other:Article Title: Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 16S rRNA gene 1492R reverse primer IDT (Edwards et al., 1989) Software and algorithms Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2 (Bolyen et al., 2019) https://qiime2.org DNAsubway CyVerse and DNA Learning Center https://dnasubway.cyverse.org iTOL (Interactive Tree of Life) (Letunic and Bork, 2021) https://itol.embl.de/ FlowJo BD Life Sciences https://www.flowjo.com/ Cell Ranger Single-Cell Software Suite v4.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ overview/welcome Seurat v4.0 (Hao et al., 2021) https://satijalab.org/seurat/ R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3) R Foundation https://www.r-project.org
Binding Assay:Article Title: Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin, Alexa FluorTM 700 conjugate Invitrogen Cat#S21383; RRID: N/A; Lot#2126789 Fc Receptor Binding Inhibitor Polyclonal Antibody Invitrogen Cat#14-9165-42; RRID: N/A; Lot#2251850 True-Stain Monocyte BlockerTM Biolegend Cat#426103; RRID: N/A Biological samples Rhesus macaque biological fluids (whole blood, whole BAL) ONPRC N/A Rhesus macaque cells (PBMCs, BAL cells) ONPRC N/A Rhesus macaque microbiome swabs (nasal, oral, fecal) ONPRC N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma Aldrich Cat#P8139-1MG Ionomycin Sigma Aldrich Cat#I9657-1MG brefeldin A Biolegend Cat#420601 Phosphate Buffered Saline (PBS) Global Life Cat#SH30028.02 Fetal Bovine Serum (FBS) Omega Scientific Cat#FB-02; Lot#881991 Bovine Serum Albumine (BSA) Gemini Cat#700-106P; Lot#C82H81J Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#d4540 GoTaq master mix Promega Cat#M71333; Lot#000428913 nuclease-free H20 Promega Cat#P1193 ODN 2216 - TLR9 ligand InvivoGen Cat#tlrl-2216-1; Lot#3603-39T ssRNA40/LyoVecTM InvivoGen Cat#tlrl-lrna40; Lot#A40-39-03 Imiquimod (R837) InvivoGen Cat#tlrl-imq; Lot#IMQ-36-02A FSL-1 InvivoGen Cat#tlrl-fsl; Lot#FSL-37-04 Pam3CSK4 InvivoGen Cat#tlrl-pms; Lot#PMS-35-03 LPS InvivoGen Cat#tlrl-b5lps Flow Cytometry Perm Buffer (10x) Tonbo Biosciences Cat#TNB-1213-L150; Lot#B1213062817TN Foxp3/Transcription Factor Fix/Perm Diluent (1x) Tonbo Biosciences Cat#TNB-1022-L160; Lot#B1022062415 Foxp3/Transcription Factor Fix/Perm Concentrate (4x) Tonbo Biosciences Cat#TNB-1020-L050; Lot#B10200322420TN Fixation Buffer Biolegend Cat#420801; Lot#B331895 Intracellular Staining Perm Wash Buffer (10x) Biolegend Cat#421002; Lot#B32433 Critical commercial assays DNeasy Powersoil Pro kit Qiagen Cat#47016; Lot#169022930 MinElute 96 UF PCR Purification Kit Qiagen Cat#28053; Lot#154032872 MiSeq Reagent Kit v3 600 cycles Illumina Cat#MS-102-3003 Chromium Single Cell 30 Feature Barcoding Library Kit v3.1 chemistry 10X Genomics Cat#1000079 Deposited data Raw sequencing data This Study Sequence Read Archive- BioProject SRA: PRJNA800766 (https://www.ncbi. nlm.nih.gov) Oligonucleotides 16S rRNA gene 515F forward primer 50-GTGYCAGCMGCCGCGGTAA-30 IDT (Parada et al., 2016) 16S rRNA gene 806R reverse primer 50-GGACTACNVGGGTWTCTAAT-30 IDT (Parada et al., 2016) 16S rRNA gene B8F forward primer IDT (Edwards et al., 1989) (Continued on next page) Cell Reports 39, 110725, April 19, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 16S rRNA gene 1492R reverse primer IDT (Edwards et al., 1989) Software and algorithms Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2 (Bolyen et al., 2019) https://qiime2.org DNAsubway CyVerse and DNA Learning Center https://dnasubway.cyverse.org iTOL (Interactive Tree of Life) (Letunic and Bork, 2021) https://itol.embl.de/ FlowJo BD Life Sciences https://www.flowjo.com/ Cell Ranger Single-Cell Software Suite v4.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ overview/welcome Seurat v4.0 (Hao et al., 2021) https://satijalab.org/seurat/ R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3) R Foundation https://www.r-project.org
