Virus:Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921 Article ll OPEN ACCESS
Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921
Bioprocessing:Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921 Article ll OPEN ACCESS
Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921
Recombinant:Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921 Article ll OPEN ACCESS
Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921
RNAscope:Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921 Article ll OPEN ACCESS
Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921
Multiplex Assay:Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921 Article ll OPEN ACCESS
Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921
Single Cell:Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921 Article ll OPEN ACCESS
Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921
DNA Library Preparation:Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921 Article ll OPEN ACCESS
Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921
RNA Sequencing:Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921 Article ll OPEN ACCESS
Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921
Expressing:Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921 Article ll OPEN ACCESS
Article Title: Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-SOX11 Merck Millipore Cat#ABN105 Mouse anti-NeuN Merck Millipore Cat#MAB377; RRID: AB_2298772 Rabbit anti-Draxin Abcam Cat#ab117452; RRID: AB_10898861 Mouse anti-Beta-tubulin Sigma CatT4026; RRID: AB_477577 AzureSpectra 700 Goat-anti-mouse secondary antibody Azure biosystem Cat#AC2129 AzureSpectra 800 Goat-anti-rabbit secondary antibody Azure biosystem Cat#AC2134 Donkey anti-Mouse Alexa 594 Molecular Probes Cat#A21203; RRID: AB_141633 Goat anti Rabbit Alexa 647 Abcam Cat#ab150079; RRID: AB_2722623 Bacterial and virus strains AAV9 pENN.AAV.CamkII.HI.GFP-Cre.WPRE.SV40 Addgene 105551-AAV9 AAV-9 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541-AAV9 AAV-9 Silc1 This study N/A AAV-9 Sox11 This study N/A Chemicals, peptides, and recombinant proteins Papain Sigma P4762 Dispase II Roche 165859 Percoll Sigma P1644 Poly L lysin Sigma P4832 Laminin Life 23017–015 Collagenase type II Worthington CSL-2 Critical commercial assays SENSE mRNA-Seq Library Prep Kit V2 Lexogen 001.96 ACD RNAscope Fluorescent Multiplex Assay ACDBio 320850 10x Genomics Chromium Single Cell Kit Version 3.1 10x Genomics Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 NovaSeq 6000 SP Flow Cell Illumina 20028401 Deposited data Raw and analyzed RNA-seq data This study GEO: GSE216643 Raw and analyzed ATAC-seq data This study GEO: GSE216643 Raw and analyzed scRNA-seq data This study GEO: GSE216643 Analyzed data of RNA-seq from the NeuroSeq atlas Sugino et al.35 GEO: GSE79238 Analyzed data of RNA-seq–based expression in the DG upon stimulation and ATAC-seq Sun et al.26 von Wittgenstein et al.28 GEO: GSE140180 Analyzed data of ATAC-seq upon kainic acid stimulation Fernandez-Albert.et al.38 GEO: GSE125068 Analyzed data from Hipposeq Cembrowski et al.39 GEO: GSE74985 Experimental models: Organisms/strains Mouse: C57black6 Ola HSD Harlan Laboratories N/A Mouse: Silc1 / mice Perry et al.9 N/A Mouse: Silc1 loxP mice This paper N/A Mouse: Silc1 polyA mice This paper N/A Mouse: Sox11 loxP mice Prof. Veronique Lefebvre lab N/A Mouse: C57black6 Ola HSD Harlan Laboratories N/A (Continued on next page) Cell Reports 42, 113168, October 31, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides For a list of oligonucleotides used in this study see Table S4 This study N/A For a list of GapmerRs used in this study see Table S5 This study N/A Recombinant DNA Silc1 pcDNA3.1(+) vector Perry et al.9 N/A pLenti-CMV-GFP-Sox11 vector Addgene 120387 pENN.AAV.CamKII0.4.eGFP.WPRE.rBG Addgene 105541 Software and algorithms STAR Dobin et al.69 https://github.com/alexdobin/STAR RSEM Li and Dewey70 https://deweylab.github.io/RSEM/ Cell Ranger 7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ Bowtie2 Langmead and Salzberg71 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Fiji (ImageJ) analysis software NIH https://fiji.sc/ IMARIS (v7.7.2) software Oxford instruments https://imaris.oxinst.com/ Other Silc1 probes- RNAscope 2.5vs. probe ״Mm GM9866״ ACD 536709 Sox11 CDS probes- RNAscope 2.5vs. probe ACD 440811 Sox11 30UTR probes- RNAscope 2.5vs. probe ACD 805071 Fos probes- RNAscope 2.5vs. probe ACD 316921
|
Azure Biosystems is a verified supplier 
Azure Biosystems manufactures this product 