Virus:Article Title: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-ATRX H-300 Santa Cruz Biotechnology, Inc sc-15408 anti-NeuN Millipore MAB377; RRID:AB_2298772 anti-GFAP Agilent Technologies, Inc M0761; RRID:AB_2109952 ;anti-IBA1 Wako Pure Chemical Corporation 019-19741; RRID:AB_839504 anti-INCENP Sigma I5283; RRID:AB_477113 anti-ATRX Abcam ab97508; RRID:AB_10680289 anti-H3K27me3 Millipore 07-449; RRID:AB_310624 anti-H3.3 Millipore 17-10245: RRID:AB_10953839 Normal rabbit IgG Cell Signaling 2729S; RRID:AB_1031062 anti-Rabbit-HRP Jackson ImmunoResearch Laboratories, Inc 111-036-003; RRID:AB_2337942 Bacterial and Virus Strains pmirGLO vector Promega E1330 PX459 plasmid (Addgene) Ran et al., 2013 62988 Lenti-III-mico-GFP vector, viral titer > 107 IU/ml Applied Biological Materials MIMAT0000149 Chemicals, Peptides, and Recombinant Proteins XbaI NEB R0145S BbsI NEB R0539S Anti-miR miRNA Inhibitor; miR-137-3p ThermoFisher AM17000 KpnI NEB R0142S Critical Commercial Assays SuperScript II Reverse Transcriptase Invitrogen 18064022 miRVANA total RNA isolation kit ThermoFisher AM1560 TaqMan Advanced MicroRNA reverse transcription kit ThermoFisher A28007 TaqMan Universal PCR Master Mix, no AmpEraseTaqMan Universal PCR Master Mix, no AmpErase ThermoFisher 4324018 Rapid GolgiStain Kit FD Neurotechnologies, Inc PK401 RNA 6000 Nano kit Caliper Life Sciences 5067-1511 ScriptSeq Complete Gold Kit (H/M/R) Illumina Inc. BHMR1205 Deposited Data RNA sequencing of hippocampi from control and Atrx-cKO males and females This study GEO: GSE129975 Experimental Models: Cell Lines Neuro2A ATCC CCL-131 Experimental Models: Organisms/Strains Mouse: CaMKII-Cre: B6.Cg-Tg(Camk2acre)T29-1Stl/J Jackson Laboratory 005359 Mouse: Atrxfl/fl Gift from Doug Higgs and Richard Gibbons N/A Oligonucleotides Oligonucleotides for qRT-PCR Table S4 N/A Oligonucleotides for sgRNA Table S4 N/A Oligonucleotides for ChIP-PCR Table S4 N/A (Continued on next page) e1 Cell Reports 31, 107838, June 30, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Adobe Photoshop CS6 Adobe RRID:SCR_014199;Version 13.0 OpenLab Agilent RRID:SCR_012158 Volocity 3D Image Analysis Software PerkinElmer RRID:SCR_002668; Demo Version 6.0.1 mni_autoreg tools Collins et al., 1994 RRID:SCR_013621; http://www.bic.mni. mcgill.ca/software/mni_autoreg/ ANTS (advanced normalization tools) Avants et al., 2011 RRID:SCR_004757; http://www.picsl. upenn.edu/ANTS/ FIJI Schindelin et al., 2012 RRID:SCR_002285 https://fiji.sc Prism 6.0 Graphpad RRID:SCR_002798; https://www. graphpad.com Simple Neurite Tracer Longair et al., 2011 RRID:SCR_016566; https://imagej.net/ Simple_Neurite_Tracer ANY-Maze Stoelting Co. RRID:SCR_014289 cutadapt Martin, 2011 RRID:SCR_011841; version 0.4.1 HISAT2 Kim et al., 2015 RRID:SCR_015530; version 2.0.4 SAMtools Li et al., 2009 RRID:SCR_002105; http://www.htslib.org/ StringTie Pertea et al., 2015 RRID:SCR_016323; v1.3.3; https://ccb.jhu. edu/software/stringtie/ tximport Soneson et al., 2015 RRID:SCR_016752; https://bioconductor. org/packages/release/bioc/html/tximport. html DESeq2 Love et al., 2014 RRID:SCR_015687; https://bioconductor. org/packages/release/bioc/html/DESeq2. html pheatmap Kolde, 2012 RRID:SCR_016418; https://cran.r-project. org/web/packages/pheatmap/index.html Lancaster method Yi et al., 2018 N/A Other Bussey-Saksida mouse touch screen chambers Lafayette Neuroscience Model 80614-20 Article ll OPEN ACCESS
Plasmid Preparation:Article Title: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-ATRX H-300 Santa Cruz Biotechnology, Inc sc-15408 anti-NeuN Millipore MAB377; RRID:AB_2298772 anti-GFAP Agilent Technologies, Inc M0761; RRID:AB_2109952 ;anti-IBA1 Wako Pure Chemical Corporation 019-19741; RRID:AB_839504 anti-INCENP Sigma I5283; RRID:AB_477113 anti-ATRX Abcam ab97508; RRID:AB_10680289 anti-H3K27me3 Millipore 07-449; RRID:AB_310624 anti-H3.3 Millipore 17-10245: RRID:AB_10953839 Normal rabbit IgG Cell Signaling 2729S; RRID:AB_1031062 anti-Rabbit-HRP Jackson ImmunoResearch Laboratories, Inc 111-036-003; RRID:AB_2337942 Bacterial and Virus Strains pmirGLO vector Promega E1330 PX459 plasmid (Addgene) Ran et al., 2013 62988 Lenti-III-mico-GFP vector, viral titer > 107 IU/ml Applied Biological Materials MIMAT0000149 Chemicals, Peptides, and Recombinant Proteins XbaI