Recombinant:Article Title: Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin, Alexa FluorTM 700 conjugate Invitrogen Cat#S21383; RRID: N/A; Lot#2126789 Fc Receptor Binding Inhibitor Polyclonal Antibody Invitrogen Cat#14-9165-42; RRID: N/A; Lot#2251850 True-Stain Monocyte BlockerTM Biolegend Cat#426103; RRID: N/A Biological samples Rhesus macaque biological fluids (whole blood, whole BAL) ONPRC N/A Rhesus macaque cells (PBMCs, BAL cells) ONPRC N/A Rhesus macaque microbiome swabs (nasal, oral, fecal) ONPRC N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma Aldrich Cat#P8139-1MG Ionomycin Sigma Aldrich Cat#I9657-1MG brefeldin A Biolegend Cat#420601 Phosphate Buffered Saline (PBS) Global Life Cat#SH30028.02 Fetal Bovine Serum (FBS) Omega Scientific Cat#FB-02; Lot#881991 Bovine Serum Albumine (BSA) Gemini Cat#700-106P; Lot#C82H81J Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#d4540 GoTaq master mix Promega Cat#M71333; Lot#000428913 nuclease-free H20 Promega Cat#P1193 ODN 2216 - TLR9 ligand InvivoGen Cat#tlrl-2216-1; Lot#3603-39T ssRNA40/LyoVecTM InvivoGen Cat#tlrl-lrna40; Lot#A40-39-03 Imiquimod (R837) InvivoGen Cat#tlrl-imq; Lot#IMQ-36-02A FSL-1 InvivoGen Cat#tlrl-fsl; Lot#FSL-37-04 Pam3CSK4 InvivoGen Cat#tlrl-pms; Lot#PMS-35-03 LPS InvivoGen Cat#tlrl-b5lps Flow Cytometry Perm Buffer (10x) Tonbo Biosciences Cat#TNB-1213-L150; Lot#B1213062817TN Foxp3/Transcription Factor Fix/Perm Diluent (1x) Tonbo Biosciences Cat#TNB-1022-L160; Lot#B1022062415 Foxp3/Transcription Factor Fix/Perm Concentrate (4x) Tonbo Biosciences Cat#TNB-1020-L050; Lot#B10200322420TN Fixation Buffer Biolegend Cat#420801; Lot#B331895 Intracellular Staining Perm Wash Buffer (10x) Biolegend Cat#421002; Lot#B32433 Critical commercial assays DNeasy Powersoil Pro kit Qiagen Cat#47016; Lot#169022930 MinElute 96 UF PCR Purification Kit Qiagen Cat#28053; Lot#154032872 MiSeq Reagent Kit v3 600 cycles Illumina Cat#MS-102-3003 Chromium Single Cell 30 Feature Barcoding Library Kit v3.1 chemistry 10X Genomics Cat#1000079 Deposited data Raw sequencing data This Study Sequence Read Archive- BioProject SRA: PRJNA800766 (https://www.ncbi. nlm.nih.gov) Oligonucleotides 16S rRNA gene 515F forward primer 50-GTGYCAGCMGCCGCGGTAA-30 IDT (Parada et al., 2016) 16S rRNA gene 806R reverse primer 50-GGACTACNVGGGTWTCTAAT-30 IDT (Parada et al., 2016) 16S rRNA gene B8F forward primer IDT (Edwards et al., 1989) (Continued on next page) Cell Reports 39, 110725, April 19, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 16S rRNA gene 1492R reverse primer IDT (Edwards et al., 1989) Software and algorithms Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2 (Bolyen et al., 2019) https://qiime2.org DNAsubway CyVerse and DNA Learning Center https://dnasubway.cyverse.org iTOL (Interactive Tree of Life) (Letunic and Bork, 2021) https://itol.embl.de/ FlowJo BD Life Sciences https://www.flowjo.com/ Cell Ranger Single-Cell Software Suite v4.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ overview/welcome Seurat v4.0 (Hao et al., 2021) https://satijalab.org/seurat/ R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3) R Foundation https://www.r-project.org
