Labeling:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Fluorescein-POD, Fab fragments Roche Cat# 11426346910; RRID: AB_840257 Anti-active-CASP3 (rabbit polyclonal Promega Cat# G7481; RRID: AB_430875 Anti-rabbit-HRP (goat polyclonal) Jackson Immuno Cat# 111-035-144; RRID: AB_2307391 Anti-OMP (goat polyclonal) Wako Cat# 544-10001; RRID: AB_664696 Anti-goat-Cy5 (donkey polyclonal) Jackson Immuno Cat# 705-175-147; RRID: AB_2340415 Anti-HA antibody (rabbit polyclonal) Abcam Cat# ab9110; RRID: AB_307019 Alexa647-anti-HA antibodies (mouse monoclonal) Biolegend Cat# 682404; RRID: AB_2566616 Chemicals, Peptides, and Recombinant Proteins DIG RNA Labeling Mix, 10 3 conc. .. Roche Cat# 11277073910 Fluorescein RNA Labeling Mix Roche Cat# 11685619910 2-Deoxy-5-ethynyluridine Carbosynth Cat# NE08701 Sulfo-Cyanine3 azide Lumiprobe Cat# A1330 Protein A/G magnetic beads ThermoFisher Cat# 88803 Tamoxifen Alfa Aesar Cat# J63509 T7 RNA Polymerase NEB Cat# M0251L Sp6 RNA Polymerase NEB Cat# M0207S RQ1 RNase-Free DNase Promega Cat# M6101 Vectashield Vector Laboratories Cat# H1000 Hibernate AB Complete medium BrainBits Cat# HAB100 Papain BrainBits Cat# PAP Hibernate A-minus Calcium medium BrainBits Cat# HACA100 NbActiv1 neuronal culturing medium BrainBits Cat# NbActiv1-100 Critical Commercial Assays Tyramide Signal Amplification Plus Fluorescein Kit Perkin Elmer Cat# NEL745B001KT Tyramide Signal Amplification Plus Cyanine 5 Kit Perkin Elmer Cat# NEL741B001KT In Situ Cell Death Detection Kit, Fluorescein Roche Cat# 11684795910 TOPO TA Cloning Kit, Dual Promoter ThermoFisher Cat# K460040 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Chromium Single Cell 30 v3 Kit 10X Genomics Cat# PN-1000075 Deposited Data Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO) (Santoro and Dulac, 2012) GEO: GSE39516; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE39516 Olfactory stimulation regulates the birth of neurons that express specific odorant receptors (SuperSeries of GSE157119 and GSE157101) Present study GEO: GSE157120; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE157120 scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157119; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157119 TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157101; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157101 (Continued on next page) Cell Reports 33, 108210, October 6, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J Jackson Labs 000664 Mouse: Ascl1-CreERT2 (Ascl1tm1.1(Cre/ERT2)Jejo/J) Jackson Labs 012882 Mouse: Ribotag (B6J.129(Cg)-Rpl22tm1.1Psam/SjJ) Jackson Labs 029977 Oligonucleotides DNA oligonucleotide primers for cloning antisense fluorescent in situ hybridization (FISH) probes This study See Table S2 Software and Algorithms Zen Blue software Zeiss https://www.zeiss.com Adobe Photoshop Adobe https://www.adobe.com Adobe Illustrator Adobe https://www.adobe.com Cell Ranger 10X Genomics https://www.10xgenomics.com Loupe Cell Browser 10X Genomics https://www.10xgenomics.com FASTQ groomer (Blankenberg et al., 2010) https://academic.oup.com/bioinformatics/ article-lookup/doi/10.1093/bioinformatics/ btq281 Trim Galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page=trimmomatic HISAT2 (Kim et al., 2015) https://daehwankimlab.github.io/hisat2/ featureCounts (Liao et al., 2014) http://bioinf.wehi.edu.au/featureCounts/ Remove Unwanted Variation (Risso et al., 2014) https://bioconductor.org/packages/RUVSeq Deseq2 (Love et al., 2014) https://bioconductor.org/packages/DESeq2 Other RNA FISH probes for specific ORs, S100a5, and Kirrel2 This paper See Table S2 Article ll OPEN ACCESS
Magnetic Beads:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Fluorescein-POD, Fab fragments Roche Cat# 11426346910; RRID: AB_840257 Anti-active-CASP3 (rabbit polyclonal Promega Cat# G7481; RRID: AB_430875 Anti-rabbit-HRP (goat polyclonal) Jackson Immuno Cat# 111-035-144; RRID: AB_2307391 Anti-OMP (goat polyclonal) Wako Cat# 544-10001; RRID: AB_664696 Anti-goat-Cy5 (donkey polyclonal) Jackson Immuno Cat# 705-175-147; RRID: AB_2340415 Anti-HA antibody (rabbit polyclonal) Abcam Cat# ab9110; RRID: AB_307019 Alexa647-anti-HA antibodies (mouse monoclonal) Biolegend Cat# 682404; RRID: AB_2566616 Chemicals, Peptides, and Recombinant Proteins DIG RNA Labeling Mix, 10 3 conc. .. Roche Cat# 11277073910 Fluorescein RNA Labeling Mix Roche Cat# 11685619910 2-Deoxy-5-ethynyluridine Carbosynth Cat# NE08701 Sulfo-Cyanine3 azide Lumiprobe Cat# A1330 Protein A/G magnetic beads ThermoFisher Cat# 88803 Tamoxifen Alfa Aesar Cat# J63509 T7 RNA Polymerase NEB Cat# M0251L Sp6 RNA Polymerase NEB Cat# M0207S RQ1 RNase-Free DNase Promega