NEB R0145S BbsI NEB R0539S Anti-miR miRNA Inhibitor; miR-137-3p ThermoFisher AM17000 KpnI NEB R0142S Critical Commercial Assays SuperScript II Reverse Transcriptase Invitrogen 18064022 miRVANA total RNA isolation kit ThermoFisher AM1560 TaqMan Advanced MicroRNA reverse transcription kit ThermoFisher A28007 TaqMan Universal PCR Master Mix, no AmpEraseTaqMan Universal PCR Master Mix, no AmpErase ThermoFisher 4324018 Rapid GolgiStain Kit FD Neurotechnologies, Inc PK401 RNA 6000 Nano kit Caliper Life Sciences 5067-1511 ScriptSeq Complete Gold Kit (H/M/R) Illumina Inc. BHMR1205 Deposited Data RNA sequencing of hippocampi from control and Atrx-cKO males and females This study GEO: GSE129975 Experimental Models: Cell Lines Neuro2A ATCC CCL-131 Experimental Models: Organisms/Strains Mouse: CaMKII-Cre: B6.Cg-Tg(Camk2acre)T29-1Stl/J Jackson Laboratory 005359 Mouse: Atrxfl/fl Gift from Doug Higgs and Richard Gibbons N/A Oligonucleotides Oligonucleotides for qRT-PCR Table S4 N/A Oligonucleotides for sgRNA Table S4 N/A Oligonucleotides for ChIP-PCR Table S4 N/A (Continued on next page) e1 Cell Reports 31, 107838, June 30, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Adobe Photoshop CS6 Adobe RRID:SCR_014199;Version 13.0 OpenLab Agilent RRID:SCR_012158 Volocity 3D Image Analysis Software PerkinElmer RRID:SCR_002668; Demo Version 6.0.1 mni_autoreg tools Collins et al., 1994 RRID:SCR_013621; http://www.bic.mni. mcgill.ca/software/mni_autoreg/ ANTS (advanced normalization tools) Avants et al., 2011 RRID:SCR_004757; http://www.picsl. upenn.edu/ANTS/ FIJI Schindelin et al., 2012 RRID:SCR_002285 https://fiji.sc Prism 6.0 Graphpad RRID:SCR_002798; https://www. graphpad.com Simple Neurite Tracer Longair et al., 2011 RRID:SCR_016566; https://imagej.net/ Simple_Neurite_Tracer ANY-Maze Stoelting Co. RRID:SCR_014289 cutadapt Martin, 2011 RRID:SCR_011841; version 0.4.1 HISAT2 Kim et al., 2015 RRID:SCR_015530; version 2.0.4 SAMtools Li et al., 2009 RRID:SCR_002105; http://www.htslib.org/ StringTie Pertea et al., 2015 RRID:SCR_016323; v1.3.3; https://ccb.jhu. edu/software/stringtie/ tximport Soneson et al., 2015 RRID:SCR_016752; https://bioconductor. org/packages/release/bioc/html/tximport. html DESeq2 Love et al., 2014 RRID:SCR_015687; https://bioconductor. org/packages/release/bioc/html/DESeq2. html pheatmap Kolde, 2012 RRID:SCR_016418; https://cran.r-project. org/web/packages/pheatmap/index.html Lancaster method Yi et al., 2018 N/A Other Bussey-Saksida mouse touch screen chambers Lafayette Neuroscience Model 80614-20 Article ll OPEN ACCESS
Recombinant:Article Title: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-ATRX H-300 Santa Cruz Biotechnology, Inc sc-15408 anti-NeuN Millipore MAB377; RRID:AB_2298772 anti-GFAP Agilent Technologies, Inc M0761; RRID:AB_2109952 ;anti-IBA1 Wako Pure Chemical Corporation 019-19741; RRID:AB_839504 anti-INCENP Sigma I5283; RRID:AB_477113 anti-ATRX Abcam ab97508; RRID:AB_10680289 anti-H3K27me3 Millipore 07-449; RRID:AB_310624 anti-H3.3 Millipore 17-10245: RRID:AB_10953839 Normal rabbit IgG Cell Signaling 2729S; RRID:AB_1031062 anti-Rabbit-HRP Jackson ImmunoResearch Laboratories, Inc 111-036-003; RRID:AB_2337942 Bacterial and Virus Strains pmirGLO vector Promega E1330 PX459 plasmid (Addgene) Ran et al., 2013 62988 Lenti-III-mico-GFP vector, viral titer > 107 IU/ml Applied Biological Materials MIMAT0000149 Chemicals, Peptides, and Recombinant Proteins XbaI NEB R0145S BbsI NEB R0539S Anti-miR miRNA Inhibitor; miR-137-3p ThermoFisher AM17000 KpnI NEB R0142S Critical Commercial Assays SuperScript II Reverse Transcriptase Invitrogen 18064022 miRVANA total RNA isolation kit ThermoFisher AM1560 TaqMan Advanced MicroRNA reverse transcription kit ThermoFisher A28007 TaqMan Universal PCR Master Mix, no AmpEraseTaqMan Universal PCR Master Mix, no AmpErase ThermoFisher 4324018 Rapid GolgiStain Kit FD Neurotechnologies, Inc PK401 RNA 6000 Nano kit Caliper Life Sciences 5067-1511 ScriptSeq Complete Gold Kit (H/M/R) Illumina Inc. BHMR1205 Deposited Data RNA sequencing of hippocampi from control and Atrx-cKO males and females This study GEO: GSE129975 Experimental Models: Cell Lines Neuro2A ATCC CCL-131 Experimental Models: Organisms/Strains Mouse: CaMKII-Cre: B6.Cg-Tg(Camk2acre)T29-1Stl/J Jackson Laboratory 005359 Mouse: Atrxfl/fl Gift from Doug Higgs and Richard Gibbons N/A Oligonucleotides Oligonucleotides for qRT-PCR Table S4 N/A Oligonucleotides for sgRNA Table S4 N/A Oligonucleotides for ChIP-PCR Table S4 N/A (Continued on next page) e1 Cell Reports 31, 107838, June 30, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Adobe Photoshop CS6 Adobe RRID:SCR_014199;Version 13.0 OpenLab Agilent RRID:SCR_012158 Volocity 3D Image Analysis Software PerkinElmer RRID:SCR_002668; Demo Version 6.0.1 mni_autoreg tools Collins et al., 1994 RRID:SCR_013621; http://www.bic.mni. mcgill.ca/software/mni_autoreg/ ANTS (advanced normalization tools) Avants et al., 2011 RRID:SCR_004757; http://www.picsl. upenn.edu/ANTS/ FIJI Schindelin et al., 2012 RRID:SCR_002285 https://fiji.sc Prism 6.0 Graphpad RRID:SCR_002798; https://www. graphpad.com Simple Neurite Tracer Longair et al., 2011 RRID:SCR_016566; https://imagej.net/ Simple_Neurite_Tracer ANY-Maze Stoelting Co. RRID:SCR_014289 cutadapt Martin, 2011 RRID:SCR_011841; version 0.4.1 HISAT2 Kim et al., 2015 RRID:SCR_015530; version 2.0.4 SAMtools Li et al., 2009 RRID:SCR_002105; http://www.htslib.org/ StringTie Pertea et al., 2015 RRID:SCR_016323; v1.3.3; https://ccb.jhu. edu/software/stringtie/ tximport Soneson et al., 2015 RRID:SCR_016752; https://bioconductor. org/packages/release/bioc/html/tximport. html DESeq2 Love et al., 2014 RRID:SCR_015687; https://bioconductor. org/packages/release/bioc/html/DESeq2. html pheatmap Kolde, 2012 RRID:SCR_016418; https://cran.r-project. org/web/packages/pheatmap/index.html Lancaster method Yi et al., 2018 N/A Other Bussey-Saksida mouse touch screen chambers Lafayette Neuroscience Model 80614-20 Article ll OPEN ACCESS
Reverse Transcription:Article Title: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-ATRX H-300 Santa Cruz Biotechnology, Inc sc-15408 anti-NeuN Millipore MAB377; RRID:AB_2298772 anti-GFAP Agilent Technologies, Inc M0761; RRID:AB_2109952 ;anti-IBA1 Wako Pure Chemical Corporation 019-19741; RRID:AB_839504 anti-INCENP Sigma I5283; RRID:AB_477113 anti-ATRX Abcam ab97508; RRID:AB_10680289 anti-H3K27me3 Millipore 07-449; RRID:AB_310624 anti-H3.3 Millipore 17-10245: RRID:AB_10953839 Normal rabbit IgG Cell Signaling 2729S; RRID:AB_1031062 anti-Rabbit-HRP Jackson ImmunoResearch Laboratories, Inc 111-036-003; RRID:AB_2337942 Bacterial and Virus Strains pmirGLO vector Promega E1330 PX459 plasmid (Addgene) Ran et al., 2013 62988 Lenti-III-mico-GFP vector, viral titer > 107 IU/ml Applied Biological Materials MIMAT0000149 Chemicals, Peptides, and Recombinant Proteins XbaI NEB R0145S BbsI NEB R0539S Anti-miR miRNA Inhibitor; miR-137-3p ThermoFisher AM17000 KpnI NEB R0142S Critical Commercial Assays SuperScript II Reverse Transcriptase Invitrogen 18064022 miRVANA total RNA isolation kit ThermoFisher AM1560 TaqMan Advanced MicroRNA reverse transcription kit ThermoFisher A28007 TaqMan Universal PCR Master Mix, no AmpEraseTaqMan Universal PCR Master Mix, no AmpErase ThermoFisher 4324018 Rapid GolgiStain Kit FD Neurotechnologies, Inc PK401 RNA 6000 Nano kit Caliper Life Sciences 5067-1511 ScriptSeq Complete Gold Kit (H/M/R) Illumina Inc. BHMR1205 Deposited Data RNA sequencing of hippocampi from control and Atrx-cKO males and females This study GEO: GSE129975 Experimental Models: Cell Lines Neuro2A ATCC CCL-131 Experimental Models: Organisms/Strains Mouse: CaMKII-Cre: B6.Cg-Tg(Camk2acre)T29-1Stl/J Jackson Laboratory 005359 Mouse: Atrxfl/fl Gift from Doug Higgs and Richard Gibbons N/A Oligonucleotides Oligonucleotides for qRT-PCR Table S4 N/A Oligonucleotides for sgRNA Table S4 N/A Oligonucleotides for ChIP-PCR Table S4 N/A (Continued on next page) e1 Cell Reports 31, 107838, June 30, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Adobe Photoshop CS6 Adobe RRID:SCR_014199;Version 13.0 OpenLab Agilent RRID:SCR_012158 Volocity 3D Image Analysis Software PerkinElmer RRID:SCR_002668; Demo Version 6.0.1 mni_autoreg tools Collins et al., 1994 RRID:SCR_013621; http://www.bic.mni. mcgill.ca/software/mni_autoreg/ ANTS (advanced normalization tools) Avants et al., 2011 RRID:SCR_004757; http://www.picsl. upenn.edu/ANTS/ FIJI Schindelin et al., 2012 RRID:SCR_002285 https://fiji.sc Prism 6.0 Graphpad RRID:SCR_002798; https://www. graphpad.com Simple Neurite Tracer Longair et al., 2011 