Saline:Article Title: Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin, Alexa FluorTM 700 conjugate Invitrogen Cat#S21383; RRID: N/A; Lot#2126789 Fc Receptor Binding Inhibitor Polyclonal Antibody Invitrogen Cat#14-9165-42; RRID: N/A; Lot#2251850 True-Stain Monocyte BlockerTM Biolegend Cat#426103; RRID: N/A Biological samples Rhesus macaque biological fluids (whole blood, whole BAL) ONPRC N/A Rhesus macaque cells (PBMCs, BAL cells) ONPRC N/A Rhesus macaque microbiome swabs (nasal, oral, fecal) ONPRC N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma Aldrich Cat#P8139-1MG Ionomycin Sigma Aldrich Cat#I9657-1MG brefeldin A Biolegend Cat#420601 Phosphate Buffered Saline (PBS) Global Life Cat#SH30028.02 Fetal Bovine Serum (FBS) Omega Scientific Cat#FB-02; Lot#881991 Bovine Serum Albumine (BSA) Gemini Cat#700-106P; Lot#C82H81J Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#d4540 GoTaq master mix Promega Cat#M71333; Lot#000428913 nuclease-free H20 Promega Cat#P1193 ODN 2216 - TLR9 ligand InvivoGen Cat#tlrl-2216-1; Lot#3603-39T ssRNA40/LyoVecTM InvivoGen Cat#tlrl-lrna40; Lot#A40-39-03 Imiquimod (R837) InvivoGen Cat#tlrl-imq; Lot#IMQ-36-02A FSL-1 InvivoGen Cat#tlrl-fsl; Lot#FSL-37-04 Pam3CSK4 InvivoGen Cat#tlrl-pms; Lot#PMS-35-03 LPS InvivoGen Cat#tlrl-b5lps Flow Cytometry Perm Buffer (10x) Tonbo Biosciences Cat#TNB-1213-L150; Lot#B1213062817TN Foxp3/Transcription Factor Fix/Perm Diluent (1x) Tonbo Biosciences Cat#TNB-1022-L160; Lot#B1022062415 Foxp3/Transcription Factor Fix/Perm Concentrate (4x) Tonbo Biosciences Cat#TNB-1020-L050; Lot#B10200322420TN Fixation Buffer Biolegend Cat#420801; Lot#B331895 Intracellular Staining Perm Wash Buffer (10x) Biolegend Cat#421002; Lot#B32433 Critical commercial assays DNeasy Powersoil Pro kit Qiagen Cat#47016; Lot#169022930 MinElute 96 UF PCR Purification Kit Qiagen Cat#28053; Lot#154032872 MiSeq Reagent Kit v3 600 cycles Illumina Cat#MS-102-3003 Chromium Single Cell 30 Feature Barcoding Library Kit v3.1 chemistry 10X Genomics Cat#1000079 Deposited data Raw sequencing data This Study Sequence Read Archive- BioProject SRA: PRJNA800766 (https://www.ncbi. nlm.nih.gov) Oligonucleotides 16S rRNA gene 515F forward primer 50-GTGYCAGCMGCCGCGGTAA-30 IDT (Parada et al., 2016) 16S rRNA gene 806R reverse primer 50-GGACTACNVGGGTWTCTAAT-30 IDT (Parada et al., 2016) 16S rRNA gene B8F forward primer IDT (Edwards et al., 1989) (Continued on next page) Cell Reports 39, 110725, April 19, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 16S rRNA gene 1492R reverse primer IDT (Edwards et al., 1989) Software and algorithms Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2 (Bolyen et al., 2019) https://qiime2.org DNAsubway CyVerse and DNA Learning Center https://dnasubway.cyverse.org iTOL (Interactive Tree of Life) (Letunic and Bork, 2021) https://itol.embl.de/ FlowJo BD Life Sciences https://www.flowjo.com/ Cell Ranger Single-Cell Software Suite v4.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ overview/welcome Seurat v4.0 (Hao et al., 2021) https://satijalab.org/seurat/ R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3) R Foundation https://www.r-project.org
Flow Cytometry:Article Title: Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin, Alexa FluorTM 700 conjugate Invitrogen Cat#S21383; RRID: N/A; Lot#2126789 Fc Receptor Binding Inhibitor Polyclonal Antibody Invitrogen Cat#14-9165-42; RRID: N/A; Lot#2251850 True-Stain Monocyte BlockerTM Biolegend Cat#426103; RRID: N/A Biological samples Rhesus macaque biological fluids (whole blood, whole BAL) ONPRC N/A Rhesus macaque cells (PBMCs, BAL cells) ONPRC N/A Rhesus macaque microbiome swabs (nasal, oral, fecal) ONPRC N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma Aldrich Cat#P8139-1MG Ionomycin Sigma Aldrich Cat#I9657-1MG brefeldin A Biolegend Cat#420601 Phosphate Buffered Saline (PBS) Global Life Cat#SH30028.02 Fetal Bovine Serum (FBS) Omega Scientific