Cat# M6101 Vectashield Vector Laboratories Cat# H1000 Hibernate AB Complete medium BrainBits Cat# HAB100 Papain BrainBits Cat# PAP Hibernate A-minus Calcium medium BrainBits Cat# HACA100 NbActiv1 neuronal culturing medium BrainBits Cat# NbActiv1-100 Critical Commercial Assays Tyramide Signal Amplification Plus Fluorescein Kit Perkin Elmer Cat# NEL745B001KT Tyramide Signal Amplification Plus Cyanine 5 Kit Perkin Elmer Cat# NEL741B001KT In Situ Cell Death Detection Kit, Fluorescein Roche Cat# 11684795910 TOPO TA Cloning Kit, Dual Promoter ThermoFisher Cat# K460040 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Chromium Single Cell 30 v3 Kit 10X Genomics Cat# PN-1000075 Deposited Data Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO) (Santoro and Dulac, 2012) GEO: GSE39516; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE39516 Olfactory stimulation regulates the birth of neurons that express specific odorant receptors (SuperSeries of GSE157119 and GSE157101) Present study GEO: GSE157120; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE157120 scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157119; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157119 TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157101; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157101 (Continued on next page) Cell Reports 33, 108210, October 6, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J Jackson Labs 000664 Mouse: Ascl1-CreERT2 (Ascl1tm1.1(Cre/ERT2)Jejo/J) Jackson Labs 012882 Mouse: Ribotag (B6J.129(Cg)-Rpl22tm1.1Psam/SjJ) Jackson Labs 029977 Oligonucleotides DNA oligonucleotide primers for cloning antisense fluorescent in situ hybridization (FISH) probes This study See Table S2 Software and Algorithms Zen Blue software Zeiss https://www.zeiss.com Adobe Photoshop Adobe https://www.adobe.com Adobe Illustrator Adobe https://www.adobe.com Cell Ranger 10X Genomics https://www.10xgenomics.com Loupe Cell Browser 10X Genomics https://www.10xgenomics.com FASTQ groomer (Blankenberg et al., 2010) https://academic.oup.com/bioinformatics/ article-lookup/doi/10.1093/bioinformatics/ btq281 Trim Galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page=trimmomatic HISAT2 (Kim et al., 2015) https://daehwankimlab.github.io/hisat2/ featureCounts (Liao et al., 2014) http://bioinf.wehi.edu.au/featureCounts/ Remove Unwanted Variation (Risso et al., 2014) https://bioconductor.org/packages/RUVSeq Deseq2 (Love et al., 2014) https://bioconductor.org/packages/DESeq2 Other RNA FISH probes for specific ORs, S100a5, and Kirrel2 This paper See Table S2 Article ll OPEN ACCESS
Amplification:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Fluorescein-POD, Fab fragments Roche Cat# 11426346910; RRID: AB_840257 Anti-active-CASP3 (rabbit polyclonal Promega Cat# G7481; RRID: AB_430875 Anti-rabbit-HRP (goat polyclonal) Jackson Immuno Cat# 111-035-144; RRID: AB_2307391 Anti-OMP (goat polyclonal) Wako Cat# 544-10001; RRID: AB_664696 Anti-goat-Cy5 (donkey polyclonal) Jackson Immuno Cat# 705-175-147; RRID: AB_2340415 Anti-HA antibody (rabbit polyclonal) Abcam Cat# ab9110; RRID: AB_307019 Alexa647-anti-HA antibodies (mouse monoclonal) Biolegend Cat# 682404; RRID: AB_2566616 Chemicals, Peptides, and Recombinant Proteins DIG RNA Labeling Mix, 10 3 conc. .. Roche Cat# 11277073910 Fluorescein RNA Labeling Mix Roche Cat# 11685619910 2-Deoxy-5-ethynyluridine Carbosynth Cat# NE08701 Sulfo-Cyanine3 azide Lumiprobe Cat# A1330 Protein A/G magnetic beads ThermoFisher Cat# 88803 Tamoxifen Alfa Aesar Cat# J63509 T7 RNA Polymerase NEB Cat# M0251L Sp6 RNA Polymerase NEB Cat# M0207S RQ1 RNase-Free DNase Promega Cat# M6101 Vectashield Vector Laboratories Cat# H1000 Hibernate AB Complete medium BrainBits Cat# HAB100 Papain BrainBits Cat# PAP Hibernate A-minus Calcium medium BrainBits Cat# HACA100 NbActiv1 neuronal culturing medium BrainBits Cat# NbActiv1-100 Critical Commercial Assays Tyramide Signal Amplification Plus Fluorescein Kit Perkin Elmer Cat# NEL745B001KT Tyramide Signal Amplification Plus Cyanine 5 Kit Perkin Elmer Cat# NEL741B001KT In Situ Cell Death Detection Kit, Fluorescein Roche Cat# 11684795910 TOPO TA Cloning Kit, Dual Promoter ThermoFisher Cat# K460040 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Chromium Single Cell 30 v3 Kit 10X Genomics Cat# PN-1000075 Deposited Data Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO) (Santoro and Dulac, 2012) GEO: GSE39516; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE39516 Olfactory stimulation regulates the birth of neurons that express specific odorant receptors (SuperSeries of GSE157119 and GSE157101) Present study GEO: GSE157120; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE157120 scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157119; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157119 TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157101; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157101 (Continued on next page) Cell Reports 33, 108210, October 6, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J Jackson Labs 000664 Mouse: Ascl1-CreERT2 (Ascl1tm1.1(Cre/ERT2)Jejo/J) Jackson Labs 012882 Mouse: Ribotag (B6J.129(Cg)-Rpl22tm1.1Psam/SjJ) Jackson Labs 029977 Oligonucleotides DNA oligonucleotide primers for cloning antisense fluorescent in situ hybridization (FISH) probes This study See Table S2 Software and Algorithms Zen Blue software Zeiss https://www.zeiss.com Adobe Photoshop Adobe https://www.adobe.com Adobe Illustrator Adobe https://www.adobe.com Cell Ranger 10X Genomics https://www.10xgenomics.com Loupe Cell Browser 10X Genomics https://www.10xgenomics.com FASTQ groomer (Blankenberg et al., 2010) https://academic.oup.com/bioinformatics/ article-lookup/doi/10.1093/bioinformatics/ btq281 Trim Galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page=trimmomatic HISAT2 (Kim et al., 2015) https://daehwankimlab.github.io/hisat2/ featureCounts (Liao et al., 2014) http://bioinf.wehi.edu.au/featureCounts/ Remove Unwanted Variation (Risso et al., 2014) https://bioconductor.org/packages/RUVSeq Deseq2 (Love et al., 2014) https://bioconductor.org/packages/DESeq2 Other RNA FISH probes for specific ORs, S100a5, and Kirrel2 This paper See Table S2 Article ll OPEN ACCESS
In Situ:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Fluorescein-POD, Fab fragments Roche Cat# 11426346910; RRID: AB_840257 Anti-active-CASP3 (rabbit polyclonal Promega Cat# G7481; RRID: AB_430875 Anti-rabbit-HRP (goat polyclonal) Jackson Immuno Cat# 111-035-144; RRID: AB_2307391 Anti-OMP (goat polyclonal) Wako Cat# 544-10001; RRID: AB_664696 Anti-goat-Cy5 (donkey polyclonal) Jackson Immuno Cat# 705-175-147; RRID: AB_2340415 Anti-HA antibody (rabbit polyclonal) Abcam Cat# ab9110; RRID: AB_307019 Alexa647-anti-HA antibodies (mouse monoclonal) Biolegend Cat# 682404; RRID: AB_2566616 Chemicals, Peptides, and Recombinant Proteins DIG RNA Labeling Mix, 10 3 conc. .. Roche Cat# 11277073910 Fluorescein RNA Labeling Mix Roche Cat# 11685619910 2-Deoxy-5-ethynyluridine Carbosynth Cat# NE08701 Sulfo-Cyanine3 azide Lumiprobe Cat# A1330 Protein A/G magnetic beads ThermoFisher Cat# 88803 Tamoxifen Alfa Aesar Cat# J63509 T7 RNA Polymerase NEB Cat# M0251L Sp6 RNA Polymerase NEB Cat# M0207S RQ1 RNase-Free DNase Promega Cat# M6101 Vectashield Vector Laboratories Cat# H1000 Hibernate AB Complete medium BrainBits Cat# HAB100 Papain BrainBits Cat# PAP Hibernate A-minus Calcium medium BrainBits Cat# HACA100 NbActiv1 neuronal culturing medium BrainBits Cat# NbActiv1-100 Critical Commercial Assays Tyramide Signal Amplification Plus Fluorescein Kit Perkin Elmer Cat# NEL745B001KT Tyramide Signal Amplification Plus Cyanine 5 Kit Perkin Elmer Cat# NEL741B001KT In Situ Cell Death Detection Kit, Fluorescein Roche Cat# 11684795910 TOPO TA Cloning Kit, Dual Promoter ThermoFisher Cat# K460040 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Chromium Single Cell 30 v3 Kit 10X Genomics Cat# PN-1000075 Deposited Data Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO) (Santoro and Dulac, 2012) GEO: GSE39516; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE39516 Olfactory stimulation regulates the birth of neurons that express specific odorant receptors (SuperSeries of GSE157119 and GSE157101) Present study GEO: GSE157120; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE157120 scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157119; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157119 TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157101; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157101 (Continued on next page) Cell Reports 33, 108210, October 6, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J Jackson Labs 000664 Mouse: Ascl1-CreERT2 (Ascl1tm1.1(Cre/ERT2)Jejo/J) Jackson Labs 012882 Mouse: Ribotag (B6J.129(Cg)-Rpl22tm1.1Psam/SjJ) Jackson Labs 029977 Oligonucleotides DNA oligonucleotide primers for cloning antisense fluorescent in situ hybridization (FISH) probes This study See Table S2 Software and Algorithms Zen Blue software Zeiss https://www.zeiss.com Adobe Photoshop Adobe https://www.adobe.com Adobe Illustrator Adobe https://www.adobe.com Cell Ranger 10X Genomics https://www.10xgenomics.com Loupe Cell Browser 10X Genomics https://www.10xgenomics.com FASTQ groomer (Blankenberg et al., 2010) https://academic.oup.com/bioinformatics/ article-lookup/doi/10.1093/bioinformatics/ btq281 Trim Galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page=trimmomatic HISAT2 (Kim et al., 2015) https://daehwankimlab.github.io/hisat2/ featureCounts (Liao et al., 2014) http://bioinf.wehi.edu.au/featureCounts/ Remove Unwanted Variation (Risso et al., 2014) https://bioconductor.org/packages/RUVSeq Deseq2 (Love et al., 2014) https://bioconductor.org/packages/DESeq2 Other RNA FISH probes for specific ORs, S100a5, and Kirrel2 This paper See Table S2 Article ll OPEN ACCESS