RRID:SCR_016566; https://imagej.net/ Simple_Neurite_Tracer ANY-Maze Stoelting Co. RRID:SCR_014289 cutadapt Martin, 2011 RRID:SCR_011841; version 0.4.1 HISAT2 Kim et al., 2015 RRID:SCR_015530; version 2.0.4 SAMtools Li et al., 2009 RRID:SCR_002105; http://www.htslib.org/ StringTie Pertea et al., 2015 RRID:SCR_016323; v1.3.3; https://ccb.jhu. edu/software/stringtie/ tximport Soneson et al., 2015 RRID:SCR_016752; https://bioconductor. org/packages/release/bioc/html/tximport. html DESeq2 Love et al., 2014 RRID:SCR_015687; https://bioconductor. org/packages/release/bioc/html/DESeq2. html pheatmap Kolde, 2012 RRID:SCR_016418; https://cran.r-project. org/web/packages/pheatmap/index.html Lancaster method Yi et al., 2018 N/A Other Bussey-Saksida mouse touch screen chambers Lafayette Neuroscience Model 80614-20 Article ll OPEN ACCESS
Isolation:Article Title: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-ATRX H-300 Santa Cruz Biotechnology, Inc sc-15408 anti-NeuN Millipore MAB377; RRID:AB_2298772 anti-GFAP Agilent Technologies, Inc M0761; RRID:AB_2109952 ;anti-IBA1 Wako Pure Chemical Corporation 019-19741; RRID:AB_839504 anti-INCENP Sigma I5283; RRID:AB_477113 anti-ATRX Abcam ab97508; RRID:AB_10680289 anti-H3K27me3 Millipore 07-449; RRID:AB_310624 anti-H3.3 Millipore 17-10245: RRID:AB_10953839 Normal rabbit IgG Cell Signaling 2729S; RRID:AB_1031062 anti-Rabbit-HRP Jackson ImmunoResearch Laboratories, Inc 111-036-003; RRID:AB_2337942 Bacterial and Virus Strains pmirGLO vector Promega E1330 PX459 plasmid (Addgene) Ran et al., 2013 62988 Lenti-III-mico-GFP vector, viral titer > 107 IU/ml Applied Biological Materials MIMAT0000149 Chemicals, Peptides, and Recombinant Proteins XbaI NEB R0145S BbsI NEB R0539S Anti-miR miRNA Inhibitor; miR-137-3p ThermoFisher AM17000 KpnI NEB R0142S Critical Commercial Assays SuperScript II Reverse Transcriptase Invitrogen 18064022 miRVANA total RNA isolation kit ThermoFisher AM1560 TaqMan Advanced MicroRNA reverse transcription kit ThermoFisher A28007 TaqMan Universal PCR Master Mix, no AmpEraseTaqMan Universal PCR Master Mix, no AmpErase ThermoFisher 4324018 Rapid GolgiStain Kit FD Neurotechnologies, Inc PK401 RNA 6000 Nano kit Caliper Life Sciences 5067-1511 ScriptSeq Complete Gold Kit (H/M/R) Illumina Inc. BHMR1205 Deposited Data RNA sequencing of hippocampi from control and Atrx-cKO males and females This study GEO: GSE129975 Experimental Models: Cell Lines Neuro2A ATCC CCL-131 Experimental Models: Organisms/Strains Mouse: CaMKII-Cre: B6.Cg-Tg(Camk2acre)T29-1Stl/J Jackson Laboratory 005359 Mouse: Atrxfl/fl Gift from Doug Higgs and Richard Gibbons N/A Oligonucleotides Oligonucleotides for qRT-PCR Table S4 N/A Oligonucleotides for sgRNA Table S4 N/A Oligonucleotides for ChIP-PCR Table S4 N/A (Continued on next page) e1 Cell Reports 31, 107838, June 30, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Adobe Photoshop CS6 Adobe RRID:SCR_014199;Version 13.0 OpenLab Agilent RRID:SCR_012158 Volocity 3D Image Analysis Software PerkinElmer RRID:SCR_002668; Demo Version 6.0.1 mni_autoreg tools Collins et al., 1994 RRID:SCR_013621; http://www.bic.mni. mcgill.ca/software/mni_autoreg/ ANTS (advanced normalization tools) Avants et al., 2011 RRID:SCR_004757; http://www.picsl. upenn.edu/ANTS/ FIJI Schindelin et al., 2012 RRID:SCR_002285 https://fiji.sc Prism 6.0 Graphpad RRID:SCR_002798; https://www. graphpad.com Simple Neurite Tracer Longair et al., 2011 RRID:SCR_016566; https://imagej.net/ Simple_Neurite_Tracer ANY-Maze Stoelting Co. RRID:SCR_014289 cutadapt Martin, 2011 RRID:SCR_011841; version 0.4.1 HISAT2 Kim et al., 2015 RRID:SCR_015530; version 2.0.4 SAMtools Li et al., 2009 RRID:SCR_002105; http://www.htslib.org/ StringTie Pertea et al., 2015 RRID:SCR_016323; v1.3.3; https://ccb.jhu. edu/software/stringtie/ tximport Soneson et al., 2015 RRID:SCR_016752; https://bioconductor. org/packages/release/bioc/html/tximport. html DESeq2 Love et al., 2014 RRID:SCR_015687; https://bioconductor. org/packages/release/bioc/html/DESeq2. html pheatmap Kolde, 2012 RRID:SCR_016418; https://cran.r-project. org/web/packages/pheatmap/index.html Lancaster method Yi et al., 2018 N/A Other Bussey-Saksida mouse touch screen chambers Lafayette Neuroscience Model 80614-20 Article ll OPEN ACCESS
