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.
Derivative Assay:Article Title: TMEM106B reduction does not rescue GRN deficiency in iPSC-derived human microglia and mouse models
Article Snippet: The PGP1 iPS cell line was obtained from Synthego and the knockout lines were generated using a nucleofection-based RNP approach to introduce Cas9 and sgRNAs against TMEM106b, GRN and TMEM106b/GRN (DKO). .. PGP1 WT, TKO, GKO and DKO iPSCs derived microglia were generated using the StemDiff hematopoietic kit (stemcell technologies cat #05310) from days 0–12, and subsequently the StemDiff microglia differentiation (stemcell technologies cat #100-0019) and maturation (cat #100-0020) kits from days 13–40+ with some adaptations to increase cell yield. ..
Generated:Article Title: TMEM106B reduction does not rescue GRN deficiency in iPSC-derived human microglia and mouse models
Article Snippet: The PGP1 iPS cell line was obtained from Synthego and the knockout lines were generated using a nucleofection-based RNP approach to introduce Cas9 and sgRNAs against TMEM106b, GRN and TMEM106b/GRN (DKO). .. PGP1 WT, TKO, GKO and DKO iPSCs derived microglia were generated using the StemDiff hematopoietic kit (stemcell technologies cat #05310) from days 0–12, and subsequently the StemDiff microglia differentiation (stemcell technologies cat #100-0019) and maturation (cat #100-0020) kits from days 13–40+ with some adaptations to increase cell yield. ..
Article Title: ATM-deficiency-induced microglial activation promotes neurodegeneration in ataxia-telangiectasia.
Article Snippet: Analysis was performed using FlowJo software. .. Differentiation of hematopoietic progenitor cells to Microglia Human iPSC-derived microglia (iMGL) were generated from human iPSC-derived hematopoietic progenitors using the STEMdiff Microglia Differentiation Kit (STEMCELL Technologies Cat# 100-0019) and STEMdiff Microglia Maturation Kit (STEMCELL Technologies Cat# 100-0020) according to manufacturer instructions. ..
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