Cat#FB-02; Lot#881991 Bovine Serum Albumine (BSA) Gemini Cat#700-106P; Lot#C82H81J Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#d4540 GoTaq master mix Promega Cat#M71333; Lot#000428913 nuclease-free H20 Promega Cat#P1193 ODN 2216 - TLR9 ligand InvivoGen Cat#tlrl-2216-1; Lot#3603-39T ssRNA40/LyoVecTM InvivoGen Cat#tlrl-lrna40; Lot#A40-39-03 Imiquimod (R837) InvivoGen Cat#tlrl-imq; Lot#IMQ-36-02A FSL-1 InvivoGen Cat#tlrl-fsl; Lot#FSL-37-04 Pam3CSK4 InvivoGen Cat#tlrl-pms; Lot#PMS-35-03 LPS InvivoGen Cat#tlrl-b5lps Flow Cytometry Perm Buffer (10x) Tonbo Biosciences Cat#TNB-1213-L150; Lot#B1213062817TN Foxp3/Transcription Factor Fix/Perm Diluent (1x) Tonbo Biosciences Cat#TNB-1022-L160; Lot#B1022062415 Foxp3/Transcription Factor Fix/Perm Concentrate (4x) Tonbo Biosciences Cat#TNB-1020-L050; Lot#B10200322420TN Fixation Buffer Biolegend Cat#420801; Lot#B331895 Intracellular Staining Perm Wash Buffer (10x) Biolegend Cat#421002; Lot#B32433 Critical commercial assays DNeasy Powersoil Pro kit Qiagen Cat#47016; Lot#169022930 MinElute 96 UF PCR Purification Kit Qiagen Cat#28053; Lot#154032872 MiSeq Reagent Kit v3 600 cycles Illumina Cat#MS-102-3003 Chromium Single Cell 30 Feature Barcoding Library Kit v3.1 chemistry 10X Genomics Cat#1000079 Deposited data Raw sequencing data This Study Sequence Read Archive- BioProject SRA: PRJNA800766 (https://www.ncbi. nlm.nih.gov) Oligonucleotides 16S rRNA gene 515F forward primer 50-GTGYCAGCMGCCGCGGTAA-30 IDT (Parada et al., 2016) 16S rRNA gene 806R reverse primer 50-GGACTACNVGGGTWTCTAAT-30 IDT (Parada et al., 2016) 16S rRNA gene B8F forward primer IDT (Edwards et al., 1989) (Continued on next page) Cell Reports 39, 110725, April 19, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 16S rRNA gene 1492R reverse primer IDT (Edwards et al., 1989) Software and algorithms Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2 (Bolyen et al., 2019) https://qiime2.org DNAsubway CyVerse and DNA Learning Center https://dnasubway.cyverse.org iTOL (Interactive Tree of Life) (Letunic and Bork, 2021) https://itol.embl.de/ FlowJo BD Life Sciences https://www.flowjo.com/ Cell Ranger Single-Cell Software Suite v4.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ overview/welcome Seurat v4.0 (Hao et al., 2021) https://satijalab.org/seurat/ R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3) R Foundation https://www.r-project.org
Staining:Article Title: Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin, Alexa FluorTM 700 conjugate Invitrogen Cat#S21383; RRID: N/A; Lot#2126789 Fc Receptor Binding Inhibitor Polyclonal Antibody Invitrogen Cat#14-9165-42; RRID: N/A; Lot#2251850 True-Stain Monocyte BlockerTM Biolegend Cat#426103; RRID: N/A Biological samples Rhesus macaque biological fluids (whole blood, whole BAL) ONPRC N/A Rhesus macaque cells (PBMCs, BAL cells) ONPRC N/A Rhesus macaque microbiome swabs (nasal, oral, fecal) ONPRC N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma Aldrich Cat#P8139-1MG Ionomycin Sigma Aldrich Cat#I9657-1MG brefeldin A Biolegend Cat#420601 Phosphate Buffered Saline (PBS) Global Life Cat#SH30028.02 Fetal Bovine Serum (FBS) Omega Scientific Cat#FB-02; Lot#881991 Bovine Serum Albumine (BSA) Gemini Cat#700-106P; Lot#C82H81J Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#d4540 GoTaq master mix Promega Cat#M71333; Lot#000428913 nuclease-free H20 Promega Cat#P1193 ODN 2216 - TLR9 ligand InvivoGen Cat#tlrl-2216-1; Lot#3603-39T ssRNA40/LyoVecTM InvivoGen Cat#tlrl-lrna40; Lot#A40-39-03 Imiquimod (R837) InvivoGen Cat#tlrl-imq; Lot#IMQ-36-02A FSL-1 InvivoGen Cat#tlrl-fsl; Lot#FSL-37-04 Pam3CSK4 InvivoGen Cat#tlrl-pms; Lot#PMS-35-03 