Polymerase Chain Reaction:Article Title: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-ATRX H-300 Santa Cruz Biotechnology, Inc sc-15408 anti-NeuN Millipore MAB377; RRID:AB_2298772 anti-GFAP Agilent Technologies, Inc M0761; RRID:AB_2109952 ;anti-IBA1 Wako Pure Chemical Corporation 019-19741; RRID:AB_839504 anti-INCENP Sigma I5283; RRID:AB_477113 anti-ATRX Abcam ab97508; RRID:AB_10680289 anti-H3K27me3 Millipore 07-449; RRID:AB_310624 anti-H3.3 Millipore 17-10245: RRID:AB_10953839 Normal rabbit IgG Cell Signaling 2729S; RRID:AB_1031062 anti-Rabbit-HRP Jackson ImmunoResearch Laboratories, Inc 111-036-003; RRID:AB_2337942 Bacterial and Virus Strains pmirGLO vector Promega E1330 PX459 plasmid (Addgene) Ran et al., 2013 62988 Lenti-III-mico-GFP vector, viral titer > 107 IU/ml Applied Biological Materials MIMAT0000149 Chemicals, Peptides, and Recombinant Proteins XbaI NEB R0145S BbsI NEB R0539S Anti-miR miRNA Inhibitor; miR-137-3p ThermoFisher AM17000 KpnI NEB R0142S Critical Commercial Assays SuperScript II Reverse Transcriptase Invitrogen 18064022 miRVANA total RNA isolation kit ThermoFisher AM1560 TaqMan Advanced MicroRNA reverse transcription kit ThermoFisher A28007 TaqMan Universal PCR Master Mix, no AmpEraseTaqMan Universal PCR Master Mix, no AmpErase ThermoFisher 4324018 Rapid GolgiStain Kit FD Neurotechnologies, Inc PK401 RNA 6000 Nano kit Caliper Life Sciences 5067-1511 ScriptSeq Complete Gold Kit (H/M/R) Illumina Inc. BHMR1205 Deposited Data RNA sequencing of hippocampi from control and Atrx-cKO males and females This study GEO: GSE129975 Experimental Models: Cell Lines Neuro2A ATCC CCL-131 Experimental Models: Organisms/Strains Mouse: CaMKII-Cre: B6.Cg-Tg(Camk2acre)T29-1Stl/J Jackson Laboratory 005359 Mouse: Atrxfl/fl Gift from Doug Higgs and Richard Gibbons N/A Oligonucleotides Oligonucleotides for qRT-PCR Table S4 N/A Oligonucleotides for sgRNA Table S4 N/A Oligonucleotides for ChIP-PCR Table S4 N/A (Continued on next page) e1 Cell Reports 31, 107838, June 30, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Adobe Photoshop CS6 Adobe RRID:SCR_014199;Version 13.0 OpenLab Agilent RRID:SCR_012158 Volocity 3D Image Analysis Software PerkinElmer RRID:SCR_002668; Demo Version 6.0.1 mni_autoreg tools Collins et al., 1994 RRID:SCR_013621; http://www.bic.mni. mcgill.ca/software/mni_autoreg/ ANTS (advanced normalization tools) Avants et al., 2011 RRID:SCR_004757; http://www.picsl. upenn.edu/ANTS/ FIJI Schindelin et al., 2012 RRID:SCR_002285 https://fiji.sc Prism 6.0 Graphpad RRID:SCR_002798; https://www. graphpad.com Simple Neurite Tracer Longair et al., 2011 RRID:SCR_016566; https://imagej.net/ Simple_Neurite_Tracer ANY-Maze Stoelting Co. RRID:SCR_014289 cutadapt Martin, 2011 RRID:SCR_011841; version 0.4.1 HISAT2 Kim et al., 2015 RRID:SCR_015530; version 2.0.4 SAMtools Li et al., 2009 RRID:SCR_002105; http://www.htslib.org/ StringTie Pertea et al., 2015 RRID:SCR_016323; v1.3.3; https://ccb.jhu. edu/software/stringtie/ tximport Soneson et al., 2015 RRID:SCR_016752; https://bioconductor. org/packages/release/bioc/html/tximport. html DESeq2 Love et al., 2014 RRID:SCR_015687; https://bioconductor. org/packages/release/bioc/html/DESeq2. html pheatmap Kolde, 2012 RRID:SCR_016418; https://cran.r-project. org/web/packages/pheatmap/index.html Lancaster method Yi et al., 2018 N/A Other Bussey-Saksida mouse touch screen chambers Lafayette Neuroscience Model 80614-20 Article ll OPEN ACCESS
RNA Sequencing:Article Title: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-ATRX H-300 Santa Cruz Biotechnology, Inc sc-15408 anti-NeuN Millipore MAB377; RRID:AB_2298772 anti-GFAP Agilent Technologies, Inc M0761; RRID:AB_2109952 ;anti-IBA1 Wako Pure Chemical Corporation 019-19741; RRID:AB_839504 anti-INCENP Sigma I5283; RRID:AB_477113 anti-ATRX Abcam ab97508; RRID:AB_10680289 anti-H3K27me3 Millipore 07-449; RRID:AB_310624 anti-H3.3 Millipore 17-10245: RRID:AB_10953839 Normal rabbit IgG Cell Signaling 2729S; RRID:AB_1031062 anti-Rabbit-HRP Jackson ImmunoResearch Laboratories, Inc 111-036-003; RRID:AB_2337942 Bacterial and Virus Strains pmirGLO vector Promega E1330 PX459 plasmid (Addgene) Ran et al., 2013 62988 Lenti-III-mico-GFP vector, viral titer > 107 IU/ml Applied Biological Materials MIMAT0000149 Chemicals, Peptides, and Recombinant Proteins XbaI NEB R0145S BbsI NEB