TA Cloning:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Fluorescein-POD, Fab fragments Roche Cat# 11426346910; RRID: AB_840257 Anti-active-CASP3 (rabbit polyclonal Promega Cat# G7481; RRID: AB_430875 Anti-rabbit-HRP (goat polyclonal) Jackson Immuno Cat# 111-035-144; RRID: AB_2307391 Anti-OMP (goat polyclonal) Wako Cat# 544-10001; RRID: AB_664696 Anti-goat-Cy5 (donkey polyclonal) Jackson Immuno Cat# 705-175-147; RRID: AB_2340415 Anti-HA antibody (rabbit polyclonal) Abcam Cat# ab9110; RRID: AB_307019 Alexa647-anti-HA antibodies (mouse monoclonal) Biolegend Cat# 682404; RRID: AB_2566616 Chemicals, Peptides, and Recombinant Proteins DIG RNA Labeling Mix, 10 3 conc. .. Roche Cat# 11277073910 Fluorescein RNA Labeling Mix Roche Cat# 11685619910 2-Deoxy-5-ethynyluridine Carbosynth Cat# NE08701 Sulfo-Cyanine3 azide Lumiprobe Cat# A1330 Protein A/G magnetic beads ThermoFisher Cat# 88803 Tamoxifen Alfa Aesar Cat# J63509 T7 RNA Polymerase NEB Cat# M0251L Sp6 RNA Polymerase NEB Cat# M0207S RQ1 RNase-Free DNase Promega Cat# M6101 Vectashield Vector Laboratories Cat# H1000 Hibernate AB Complete medium BrainBits Cat# HAB100 Papain BrainBits Cat# PAP Hibernate A-minus Calcium medium BrainBits Cat# HACA100 NbActiv1 neuronal culturing medium BrainBits Cat# NbActiv1-100 Critical Commercial Assays Tyramide Signal Amplification Plus Fluorescein Kit Perkin Elmer Cat# NEL745B001KT Tyramide Signal Amplification Plus Cyanine 5 Kit Perkin Elmer Cat# NEL741B001KT In Situ Cell Death Detection Kit, Fluorescein Roche Cat# 11684795910 TOPO TA Cloning Kit, Dual Promoter ThermoFisher Cat# K460040 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Chromium Single Cell 30 v3 Kit 10X Genomics Cat# PN-1000075 Deposited Data Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO) (Santoro and Dulac, 2012) GEO: GSE39516; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE39516 Olfactory stimulation regulates the birth of neurons that express specific odorant receptors (SuperSeries of GSE157119 and GSE157101) Present study GEO: GSE157120; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE157120 scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157119; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157119 TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157101; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157101 (Continued on next page) Cell Reports 33, 108210, October 6, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J Jackson Labs 000664 Mouse: Ascl1-CreERT2 (Ascl1tm1.1(Cre/ERT2)Jejo/J) Jackson Labs 012882 Mouse: Ribotag (B6J.129(Cg)-Rpl22tm1.1Psam/SjJ) Jackson Labs 029977 Oligonucleotides DNA oligonucleotide primers for cloning antisense fluorescent in situ hybridization (FISH) probes This study See Table S2 Software and Algorithms Zen Blue software Zeiss https://www.zeiss.com Adobe Photoshop Adobe https://www.adobe.com Adobe Illustrator Adobe https://www.adobe.com Cell Ranger 10X Genomics https://www.10xgenomics.com Loupe Cell Browser 10X Genomics https://www.10xgenomics.com FASTQ groomer (Blankenberg et al., 2010) https://academic.oup.com/bioinformatics/ article-lookup/doi/10.1093/bioinformatics/ btq281 Trim Galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page=trimmomatic HISAT2 (Kim et al., 2015) https://daehwankimlab.github.io/hisat2/ featureCounts (Liao et al., 2014) http://bioinf.wehi.edu.au/featureCounts/ Remove Unwanted Variation (Risso et al., 2014) https://bioconductor.org/packages/RUVSeq Deseq2 (Love et al., 2014) https://bioconductor.org/packages/DESeq2 Other RNA FISH probes for specific ORs, S100a5, and Kirrel2 This paper See Table S2 Article ll OPEN ACCESS