LPS InvivoGen Cat#tlrl-b5lps Flow Cytometry Perm Buffer (10x) Tonbo Biosciences Cat#TNB-1213-L150; Lot#B1213062817TN Foxp3/Transcription Factor Fix/Perm Diluent (1x) Tonbo Biosciences Cat#TNB-1022-L160; Lot#B1022062415 Foxp3/Transcription Factor Fix/Perm Concentrate (4x) Tonbo Biosciences Cat#TNB-1020-L050; Lot#B10200322420TN Fixation Buffer Biolegend Cat#420801; Lot#B331895 Intracellular Staining Perm Wash Buffer (10x) Biolegend Cat#421002; Lot#B32433 Critical commercial assays DNeasy Powersoil Pro kit Qiagen Cat#47016; Lot#169022930 MinElute 96 UF PCR Purification Kit Qiagen Cat#28053; Lot#154032872 MiSeq Reagent Kit v3 600 cycles Illumina Cat#MS-102-3003 Chromium Single Cell 30 Feature Barcoding Library Kit v3.1 chemistry 10X Genomics Cat#1000079 Deposited data Raw sequencing data This Study Sequence Read Archive- BioProject SRA: PRJNA800766 (https://www.ncbi. nlm.nih.gov) Oligonucleotides 16S rRNA gene 515F forward primer 50-GTGYCAGCMGCCGCGGTAA-30 IDT (Parada et al., 2016) 16S rRNA gene 806R reverse primer 50-GGACTACNVGGGTWTCTAAT-30 IDT (Parada et al., 2016) 16S rRNA gene B8F forward primer IDT (Edwards et al., 1989) (Continued on next page) Cell Reports 39, 110725, April 19, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 16S rRNA gene 1492R reverse primer IDT (Edwards et al., 1989) Software and algorithms Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2 (Bolyen et al., 2019) https://qiime2.org DNAsubway CyVerse and DNA Learning Center https://dnasubway.cyverse.org iTOL (Interactive Tree of Life) (Letunic and Bork, 2021) https://itol.embl.de/ FlowJo BD Life Sciences https://www.flowjo.com/ Cell Ranger Single-Cell Software Suite v4.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ overview/welcome Seurat v4.0 (Hao et al., 2021) https://satijalab.org/seurat/ R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3) R Foundation https://www.r-project.org
Polymerase Chain Reaction:Article Title: Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin, Alexa FluorTM 700 conjugate Invitrogen Cat#S21383; RRID: N/A; Lot#2126789 Fc Receptor Binding Inhibitor Polyclonal Antibody Invitrogen Cat#14-9165-42; RRID: N/A; Lot#2251850 True-Stain Monocyte BlockerTM Biolegend Cat#426103; RRID: N/A Biological samples Rhesus macaque biological fluids (whole blood, whole BAL) ONPRC N/A Rhesus macaque cells (PBMCs, BAL cells) ONPRC N/A Rhesus macaque microbiome swabs (nasal, oral, fecal) ONPRC N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma Aldrich Cat#P8139-1MG Ionomycin Sigma Aldrich Cat#I9657-1MG brefeldin A Biolegend Cat#420601 Phosphate Buffered Saline (PBS) Global Life Cat#SH30028.02 Fetal Bovine Serum (FBS) Omega Scientific Cat#FB-02; Lot#881991 Bovine Serum Albumine (BSA) Gemini Cat#700-106P; Lot#C82H81J Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#d4540 GoTaq master mix Promega Cat#M71333; Lot#000428913 nuclease-free H20 Promega Cat#P1193 ODN 2216 - TLR9 ligand InvivoGen Cat#tlrl-2216-1; Lot#3603-39T ssRNA40/LyoVecTM InvivoGen Cat#tlrl-lrna40; Lot#A40-39-03 Imiquimod (R837) InvivoGen Cat#tlrl-imq; Lot#IMQ-36-02A FSL-1 InvivoGen Cat#tlrl-fsl; Lot#FSL-37-04 Pam3CSK4 InvivoGen Cat#tlrl-pms; Lot#PMS-35-03 LPS InvivoGen Cat#tlrl-b5lps Flow Cytometry Perm Buffer (10x) Tonbo Biosciences Cat#TNB-1213-L150; Lot#B1213062817TN Foxp3/Transcription Factor Fix/Perm Diluent (1x) Tonbo Biosciences Cat#TNB-1022-L160; Lot#B1022062415 Foxp3/Transcription Factor Fix/Perm Concentrate (4x) Tonbo Biosciences Cat#TNB-1020-L050; Lot#B10200322420TN Fixation Buffer Biolegend Cat#420801; Lot#B331895 Intracellular Staining Perm Wash Buffer (10x) Biolegend Cat#421002; Lot#B32433 Critical commercial assays