: 339112 YD006186863-BEG Primers used in this study, see Table S5 This paper N/A Recombinant DNA psiCHECK-2-Jdp2-30UTR This paper N/A psiCHECK-2-Jdp2-mut-30UTR This paper N/A pCR2.1 TOPO-U6-miR-137 Cheng et al.30 N/A pLKO.1 mouse-shRNA-Jdp2 This paper N/A pET28a-MBP-Pu.1 This paper N/A Software and algorithms Prisim9 Graphpad https://www.graphpad.com/ scientific-software/prism/ Tree Star FlowJo X 10.0.7 R2 x64 Tree Star https://www.flowjo.com/ ZEN 3.3 ZEISS https://www.zeiss.com.cn/ Imaris 9.0.1 Win64 Imaris https://imaris.oxinst.com/support/ imaris-release-notes/9-0-0#9-0-1 Case Viewer (Version 2.4) 3DHISTECH Download caseviewer 3.3.6 for free (Windows) (freedownloadmanager.org) Skewer (Version 0.2.2) Jiang et al.60 https://www.skewers.cn/ R (Version 4.1.3) R https://www.r-project.org/ STAR (Version 2.7.9a) Dobin et al.61 https://github.com/alexdobin/STAR/tree/ 2.7.9a RSEM (Version1.3.1) Li and Dewey,62 http://deweylab.github.io/RSEM/ DAVID (Version 2021) Sherman et al.63 https://david.ncifcrf.gov/ bowtie2 (Version 2.4.4) Langmead and Salzberg,64 https://sourceforge.net/projects/ bowtie-bio/files/bowtie2/2.4.4/ GREAT (Version 4.0.4) McLean et al.65 http://great.stanford.edu/public/html/ DESeq2 (Version 1.34.0) Love et al.66 https://www.rdocumentation.org/search? q=deseq2 pheatmap (Version 1.0.12) Raivo Kolde https://CRAN.R-project.org/ package=pheatmap (Continued on next page) 20 Cell Reports 43, 113964, March 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER ggplot2 (Version 3.4.0) Hadley Wickham https://www.rdocumentation.org/ packages/ggplot2/versions/3.4.0 ggpubr (Version 0.5.0) Alboukadel Kassambara https://www.rdocumentation.org/ packages/ggpubr/versions/0.5.0 MACS2 (Version 2.2.7.1) Zhang et al.67 https://github.com/macs3-project/MACS/ tree/v2.2.7.1 chip-r (Version 1.2.0) Newell et al.68 https://github.com/rhysnewell/ChIP-R Bedtools (Version 2.30.0) Quinlan and Hall,69 https://bedtools.readthedocs.io/en/latest/ HOMER (Version 4.11) Heinz et al.70 http://homer.ucsd.edu/homer/ deepTools (Version 3.5.1) Ramı́rez et al.71 https://github.com/deeptools/deepTools Cell Ranger (Version 6.1.2) 10X Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/using/tutorial_in Seurat (Version 4.1.0) Stuart et al.72 https://www.rdocumentation.org/ packages/Seurat/versions/4.1.0 Ggcor (Version 0.9.8.1) Huang et al. https://github.com/Github-Yilei/ggcor DEsingle (Version 1.14.0) Miao et al.73 https://anaconda.org/bioconda/ bioconductor-desingle/files pyGenomeTracks (Version 3.7) Lopez-Delisle et al.74 https://github.com/deeptools/ pyGenomeTracks eisaR (Version 1.8.0) Gaidatzis et al.47 https://www.nature.com/articles/ s41586-018-0414-6 Velocyto (Version 0.17.17) La Manno et al.75 http://velocyto.org/velocyto.py/index.html QuasR (Version 1.38.0) Gaidatzis et al.76 https://bioconductor.org/packages/ release/bioc/html/QuasR.html Sylamer van Dongen et al.46 https://www.nature.com/articles/nmeth.
Marker:Article Title: PILRA regulates microglial neuroinflammation and lipid metabolism as a candidate therapeutic target for Alzheimer’s disease
Article Snippet: From this point 478 onward all steps from STEMCELL Technologies protocol were followed to generate highly 479 pure HPCs. .. Collected HPCs were confirmed to be >90% positive for marker CD43 and 480 seeded directly onto astrocyte feeder layers to generate iMG as previously reported22,33, 481 differentiated using STEMCELL Technolgies STEMDiff Microglia Differentiation (100-482 0019) and STEMDiff Microglia Maturation (100-0020) protocols or cryopreserved in 483 Cryostor CS5 (STEMcell Technologies, 07933)22. .. 484 Hematopoietic and iMicroglia differentiation - iPSC line 2 485 22 The parental WTC11-mEGFP (Coriell, AICS-0036-006) human iPSC line was acquired 486 through the Allen Cell Collection, available from Coriell Institute for Medical Research, 487 referred to herein as iPSC line 2. iPSCs were confirmed to be karyotypically normal by 488 Array Comparative Genomic Hybridization (Cell Line Genetics), sterile, and pluripotent 489 through trilineage in vitro differentiation. iPSCs were maintained on matrigel-coated plates 490 (Corning, CB356238) according to the manufacturer’s specifications in TeSR-E8 491 (STEMCELL Technologies, 05990).
Cell Culture:Article Title: Triglyceride metabolism controls inflammation and APOE4 -associated disease states in microglia
Article Snippet: .. For the last 4 days, microglia progenitors were cultured in the STEMdiff Microglia Maturation Kit (StemCell Technologies) medium to mature the microglia. .. Flow cytometry (CD11+ APC, Miltenyi Biotec) and immunocytochemistry (antibodies, see below) were used to assess purity.
Article Title: Triglyceride metabolism controls inflammation and microglial phenotypes associated with APOE4.
Article Snippet: .. For the last 4 days, microglia progenitors were cultured in the STEMdiff Microglia Maturation Kit (StemCell Technologies) medium to mature the microglia. .. Flow cytometry (CD11+ APC, Miltenyi Biotec) and immunocytochemistry were used to assess purity, as described below. iTF microglia differentiation iTF-Microglia were generated based on previously published protocols.32 Parental line WTC-11 (male, UCSF, MTA obtained) and KOLF2.1J iPSCs (male, available through iNDI project from JAX labs, https://www.jax.org/jax-mice-and-services/ipsc) expressing six inducible transcription factors (MAFB, CEBPα, IRF, PU.1, CEBPβ, IRF5) were dissociated using StemPro Accutase (Gibco) and plated in Induction Medium (Essential 8 Medium,10 μM Chroman1, MedChemExpress, and 2 μg/mL Doxycycline hydrochloride, Sigma) at 400,000 cells per well on double-coated [hESC-qualified Matrigel Matrix and Poly-L-Ornithine (Sigma)] 10 cm tissue-culture treated plates.
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