Single Cell:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Fluorescein-POD, Fab fragments Roche Cat# 11426346910; RRID: AB_840257 Anti-active-CASP3 (rabbit polyclonal Promega Cat# G7481; RRID: AB_430875 Anti-rabbit-HRP (goat polyclonal) Jackson Immuno Cat# 111-035-144; RRID: AB_2307391 Anti-OMP (goat polyclonal) Wako Cat# 544-10001; RRID: AB_664696 Anti-goat-Cy5 (donkey polyclonal) Jackson Immuno Cat# 705-175-147; RRID: AB_2340415 Anti-HA antibody (rabbit polyclonal) Abcam Cat# ab9110; RRID: AB_307019 Alexa647-anti-HA antibodies (mouse monoclonal) Biolegend Cat# 682404; RRID: AB_2566616 Chemicals, Peptides, and Recombinant Proteins DIG RNA Labeling Mix, 10 3 conc. .. Roche Cat# 11277073910 Fluorescein RNA Labeling Mix Roche Cat# 11685619910 2-Deoxy-5-ethynyluridine Carbosynth Cat# NE08701 Sulfo-Cyanine3 azide Lumiprobe Cat# A1330 Protein A/G magnetic beads ThermoFisher Cat# 88803 Tamoxifen Alfa Aesar Cat# J63509 T7 RNA Polymerase NEB Cat# M0251L Sp6 RNA Polymerase NEB Cat# M0207S RQ1 RNase-Free DNase Promega Cat# M6101 Vectashield Vector Laboratories Cat# H1000 Hibernate AB Complete medium BrainBits Cat# HAB100 Papain BrainBits Cat# PAP Hibernate A-minus Calcium medium BrainBits Cat# HACA100 NbActiv1 neuronal culturing medium BrainBits Cat# NbActiv1-100 Critical Commercial Assays Tyramide Signal Amplification Plus Fluorescein Kit Perkin Elmer Cat# NEL745B001KT Tyramide Signal Amplification Plus Cyanine 5 Kit Perkin Elmer Cat# NEL741B001KT In Situ Cell Death Detection Kit, Fluorescein Roche Cat# 11684795910 TOPO TA Cloning Kit, Dual Promoter ThermoFisher Cat# K460040 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Chromium Single Cell 30 v3 Kit 10X Genomics Cat# PN-1000075 Deposited Data Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO) (Santoro and Dulac, 2012) GEO: GSE39516; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE39516 Olfactory stimulation regulates the birth of neurons that express specific odorant receptors (SuperSeries of GSE157119 and GSE157101) Present study GEO: GSE157120; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE157120 scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157119; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157119 TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157101; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157101 (Continued on next page) Cell Reports 33, 108210, October 6, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J Jackson Labs 000664 Mouse: Ascl1-CreERT2 (Ascl1tm1.1(Cre/ERT2)Jejo/J) Jackson Labs 012882 Mouse: Ribotag (B6J.129(Cg)-Rpl22tm1.1Psam/SjJ) Jackson Labs 029977 Oligonucleotides DNA oligonucleotide primers for cloning antisense fluorescent in situ hybridization (FISH) probes This study See Table S2 Software and Algorithms Zen Blue software Zeiss https://www.zeiss.com Adobe Photoshop Adobe https://www.adobe.com Adobe Illustrator Adobe https://www.adobe.com Cell Ranger 10X Genomics https://www.10xgenomics.com Loupe Cell Browser 10X Genomics https://www.10xgenomics.com FASTQ groomer (Blankenberg et al., 2010) https://academic.oup.com/bioinformatics/ article-lookup/doi/10.1093/bioinformatics/ btq281 Trim Galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page=trimmomatic HISAT2 (Kim et al., 2015) https://daehwankimlab.github.io/hisat2/ featureCounts (Liao et al., 2014) http://bioinf.wehi.edu.au/featureCounts/ Remove Unwanted Variation (Risso et al., 2014) https://bioconductor.org/packages/RUVSeq Deseq2 (Love et al., 2014) https://bioconductor.org/packages/DESeq2 Other RNA FISH probes for specific ORs, S100a5, and Kirrel2 This paper See Table S2 Article ll OPEN ACCESS
Gene Expression:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Fluorescein-POD, Fab fragments Roche Cat# 11426346910; RRID: AB_840257 Anti-active-CASP3 (rabbit polyclonal Promega Cat# G7481; RRID: AB_430875 Anti-rabbit-HRP (goat polyclonal) Jackson Immuno Cat# 111-035-144; RRID: AB_2307391 Anti-OMP (goat polyclonal) Wako Cat# 544-10001; RRID: AB_664696 Anti-goat-Cy5 (donkey polyclonal) Jackson Immuno Cat# 705-175-147; RRID: AB_2340415 Anti-HA antibody (rabbit polyclonal) Abcam Cat# ab9110; RRID: AB_307019 Alexa647-anti-HA antibodies (mouse monoclonal) Biolegend Cat# 682404; RRID: AB_2566616 Chemicals, Peptides, and Recombinant Proteins DIG RNA Labeling Mix, 10 3 conc. .. Roche Cat# 11277073910 Fluorescein RNA Labeling Mix Roche Cat# 11685619910 2-Deoxy-5-ethynyluridine Carbosynth Cat# NE08701 Sulfo-Cyanine3 azide Lumiprobe Cat# A1330 Protein A/G magnetic beads ThermoFisher Cat# 88803 Tamoxifen Alfa Aesar Cat# J63509 T7 RNA Polymerase NEB Cat# M0251L Sp6 RNA Polymerase NEB Cat# M0207S RQ1 RNase-Free DNase Promega Cat# M6101 Vectashield Vector Laboratories Cat# H1000 Hibernate AB Complete medium BrainBits Cat# HAB100 Papain BrainBits Cat# PAP Hibernate A-minus Calcium medium BrainBits Cat# HACA100 NbActiv1 neuronal culturing medium BrainBits Cat# NbActiv1-100 Critical Commercial Assays Tyramide Signal Amplification Plus Fluorescein Kit Perkin Elmer Cat# NEL745B001KT Tyramide Signal Amplification Plus Cyanine 5 Kit Perkin Elmer Cat# NEL741B001KT In Situ Cell Death Detection Kit, Fluorescein