R0539S Anti-miR miRNA Inhibitor; miR-137-3p ThermoFisher AM17000 KpnI NEB R0142S Critical Commercial Assays SuperScript II Reverse Transcriptase Invitrogen 18064022 miRVANA total RNA isolation kit ThermoFisher AM1560 TaqMan Advanced MicroRNA reverse transcription kit ThermoFisher A28007 TaqMan Universal PCR Master Mix, no AmpEraseTaqMan Universal PCR Master Mix, no AmpErase ThermoFisher 4324018 Rapid GolgiStain Kit FD Neurotechnologies, Inc PK401 RNA 6000 Nano kit Caliper Life Sciences 5067-1511 ScriptSeq Complete Gold Kit (H/M/R) Illumina Inc. BHMR1205 Deposited Data RNA sequencing of hippocampi from control and Atrx-cKO males and females This study GEO: GSE129975 Experimental Models: Cell Lines Neuro2A ATCC CCL-131 Experimental Models: Organisms/Strains Mouse: CaMKII-Cre: B6.Cg-Tg(Camk2acre)T29-1Stl/J Jackson Laboratory 005359 Mouse: Atrxfl/fl Gift from Doug Higgs and Richard Gibbons N/A Oligonucleotides Oligonucleotides for qRT-PCR Table S4 N/A Oligonucleotides for sgRNA Table S4 N/A Oligonucleotides for ChIP-PCR Table S4 N/A (Continued on next page) e1 Cell Reports 31, 107838, June 30, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Adobe Photoshop CS6 Adobe RRID:SCR_014199;Version 13.0 OpenLab Agilent RRID:SCR_012158 Volocity 3D Image Analysis Software PerkinElmer RRID:SCR_002668; Demo Version 6.0.1 mni_autoreg tools Collins et al., 1994 RRID:SCR_013621; http://www.bic.mni. mcgill.ca/software/mni_autoreg/ ANTS (advanced normalization tools) Avants et al., 2011 RRID:SCR_004757; http://www.picsl. upenn.edu/ANTS/ FIJI Schindelin et al., 2012 RRID:SCR_002285 https://fiji.sc Prism 6.0 Graphpad RRID:SCR_002798; https://www. graphpad.com Simple Neurite Tracer Longair et al., 2011 RRID:SCR_016566; https://imagej.net/ Simple_Neurite_Tracer ANY-Maze Stoelting Co. RRID:SCR_014289 cutadapt Martin, 2011 RRID:SCR_011841; version 0.4.1 HISAT2 Kim et al., 2015 RRID:SCR_015530; version 2.0.4 SAMtools Li et al., 2009 RRID:SCR_002105; http://www.htslib.org/ StringTie Pertea et al., 2015 RRID:SCR_016323; v1.3.3; https://ccb.jhu. edu/software/stringtie/ tximport Soneson et al., 2015 RRID:SCR_016752; https://bioconductor. org/packages/release/bioc/html/tximport. html DESeq2 Love et al., 2014 RRID:SCR_015687; https://bioconductor. org/packages/release/bioc/html/DESeq2. html pheatmap Kolde, 2012 RRID:SCR_016418; https://cran.r-project. org/web/packages/pheatmap/index.html Lancaster method Yi et al., 2018 N/A Other Bussey-Saksida mouse touch screen chambers Lafayette Neuroscience Model 80614-20 Article ll OPEN ACCESS
Control:Article Title: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-ATRX H-300 Santa Cruz Biotechnology, Inc sc-15408 anti-NeuN Millipore MAB377; RRID:AB_2298772 anti-GFAP Agilent Technologies, Inc M0761; RRID:AB_2109952 ;anti-IBA1 Wako Pure Chemical Corporation 019-19741; RRID:AB_839504 anti-INCENP Sigma I5283; RRID:AB_477113 anti-ATRX Abcam ab97508; RRID:AB_10680289 anti-H3K27me3 Millipore 07-449; RRID:AB_310624 anti-H3.3 Millipore 17-10245: RRID:AB_10953839 Normal rabbit IgG Cell Signaling 2729S; RRID:AB_1031062 anti-Rabbit-HRP Jackson ImmunoResearch Laboratories, Inc 111-036-003; RRID:AB_2337942 Bacterial and Virus Strains pmirGLO vector Promega E1330 PX459 plasmid (Addgene) Ran et al., 2013 62988 Lenti-III-mico-GFP vector, viral titer > 107 IU/ml Applied Biological Materials MIMAT0000149 Chemicals, Peptides, and Recombinant Proteins XbaI NEB R0145S BbsI NEB R0539S Anti-miR miRNA Inhibitor; miR-137-3p ThermoFisher AM17000 KpnI NEB R0142S Critical Commercial Assays SuperScript II Reverse Transcriptase Invitrogen 18064022 miRVANA total RNA isolation kit ThermoFisher AM1560 TaqMan Advanced MicroRNA reverse transcription kit ThermoFisher A28007 TaqMan Universal PCR Master Mix, no AmpEraseTaqMan Universal PCR Master Mix, no AmpErase ThermoFisher 4324018 Rapid GolgiStain Kit FD Neurotechnologies, Inc PK401 RNA 6000 Nano kit Caliper Life Sciences 5067-1511 ScriptSeq Complete Gold Kit (H/M/R) Illumina Inc. BHMR1205 Deposited Data RNA sequencing of hippocampi from control and Atrx-cKO males and females This study GEO: GSE129975 Experimental Models: Cell Lines Neuro2A ATCC CCL-131 Experimental Models: Organisms/Strains Mouse: CaMKII-Cre: B6.Cg-Tg(Camk2acre)T29-1Stl/J Jackson Laboratory 005359 Mouse: Atrxfl/fl Gift from Doug