DNeasy Powersoil Pro kit Qiagen Cat#47016; Lot#169022930 MinElute 96 UF PCR Purification Kit Qiagen Cat#28053; Lot#154032872 MiSeq Reagent Kit v3 600 cycles Illumina Cat#MS-102-3003 Chromium Single Cell 30 Feature Barcoding Library Kit v3.1 chemistry 10X Genomics Cat#1000079 Deposited data Raw sequencing data This Study Sequence Read Archive- BioProject SRA: PRJNA800766 (https://www.ncbi. nlm.nih.gov) Oligonucleotides 16S rRNA gene 515F forward primer 50-GTGYCAGCMGCCGCGGTAA-30 IDT (Parada et al., 2016) 16S rRNA gene 806R reverse primer 50-GGACTACNVGGGTWTCTAAT-30 IDT (Parada et al., 2016) 16S rRNA gene B8F forward primer IDT (Edwards et al., 1989) (Continued on next page) Cell Reports 39, 110725, April 19, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 16S rRNA gene 1492R reverse primer IDT (Edwards et al., 1989) Software and algorithms Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2 (Bolyen et al., 2019) https://qiime2.org DNAsubway CyVerse and DNA Learning Center https://dnasubway.cyverse.org iTOL (Interactive Tree of Life) (Letunic and Bork, 2021) https://itol.embl.de/ FlowJo BD Life Sciences https://www.flowjo.com/ Cell Ranger Single-Cell Software Suite v4.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ overview/welcome Seurat v4.0 (Hao et al., 2021) https://satijalab.org/seurat/ R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3) R Foundation https://www.r-project.org
Purification:Article Title: Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin, Alexa FluorTM 700 conjugate Invitrogen Cat#S21383; RRID: N/A; Lot#2126789 Fc Receptor Binding Inhibitor Polyclonal Antibody Invitrogen Cat#14-9165-42; RRID: N/A; Lot#2251850 True-Stain Monocyte BlockerTM Biolegend Cat#426103; RRID: N/A Biological samples Rhesus macaque biological fluids (whole blood, whole BAL) ONPRC N/A Rhesus macaque cells (PBMCs, BAL cells) ONPRC N/A Rhesus macaque microbiome swabs (nasal, oral, fecal) ONPRC N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma Aldrich Cat#P8139-1MG Ionomycin Sigma Aldrich Cat#I9657-1MG brefeldin A Biolegend Cat#420601 Phosphate Buffered Saline (PBS) Global Life Cat#SH30028.02 Fetal Bovine Serum (FBS) Omega Scientific Cat#FB-02; Lot#881991 Bovine Serum Albumine (BSA) Gemini Cat#700-106P; Lot#C82H81J Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#d4540 GoTaq master mix Promega Cat#M71333; Lot#000428913 nuclease-free H20 Promega Cat#P1193 ODN 2216 - TLR9 ligand InvivoGen Cat#tlrl-2216-1; Lot#3603-39T ssRNA40/LyoVecTM InvivoGen Cat#tlrl-lrna40; Lot#A40-39-03 Imiquimod (R837) InvivoGen Cat#tlrl-imq; Lot#IMQ-36-02A FSL-1 InvivoGen Cat#tlrl-fsl; Lot#FSL-37-04 Pam3CSK4 InvivoGen Cat#tlrl-pms; Lot#PMS-35-03 LPS InvivoGen Cat#tlrl-b5lps Flow Cytometry Perm Buffer (10x) Tonbo Biosciences Cat#TNB-1213-L150; Lot#B1213062817TN Foxp3/Transcription Factor Fix/Perm Diluent (1x) Tonbo Biosciences Cat#TNB-1022-L160; Lot#B1022062415 Foxp3/Transcription Factor Fix/Perm Concentrate (4x) Tonbo Biosciences Cat#TNB-1020-L050; Lot#B10200322420TN Fixation Buffer Biolegend Cat#420801; Lot#B331895 Intracellular Staining Perm Wash Buffer (10x) Biolegend Cat#421002; Lot#B32433 Critical commercial assays DNeasy Powersoil Pro kit Qiagen Cat#47016; Lot#169022930 MinElute 96 UF PCR Purification Kit Qiagen Cat#28053; Lot#154032872 MiSeq Reagent Kit v3 600 cycles Illumina Cat#MS-102-3003 Chromium Single Cell 30 Feature Barcoding Library Kit v3.1 chemistry 10X Genomics Cat#1000079 Deposited data Raw sequencing data This Study Sequence Read Archive- BioProject SRA: PRJNA800766 (https://www.ncbi. nlm.nih.gov) Oligonucleotides 16S rRNA gene 515F forward primer 50-GTGYCAGCMGCCGCGGTAA-30 IDT (Parada et