Roche Cat# 11684795910 TOPO TA Cloning Kit, Dual Promoter ThermoFisher Cat# K460040 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Chromium Single Cell 30 v3 Kit 10X Genomics Cat# PN-1000075 Deposited Data Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO) (Santoro and Dulac, 2012) GEO: GSE39516; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE39516 Olfactory stimulation regulates the birth of neurons that express specific odorant receptors (SuperSeries of GSE157119 and GSE157101) Present study GEO: GSE157120; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE157120 scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157119; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157119 TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157101; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157101 (Continued on next page) Cell Reports 33, 108210, October 6, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J Jackson Labs 000664 Mouse: Ascl1-CreERT2 (Ascl1tm1.1(Cre/ERT2)Jejo/J) Jackson Labs 012882 Mouse: Ribotag (B6J.129(Cg)-Rpl22tm1.1Psam/SjJ) Jackson Labs 029977 Oligonucleotides DNA oligonucleotide primers for cloning antisense fluorescent in situ hybridization (FISH) probes This study See Table S2 Software and Algorithms Zen Blue software Zeiss https://www.zeiss.com Adobe Photoshop Adobe https://www.adobe.com Adobe Illustrator Adobe https://www.adobe.com Cell Ranger 10X Genomics https://www.10xgenomics.com Loupe Cell Browser 10X Genomics https://www.10xgenomics.com FASTQ groomer (Blankenberg et al., 2010) https://academic.oup.com/bioinformatics/ article-lookup/doi/10.1093/bioinformatics/ btq281 Trim Galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page=trimmomatic HISAT2 (Kim et al., 2015) https://daehwankimlab.github.io/hisat2/ featureCounts (Liao et al., 2014) http://bioinf.wehi.edu.au/featureCounts/ Remove Unwanted Variation (Risso et al., 2014) https://bioconductor.org/packages/RUVSeq Deseq2 (Love et al., 2014) https://bioconductor.org/packages/DESeq2 Other RNA FISH probes for specific ORs, S100a5, and Kirrel2 This paper See Table S2 Article ll OPEN ACCESS
Olfactory:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Fluorescein-POD, Fab fragments Roche Cat# 11426346910; RRID: AB_840257 Anti-active-CASP3 (rabbit polyclonal Promega Cat# G7481; RRID: AB_430875 Anti-rabbit-HRP (goat polyclonal) Jackson Immuno Cat# 111-035-144; RRID: AB_2307391 Anti-OMP (goat polyclonal) Wako Cat# 544-10001; RRID: AB_664696 Anti-goat-Cy5 (donkey polyclonal) Jackson Immuno Cat# 705-175-147; RRID: AB_2340415 Anti-HA antibody (rabbit polyclonal) Abcam Cat# ab9110; RRID: AB_307019 Alexa647-anti-HA antibodies (mouse monoclonal) Biolegend Cat# 682404; RRID: AB_2566616 Chemicals, Peptides, and Recombinant Proteins DIG RNA Labeling Mix, 10 3 conc. .. Roche Cat# 11277073910 Fluorescein RNA Labeling Mix Roche Cat# 11685619910 2-Deoxy-5-ethynyluridine Carbosynth Cat# NE08701 Sulfo-Cyanine3 azide Lumiprobe Cat# A1330 Protein A/G magnetic beads ThermoFisher Cat# 88803 Tamoxifen Alfa Aesar Cat# J63509 T7 RNA Polymerase NEB Cat# M0251L Sp6 RNA Polymerase NEB Cat# M0207S RQ1 RNase-Free DNase Promega Cat# M6101 Vectashield Vector Laboratories Cat# H1000 Hibernate AB Complete medium BrainBits Cat# HAB100 Papain BrainBits Cat# PAP Hibernate A-minus Calcium medium BrainBits Cat# HACA100 NbActiv1 neuronal culturing medium BrainBits Cat# NbActiv1-100 Critical Commercial Assays Tyramide Signal Amplification Plus Fluorescein Kit Perkin Elmer Cat# NEL745B001KT Tyramide Signal Amplification Plus Cyanine 5 Kit Perkin Elmer Cat# NEL741B001KT In Situ Cell Death Detection Kit, Fluorescein Roche Cat# 11684795910 TOPO TA Cloning Kit, Dual Promoter ThermoFisher Cat# K460040 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Chromium Single Cell 30 v3 Kit 10X Genomics Cat# PN-1000075 Deposited Data Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO) (Santoro and Dulac, 2012) GEO: GSE39516; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE39516 Olfactory stimulation regulates the birth of neurons that express specific odorant receptors (SuperSeries of GSE157119 and GSE157101) Present study GEO: GSE157120; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE157120 scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157119; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157119 TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157101; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157101 (Continued on next page) Cell Reports 33, 108210, October 6, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J Jackson Labs 000664 Mouse: Ascl1-CreERT2 (Ascl1tm1.1(Cre/ERT2)Jejo/J) Jackson Labs 