Higgs and Richard Gibbons N/A Oligonucleotides Oligonucleotides for qRT-PCR Table S4 N/A Oligonucleotides for sgRNA Table S4 N/A Oligonucleotides for ChIP-PCR Table S4 N/A (Continued on next page) e1 Cell Reports 31, 107838, June 30, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Adobe Photoshop CS6 Adobe RRID:SCR_014199;Version 13.0 OpenLab Agilent RRID:SCR_012158 Volocity 3D Image Analysis Software PerkinElmer RRID:SCR_002668; Demo Version 6.0.1 mni_autoreg tools Collins et al., 1994 RRID:SCR_013621; http://www.bic.mni. mcgill.ca/software/mni_autoreg/ ANTS (advanced normalization tools) Avants et al., 2011 RRID:SCR_004757; http://www.picsl. upenn.edu/ANTS/ FIJI Schindelin et al., 2012 RRID:SCR_002285 https://fiji.sc Prism 6.0 Graphpad RRID:SCR_002798; https://www. graphpad.com Simple Neurite Tracer Longair et al., 2011 RRID:SCR_016566; https://imagej.net/ Simple_Neurite_Tracer ANY-Maze Stoelting Co. RRID:SCR_014289 cutadapt Martin, 2011 RRID:SCR_011841; version 0.4.1 HISAT2 Kim et al., 2015 RRID:SCR_015530; version 2.0.4 SAMtools Li et al., 2009 RRID:SCR_002105; http://www.htslib.org/ StringTie Pertea et al., 2015 RRID:SCR_016323; v1.3.3; https://ccb.jhu. edu/software/stringtie/ tximport Soneson et al., 2015 RRID:SCR_016752; https://bioconductor. org/packages/release/bioc/html/tximport. html DESeq2 Love et al., 2014 RRID:SCR_015687; https://bioconductor. org/packages/release/bioc/html/DESeq2. html pheatmap Kolde, 2012 RRID:SCR_016418; https://cran.r-project. org/web/packages/pheatmap/index.html Lancaster method Yi et al., 2018 N/A Other Bussey-Saksida mouse touch screen chambers Lafayette Neuroscience Model 80614-20 Article ll OPEN ACCESS
Quantitative RT-PCR:Article Title: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-ATRX H-300 Santa Cruz Biotechnology, Inc sc-15408 anti-NeuN Millipore MAB377; RRID:AB_2298772 anti-GFAP Agilent Technologies, Inc M0761; RRID:AB_2109952 ;anti-IBA1 Wako Pure Chemical Corporation 019-19741; RRID:AB_839504 anti-INCENP Sigma I5283; RRID:AB_477113 anti-ATRX Abcam ab97508; RRID:AB_10680289 anti-H3K27me3 Millipore 07-449; RRID:AB_310624 anti-H3.3 Millipore 17-10245: RRID:AB_10953839 Normal rabbit IgG Cell Signaling 2729S; RRID:AB_1031062 anti-Rabbit-HRP Jackson ImmunoResearch Laboratories, Inc 111-036-003; RRID:AB_2337942 Bacterial and Virus Strains pmirGLO vector Promega E1330 PX459 plasmid (Addgene) Ran et al., 2013 62988 Lenti-III-mico-GFP vector, viral titer > 107 IU/ml Applied Biological Materials MIMAT0000149 Chemicals, Peptides, and Recombinant Proteins XbaI NEB R0145S BbsI NEB R0539S Anti-miR miRNA Inhibitor; miR-137-3p ThermoFisher AM17000 KpnI NEB R0142S Critical Commercial Assays SuperScript II Reverse Transcriptase Invitrogen 18064022 miRVANA total RNA isolation kit ThermoFisher AM1560 TaqMan Advanced MicroRNA reverse transcription kit ThermoFisher A28007 TaqMan Universal PCR Master Mix, no AmpEraseTaqMan Universal PCR Master Mix, no AmpErase ThermoFisher 4324018 Rapid GolgiStain Kit FD Neurotechnologies, Inc PK401 RNA 6000 Nano kit Caliper Life Sciences 5067-1511 ScriptSeq Complete Gold Kit (H/M/R) Illumina Inc. BHMR1205 Deposited Data RNA sequencing of hippocampi from control and Atrx-cKO males and females This study GEO: GSE129975 Experimental Models: Cell Lines Neuro2A ATCC CCL-131 Experimental Models: Organisms/Strains Mouse: CaMKII-Cre: B6.Cg-Tg(Camk2acre)T29-1Stl/J Jackson Laboratory 005359 Mouse: Atrxfl/fl Gift from Doug Higgs and Richard Gibbons N/A Oligonucleotides Oligonucleotides for qRT-PCR Table S4 N/A Oligonucleotides for sgRNA Table S4 N/A Oligonucleotides for ChIP-PCR Table S4 N/A (Continued on next page) e1 Cell Reports 31, 107838, June 30, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Adobe Photoshop CS6 Adobe RRID:SCR_014199;Version 13.0 OpenLab Agilent RRID:SCR_012158 Volocity 3D Image Analysis Software PerkinElmer RRID:SCR_002668; Demo Version 6.0.1 mni_autoreg tools Collins et al., 1994 RRID:SCR_013621; http://www.bic.mni. mcgill.ca/software/mni_autoreg/ ANTS (advanced normalization tools) Avants et al., 2011 RRID:SCR_004757; http://www.picsl. upenn.edu/ANTS/ FIJI Schindelin et al., 2012 RRID:SCR_002285 https://fiji.sc Prism 6.0 Graphpad RRID:SCR_002798; https://www. graphpad.com Simple Neurite Tracer Longair et al., 2011 RRID:SCR_016566; https://imagej.net/ Simple_Neurite_Tracer ANY-Maze Stoelting Co. RRID:SCR_014289 cutadapt Martin, 2011 RRID:SCR_011841; version 0.4.1 HISAT2 Kim et al., 2015 RRID:SCR_015530; version 2.0.4 SAMtools Li et al., 2009 RRID:SCR_002105; http://www.htslib.org/ StringTie Pertea et al., 2015 RRID:SCR_016323; v1.3.3; https://ccb.jhu. edu/software/stringtie/ tximport Soneson et al., 2015 RRID:SCR_016752; https://bioconductor. org/packages/release/bioc/html/tximport. html DESeq2 Love et al., 2014 RRID:SCR_015687; https://bioconductor. org/packages/release/bioc/html/DESeq2. html pheatmap Kolde, 2012 RRID:SCR_016418; https://cran.r-project. org/web/packages/pheatmap/index.html Lancaster method Yi et al., 2018 N/A Other Bussey-Saksida mouse touch screen chambers Lafayette Neuroscience Model 80614-20 Article ll OPEN ACCESS
Chromatin Immunoprecipitation:Article Title: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-ATRX H-300 Santa Cruz Biotechnology, Inc sc-15408 anti-NeuN Millipore MAB377; RRID:AB_2298772 anti-GFAP Agilent Technologies, Inc M0761; RRID:AB_2109952 ;anti-IBA1 Wako Pure Chemical Corporation 019-19741; RRID:AB_839504 anti-INCENP Sigma I5283; RRID:AB_477113 anti-ATRX Abcam ab97508; RRID:AB_10680289 anti-H3K27me3 Millipore 07-449; RRID:AB_310624 anti-H3.3 Millipore 17-10245: RRID:AB_10953839 Normal rabbit IgG Cell Signaling 2729S; RRID:AB_1031062 anti-Rabbit-HRP Jackson ImmunoResearch Laboratories, Inc 111-036-003; RRID:AB_2337942 Bacterial and Virus Strains pmirGLO vector Promega E1330 PX459 plasmid (Addgene) Ran et al., 2013 62988 Lenti-III-mico-GFP vector, viral titer > 107 IU/ml Applied Biological Materials MIMAT0000149 Chemicals, Peptides, and Recombinant Proteins XbaI NEB R0145S BbsI NEB R0539S Anti-miR miRNA Inhibitor; miR-137-3p ThermoFisher AM17000 KpnI NEB R0142S Critical Commercial Assays SuperScript II Reverse Transcriptase Invitrogen 18064022 miRVANA total RNA isolation kit ThermoFisher AM1560 TaqMan Advanced MicroRNA reverse transcription kit ThermoFisher A28007 TaqMan Universal PCR Master Mix, no AmpEraseTaqMan Universal PCR Master Mix, no AmpErase ThermoFisher 4324018 Rapid GolgiStain Kit FD Neurotechnologies, Inc PK401 RNA 6000 Nano kit Caliper Life Sciences 5067-1511 ScriptSeq Complete Gold Kit (H/M/R) Illumina Inc. BHMR1205 Deposited Data RNA sequencing of hippocampi from control and Atrx-cKO males and females This study GEO: GSE129975 Experimental Models: Cell Lines Neuro2A ATCC CCL-131 Experimental Models: Organisms/Strains Mouse: CaMKII-Cre: B6.Cg-Tg(Camk2acre)T29-1Stl/J Jackson Laboratory 005359 Mouse: Atrxfl/fl Gift from Doug Higgs and Richard Gibbons N/A Oligonucleotides Oligonucleotides for qRT-PCR Table S4 N/A Oligonucleotides for sgRNA Table S4 N/A Oligonucleotides for ChIP-PCR Table S4 N/A (Continued on next page) e1 Cell Reports 31, 107838, June 30, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Adobe Photoshop CS6 Adobe RRID:SCR_014199;Version 13.0 OpenLab Agilent RRID:SCR_012158 Volocity 3D Image Analysis Software PerkinElmer RRID:SCR_002668; Demo Version 6.0.1 mni_autoreg tools Collins et al., 1994 RRID:SCR_013621; http://www.bic.mni. mcgill.ca/software/mni_autoreg/ ANTS (advanced normalization tools) Avants et al., 2011 RRID:SCR_004757; http://www.picsl. upenn.edu/ANTS/ FIJI Schindelin et al., 2012 RRID:SCR_002285 https://fiji.sc Prism 6.0 Graphpad RRID:SCR_002798; https://www. graphpad.com Simple Neurite Tracer Longair et al., 2011 RRID:SCR_016566; https://imagej.net/ Simple_Neurite_Tracer ANY-Maze Stoelting Co. RRID:SCR_014289 cutadapt Martin, 2011 RRID:SCR_011841; version 0.4.1 HISAT2 Kim et al., 2015 RRID:SCR_015530; version 2.0.4 SAMtools Li et al., 2009 RRID:SCR_002105; http://www.htslib.org/ StringTie Pertea et al., 2015 RRID:SCR_016323; v1.3.3; https://ccb.jhu. edu/software/stringtie/ tximport Soneson et al., 2015 RRID:SCR_016752; https://bioconductor. org/packages/release/bioc/html/tximport. html DESeq2 Love et al., 2014 RRID:SCR_015687; https://bioconductor. org/packages/release/bioc/html/DESeq2. html pheatmap Kolde, 2012 RRID:SCR_016418; https://cran.r-project. org/web/packages/pheatmap/index.html Lancaster method Yi et al., 2018 N/A Other Bussey-Saksida mouse touch screen chambers Lafayette Neuroscience Model 80614-20 Article ll OPEN ACCESS
|
Addgene inc is a verified supplier 