al., 2016) 16S rRNA gene 806R reverse primer 50-GGACTACNVGGGTWTCTAAT-30 IDT (Parada et al., 2016) 16S rRNA gene B8F forward primer IDT (Edwards et al., 1989) (Continued on next page) Cell Reports 39, 110725, April 19, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 16S rRNA gene 1492R reverse primer IDT (Edwards et al., 1989) Software and algorithms Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2 (Bolyen et al., 2019) https://qiime2.org DNAsubway CyVerse and DNA Learning Center https://dnasubway.cyverse.org iTOL (Interactive Tree of Life) (Letunic and Bork, 2021) https://itol.embl.de/ FlowJo BD Life Sciences https://www.flowjo.com/ Cell Ranger Single-Cell Software Suite v4.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ overview/welcome Seurat v4.0 (Hao et al., 2021) https://satijalab.org/seurat/ R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3) R Foundation https://www.r-project.org
Single Cell:Article Title: Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin, Alexa FluorTM 700 conjugate Invitrogen Cat#S21383; RRID: N/A; Lot#2126789 Fc Receptor Binding Inhibitor Polyclonal Antibody Invitrogen Cat#14-9165-42; RRID: N/A; Lot#2251850 True-Stain Monocyte BlockerTM Biolegend Cat#426103; RRID: N/A Biological samples Rhesus macaque biological fluids (whole blood, whole BAL) ONPRC N/A Rhesus macaque cells (PBMCs, BAL cells) ONPRC N/A Rhesus macaque microbiome swabs (nasal, oral, fecal) ONPRC N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma Aldrich Cat#P8139-1MG Ionomycin Sigma Aldrich Cat#I9657-1MG brefeldin A Biolegend Cat#420601 Phosphate Buffered Saline (PBS) Global Life Cat#SH30028.02 Fetal Bovine Serum (FBS) Omega Scientific Cat#FB-02; Lot#881991 Bovine Serum Albumine (BSA) Gemini Cat#700-106P; Lot#C82H81J Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#d4540 GoTaq master mix Promega Cat#M71333; Lot#000428913 nuclease-free H20 Promega Cat#P1193 ODN 2216 - TLR9 ligand InvivoGen Cat#tlrl-2216-1; Lot#3603-39T ssRNA40/LyoVecTM InvivoGen Cat#tlrl-lrna40; Lot#A40-39-03 Imiquimod (R837) InvivoGen Cat#tlrl-imq; Lot#IMQ-36-02A FSL-1 InvivoGen Cat#tlrl-fsl; Lot#FSL-37-04 Pam3CSK4 InvivoGen Cat#tlrl-pms; Lot#PMS-35-03 LPS InvivoGen Cat#tlrl-b5lps Flow Cytometry Perm Buffer (10x) Tonbo Biosciences Cat#TNB-1213-L150; Lot#B1213062817TN Foxp3/Transcription Factor Fix/Perm Diluent (1x) Tonbo Biosciences Cat#TNB-1022-L160; Lot#B1022062415 Foxp3/Transcription Factor Fix/Perm Concentrate (4x) Tonbo Biosciences Cat#TNB-1020-L050; Lot#B10200322420TN Fixation Buffer Biolegend Cat#420801; Lot#B331895 Intracellular Staining Perm Wash Buffer (10x) Biolegend Cat#421002; Lot#B32433 Critical commercial assays DNeasy Powersoil Pro kit Qiagen Cat#47016; Lot#169022930 MinElute 96 UF PCR Purification Kit Qiagen Cat#28053; Lot#154032872 MiSeq Reagent Kit v3 600 cycles Illumina Cat#MS-102-3003 Chromium Single Cell 30 Feature Barcoding Library Kit v3.1 chemistry 10X Genomics Cat#1000079 Deposited data Raw sequencing data This Study Sequence Read Archive- BioProject SRA: PRJNA800766 (https://www.ncbi. nlm.nih.gov) Oligonucleotides 16S rRNA gene 515F forward primer 50-GTGYCAGCMGCCGCGGTAA-30 IDT (Parada et al., 2016) 16S rRNA gene 806R reverse primer 50-GGACTACNVGGGTWTCTAAT-30 IDT (Parada et al., 2016) 16S rRNA gene B8F forward primer IDT (Edwards et al., 1989) (Continued on next page) Cell Reports 39, 110725, April 19, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 16S rRNA gene 1492R reverse primer IDT (Edwards et al., 1989) Software and algorithms Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2 (Bolyen et al., 2019) https://qiime2.org DNAsubway CyVerse and DNA Learning Center https://dnasubway.cyverse.org iTOL (Interactive Tree of Life) (Letunic and Bork, 2021) https://itol.embl.de/ FlowJo BD Life Sciences https://www.flowjo.com/ Cell Ranger Single-Cell Software Suite v4.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ overview/welcome Seurat v4.0 (Hao et al., 2021) https://satijalab.org/seurat/ R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3) R Foundation https://www.r-project.org