012882 Mouse: Ribotag (B6J.129(Cg)-Rpl22tm1.1Psam/SjJ) Jackson Labs 029977 Oligonucleotides DNA oligonucleotide primers for cloning antisense fluorescent in situ hybridization (FISH) probes This study See Table S2 Software and Algorithms Zen Blue software Zeiss https://www.zeiss.com Adobe Photoshop Adobe https://www.adobe.com Adobe Illustrator Adobe https://www.adobe.com Cell Ranger 10X Genomics https://www.10xgenomics.com Loupe Cell Browser 10X Genomics https://www.10xgenomics.com FASTQ groomer (Blankenberg et al., 2010) https://academic.oup.com/bioinformatics/ article-lookup/doi/10.1093/bioinformatics/ btq281 Trim Galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page=trimmomatic HISAT2 (Kim et al., 2015) https://daehwankimlab.github.io/hisat2/ featureCounts (Liao et al., 2014) http://bioinf.wehi.edu.au/featureCounts/ Remove Unwanted Variation (Risso et al., 2014) https://bioconductor.org/packages/RUVSeq Deseq2 (Love et al., 2014) https://bioconductor.org/packages/DESeq2 Other RNA FISH probes for specific ORs, S100a5, and Kirrel2 This paper See Table S2 Article ll OPEN ACCESS
Activity Assay:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Fluorescein-POD, Fab fragments Roche Cat# 11426346910; RRID: AB_840257 Anti-active-CASP3 (rabbit polyclonal Promega Cat# G7481; RRID: AB_430875 Anti-rabbit-HRP (goat polyclonal) Jackson Immuno Cat# 111-035-144; RRID: AB_2307391 Anti-OMP (goat polyclonal) Wako Cat# 544-10001; RRID: AB_664696 Anti-goat-Cy5 (donkey polyclonal) Jackson Immuno Cat# 705-175-147; RRID: AB_2340415 Anti-HA antibody (rabbit polyclonal) Abcam Cat# ab9110; RRID: AB_307019 Alexa647-anti-HA antibodies (mouse monoclonal) Biolegend Cat# 682404; RRID: AB_2566616 Chemicals, Peptides, and Recombinant Proteins DIG RNA Labeling Mix, 10 3 conc. .. Roche Cat# 11277073910 Fluorescein RNA Labeling Mix Roche Cat# 11685619910 2-Deoxy-5-ethynyluridine Carbosynth Cat# NE08701 Sulfo-Cyanine3 azide Lumiprobe Cat# A1330 Protein A/G magnetic beads ThermoFisher Cat# 88803 Tamoxifen Alfa Aesar Cat# J63509 T7 RNA Polymerase NEB Cat# M0251L Sp6 RNA Polymerase NEB Cat# M0207S RQ1 RNase-Free DNase Promega Cat# M6101 Vectashield Vector Laboratories Cat# H1000 Hibernate AB Complete medium BrainBits Cat# HAB100 Papain BrainBits Cat# PAP Hibernate A-minus Calcium medium BrainBits Cat# HACA100 NbActiv1 neuronal culturing medium BrainBits Cat# NbActiv1-100 Critical Commercial Assays Tyramide Signal Amplification Plus Fluorescein Kit Perkin Elmer Cat# NEL745B001KT Tyramide Signal Amplification Plus Cyanine 5 Kit Perkin Elmer Cat# NEL741B001KT In Situ Cell Death Detection Kit, Fluorescein Roche Cat# 11684795910 TOPO TA Cloning Kit, Dual Promoter ThermoFisher Cat# K460040 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Chromium Single Cell 30 v3 Kit 10X Genomics Cat# PN-1000075 Deposited Data Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO) (Santoro and Dulac, 2012) GEO: GSE39516; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE39516 Olfactory stimulation regulates the birth of neurons that express specific odorant receptors (SuperSeries of GSE157119 and GSE157101) Present study GEO: GSE157120; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE157120 scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157119; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157119 TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157101; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157101 (Continued on next page) Cell Reports 33, 108210, October 6, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J Jackson Labs 000664 Mouse: Ascl1-CreERT2 (Ascl1tm1.1(Cre/ERT2)Jejo/J) Jackson Labs 012882 Mouse: Ribotag (B6J.129(Cg)-Rpl22tm1.1Psam/SjJ) Jackson Labs 029977 Oligonucleotides DNA oligonucleotide primers for cloning antisense fluorescent in situ hybridization (FISH) probes This study See Table S2 Software and Algorithms Zen Blue software Zeiss https://www.zeiss.com Adobe Photoshop Adobe https://www.adobe.com Adobe Illustrator Adobe https://www.adobe.com Cell Ranger 10X Genomics https://www.10xgenomics.com Loupe Cell Browser 10X Genomics https://www.10xgenomics.com FASTQ groomer (Blankenberg et al., 2010) https://academic.oup.com/bioinformatics/ article-lookup/doi/10.1093/bioinformatics/ btq281 Trim Galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page=trimmomatic HISAT2 (Kim et al., 2015) https://daehwankimlab.github.io/hisat2/ featureCounts (Liao et al., 2014) http://bioinf.wehi.edu.au/featureCounts/ Remove Unwanted Variation (Risso et al., 2014) https://bioconductor.org/packages/RUVSeq Deseq2 (Love et al., 2014) https://bioconductor.org/packages/DESeq2 Other RNA FISH probes for specific ORs, S100a5, and Kirrel2 This paper See Table S2 Article ll OPEN ACCESS
Generated:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Fluorescein-POD, Fab fragments Roche Cat# 11426346910; RRID: AB_840257 Anti-active-CASP3 (rabbit polyclonal Promega Cat# G7481; RRID: AB_430875 Anti-rabbit-HRP (goat polyclonal) Jackson Immuno Cat# 111-035-144; RRID: AB_2307391 Anti-OMP (goat polyclonal) Wako Cat# 544-10001; RRID: AB_664696 Anti-goat-Cy5 (donkey polyclonal) Jackson Immuno Cat# 705-175-147; RRID: AB_2340415 Anti-HA antibody (rabbit polyclonal) Abcam Cat# ab9110; RRID: AB_307019 Alexa647-anti-HA antibodies (mouse monoclonal) Biolegend Cat# 682404; RRID: AB_2566616 Chemicals, Peptides, and Recombinant Proteins DIG RNA Labeling Mix, 10 3 conc. .. Roche Cat# 11277073910 Fluorescein RNA Labeling Mix Roche Cat# 11685619910 2-Deoxy-5-ethynyluridine Carbosynth Cat# NE08701 Sulfo-Cyanine3 azide Lumiprobe Cat# A1330 Protein A/G magnetic beads ThermoFisher Cat# 88803 Tamoxifen Alfa Aesar Cat# J63509 T7 RNA Polymerase NEB Cat# M0251L Sp6 RNA Polymerase NEB Cat# M0207S RQ1 RNase-Free DNase Promega Cat# M6101 Vectashield Vector Laboratories Cat# H1000 Hibernate AB Complete medium BrainBits Cat# HAB100 Papain BrainBits Cat# PAP Hibernate A-minus Calcium medium BrainBits Cat# HACA100 NbActiv1 neuronal culturing medium BrainBits Cat# NbActiv1-100 Critical Commercial Assays Tyramide Signal Amplification Plus Fluorescein Kit Perkin Elmer Cat# NEL745B001KT Tyramide Signal Amplification Plus Cyanine 5 Kit Perkin Elmer Cat# NEL741B001KT In Situ Cell Death Detection Kit, Fluorescein Roche Cat# 11684795910 TOPO TA Cloning Kit, Dual Promoter ThermoFisher Cat# K460040 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Chromium Single Cell 30 v3 Kit 10X Genomics Cat# PN-1000075 Deposited Data Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO) (Santoro and Dulac, 2012) GEO: GSE39516; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE39516 Olfactory stimulation regulates the birth of neurons that express specific odorant receptors (SuperSeries of GSE157119 and GSE157101) Present study GEO: GSE157120; https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE157120 scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157119; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157119 TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion (SubSeries of GSE157120) Present study GEO: GSE157101; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE157101 (Continued on next page) Cell Reports 33, 108210, October 6, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J Jackson Labs 000664 Mouse: Ascl1-CreERT2 (Ascl1tm1.1(Cre/ERT2)Jejo/J) Jackson Labs 012882 Mouse: Ribotag (B6J.129(Cg)-Rpl22tm1.1Psam/SjJ) Jackson Labs 029977 Oligonucleotides DNA oligonucleotide primers for cloning antisense fluorescent in situ hybridization (FISH) probes This study See Table S2 Software and Algorithms Zen Blue software Zeiss https://www.zeiss.com Adobe Photoshop Adobe https://www.adobe.com Adobe Illustrator Adobe https://www.adobe.com Cell Ranger 10X Genomics https://www.10xgenomics.com Loupe Cell Browser 10X Genomics https://www.10xgenomics.com FASTQ groomer (Blankenberg et al., 2010) https://academic.oup.com/bioinformatics/ article-lookup/doi/10.1093/bioinformatics/ btq281 Trim Galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page=trimmomatic HISAT2 (Kim et al., 2015) https://daehwankimlab.github.io/hisat2/ featureCounts (Liao et al., 2014) http://bioinf.wehi.edu.au/featureCounts/ Remove Unwanted Variation (Risso et al., 2014) https://bioconductor.org/packages/RUVSeq Deseq2 (Love et al., 2014) https://bioconductor.org/packages/DESeq2 Other RNA FISH probes for specific ORs, S100a5, and Kirrel2 This paper See Table S2 Article ll OPEN ACCESS
Transferring:Article Title: Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors
Article Snippet: Tissue was dissociated by incubation in papain solution (2 mL; 2 mg/mL papain [BrainBits; PAP] in Hibernate A-minus Calcium medium [HA-Ca; BrainBits; HACA100]; 20 min, 37°C) with periodic gentle swirling. .. Following careful removal of the papain solution, the dissociated tissue was re-suspended in HAB medium (2 mL), triturated 10–15 times using a fire-polished Pasteur pipette, and allowed to settle for 20 s. The supernatant containing dispersed cells was transferred to a new 15-mL conical tube, avoiding large debris, pelleted (200 RCF; 2 min, RT), re-suspended in pre-warmed NbActiv1 neuronal culturing medium (1 mL; BrainBits; NbActiv1–100), and filtered into a 1.5 mL microcentrifuge tube using a 40-μm Flowmi cell strainer (Bel-Art). ..
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