Sequencing:Article Title: Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin, Alexa FluorTM 700 conjugate Invitrogen Cat#S21383; RRID: N/A; Lot#2126789 Fc Receptor Binding Inhibitor Polyclonal Antibody Invitrogen Cat#14-9165-42; RRID: N/A; Lot#2251850 True-Stain Monocyte BlockerTM Biolegend Cat#426103; RRID: N/A Biological samples Rhesus macaque biological fluids (whole blood, whole BAL) ONPRC N/A Rhesus macaque cells (PBMCs, BAL cells) ONPRC N/A Rhesus macaque microbiome swabs (nasal, oral, fecal) ONPRC N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma Aldrich Cat#P8139-1MG Ionomycin Sigma Aldrich Cat#I9657-1MG brefeldin A Biolegend Cat#420601 Phosphate Buffered Saline (PBS) Global Life Cat#SH30028.02 Fetal Bovine Serum (FBS) Omega Scientific Cat#FB-02; Lot#881991 Bovine Serum Albumine (BSA) Gemini Cat#700-106P; Lot#C82H81J Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#d4540 GoTaq master mix Promega Cat#M71333; Lot#000428913 nuclease-free H20 Promega Cat#P1193 ODN 2216 - TLR9 ligand InvivoGen Cat#tlrl-2216-1; Lot#3603-39T ssRNA40/LyoVecTM InvivoGen Cat#tlrl-lrna40; Lot#A40-39-03 Imiquimod (R837) InvivoGen Cat#tlrl-imq; Lot#IMQ-36-02A FSL-1 InvivoGen Cat#tlrl-fsl; Lot#FSL-37-04 Pam3CSK4 InvivoGen Cat#tlrl-pms; Lot#PMS-35-03 LPS InvivoGen Cat#tlrl-b5lps Flow Cytometry Perm Buffer (10x) Tonbo Biosciences Cat#TNB-1213-L150; Lot#B1213062817TN Foxp3/Transcription Factor Fix/Perm Diluent (1x) Tonbo Biosciences Cat#TNB-1022-L160; Lot#B1022062415 Foxp3/Transcription Factor Fix/Perm Concentrate (4x) Tonbo Biosciences Cat#TNB-1020-L050; Lot#B10200322420TN Fixation Buffer Biolegend Cat#420801; Lot#B331895 Intracellular Staining Perm Wash Buffer (10x) Biolegend Cat#421002; Lot#B32433 Critical commercial assays DNeasy Powersoil Pro kit Qiagen Cat#47016; Lot#169022930 MinElute 96 UF PCR Purification Kit Qiagen Cat#28053; Lot#154032872 MiSeq Reagent Kit v3 600 cycles Illumina Cat#MS-102-3003 Chromium Single Cell 30 Feature Barcoding Library Kit v3.1 chemistry 10X Genomics Cat#1000079 Deposited data Raw sequencing data This Study Sequence Read Archive- BioProject SRA: PRJNA800766 (https://www.ncbi. nlm.nih.gov) Oligonucleotides 16S rRNA gene 515F forward primer 50-GTGYCAGCMGCCGCGGTAA-30 IDT (Parada et al., 2016) 16S rRNA gene 806R reverse primer 50-GGACTACNVGGGTWTCTAAT-30 IDT (Parada et al., 2016) 16S rRNA gene B8F forward primer IDT (Edwards et al., 1989) (Continued on next page) Cell Reports 39, 110725, April 19, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 16S rRNA gene 1492R reverse primer IDT (Edwards et al., 1989) Software and algorithms Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2 (Bolyen et al., 2019) https://qiime2.org DNAsubway CyVerse and DNA Learning Center https://dnasubway.cyverse.org iTOL (Interactive Tree of Life) (Letunic and Bork, 2021) https://itol.embl.de/ FlowJo BD Life Sciences https://www.flowjo.com/ Cell Ranger Single-Cell Software Suite v4.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ overview/welcome Seurat v4.0 (Hao et al., 2021) https://satijalab.org/seurat/ R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3) R Foundation https://www.r-project.org
|
InvivoGen is a verified supplier 
InvivoGen manufactures this product 