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cd8 dendritic cell isolation kit miltenyi biotec  (Miltenyi Biotec)


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    Miltenyi Biotec cd8 dendritic cell isolation kit miltenyi biotec
    Cd8 Dendritic Cell Isolation Kit Miltenyi Biotec, supplied by Miltenyi Biotec, used in various techniques. Bioz Stars score: 93/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cd8+dendritic+cell+isolation+kit/CD8%2B+Dendritic+Cell+Isolation+Kit%2C+mouse/pm41990746-643-39-44
    Average 93 stars, based on 23 article reviews
    cd8 dendritic cell isolation kit miltenyi biotec - by Bioz Stars, 2026-09
    93/100 stars

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    Article Title: PU.1 regulation of type 1 dendritic cell function via NF-κB pathway in inhibition of non-small cell lung cancer progression
    Article Snippet: Filtering was applied to the cell suspension through a 40-μm filter, followed by a wash with magnetic-activated cell sorting (MACS) buffer (130-091-376; Miltenyi Biotec, Bergisch Gladbach, Germany). .. Positive selection of CD8+cDC1 cells Jo urn al Pr e-p roo f 7 / 32 was performed using the CD8+ dendritic cell isolation kit (130-091-169; Miltenyi Biotec). ..

    Article Title: Differential Activation of Splenic cDC1 and cDC2 Cell Subsets following Poxvirus Infection of BALB/c and C57BL/6 Mice
    Article Snippet: .. In some experiments, freshly obtained splenocytes were subjected to the magnetic cell separation system (MACS) for the positive selection of the cDC1 (CD8α + ) population using CD8 + Dendritic Cell Isolation Kit (Miltenyi Biotec), in accordance with the manufacturer’s instructions. .. During the first step of separation, the splenocytes were depleted of T, B, and NK cells using a cocktail of biotinylated antibodies against CD90.2, CD45R, and CD49b, followed by incubation with anti-biotin MicroBeads.

    Article Title: Differential Activation of Splenic cDC1 and cDC2 Cell Subsets following Poxvirus Infection of BALB/c and C57BL/6 Mice.
    Article Snippet: .. In some experiments, freshly obtained splenocytes were subjected to the magnetic cell separation system (MACS) for the positive selection of the cDC1 (CD8α+) population using CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec), in accordance with the manufacturer’s instructions. .. During the first step of separation, the splenocytes were depleted of T, B, and NK cells using a cocktail of biotinylated antibodies against CD90.2, CD45R, and CD49b, followed by incubation with anti-biotin MicroBeads.

    Cell Isolation:

    Article Title: PU.1 regulation of type 1 dendritic cell function via NF-κB pathway in inhibition of non-small cell lung cancer progression
    Article Snippet: Filtering was applied to the cell suspension through a 40-μm filter, followed by a wash with magnetic-activated cell sorting (MACS) buffer (130-091-376; Miltenyi Biotec, Bergisch Gladbach, Germany). .. Positive selection of CD8+cDC1 cells Jo urn al Pr e-p roo f 7 / 32 was performed using the CD8+ dendritic cell isolation kit (130-091-169; Miltenyi Biotec). ..

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: FlowJo software (version 10.8.1, BD Life Sciences Cat# 663335) was used for data analysis. .. Cell sorting was performed using FACSAria II (BD Biosciences). cDC1s and cDC2s from mice for RNA-seq, CUT&Tag, or Tiled-C experiments were isolated from splenocytes using a CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec Cat# 130-091-169) or a CD4+ Dendritic Cell Isolation Kit (Miltenyi Biotec Cat# 130-091-262), respectively. ..

    Article Title: Differential Activation of Splenic cDC1 and cDC2 Cell Subsets following Poxvirus Infection of BALB/c and C57BL/6 Mice
    Article Snippet: .. In some experiments, freshly obtained splenocytes were subjected to the magnetic cell separation system (MACS) for the positive selection of the cDC1 (CD8α + ) population using CD8 + Dendritic Cell Isolation Kit (Miltenyi Biotec), in accordance with the manufacturer’s instructions. .. During the first step of separation, the splenocytes were depleted of T, B, and NK cells using a cocktail of biotinylated antibodies against CD90.2, CD45R, and CD49b, followed by incubation with anti-biotin MicroBeads.

    Article Title: Differential Activation of Splenic cDC1 and cDC2 Cell Subsets following Poxvirus Infection of BALB/c and C57BL/6 Mice.
    Article Snippet: .. In some experiments, freshly obtained splenocytes were subjected to the magnetic cell separation system (MACS) for the positive selection of the cDC1 (CD8α+) population using CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec), in accordance with the manufacturer’s instructions. .. During the first step of separation, the splenocytes were depleted of T, B, and NK cells using a cocktail of biotinylated antibodies against CD90.2, CD45R, and CD49b, followed by incubation with anti-biotin MicroBeads.

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-conjugated Armenian Hamster Anti-Mouse CD3ε (clone 145-2C11) BioLegend Cat# 100304 Biotin-conjugated Rat Anti-Mouse F4/80 (clone BM8) BioLegend Cat# 123106 Biotin-conjugated Rat Anti-mouse IL-7R (clone A7R34) BioLegend Cat# 135006 Biotin-conjugated Rat Anti-mouse Ly-6G (clone 1A8) BioLegend Cat# 127604 Biotin-conjugated Mouse Anti-Mouse NK1.1 (clone PK136) BD Biosciences Cat# 553163 Biotin-conjugated Rat Anti-Mouse Ter119 (clone TER-119) BioLegend Cat# 116204 Purified Rat anti-mouse CD16/32 (clone 93) BioLegend Cat# 101302 Rabbit Polyclonal Anti-Mouse Histone H3 (acetyl K27) Antibody Abcam Cat# ab4729 Guinea Pig Polyclonal Anti-Rabbit IgG (Heavy & Light Chain) Antibody Antibodies online Cat# ABIN101961 Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (PE Conjugate) Cell Signaling Cat# 15562S Rabbit (DA1E) mAb IgG XP Isotype Control (PE Conjugate) Cell Signaling Cat# 5742S Bacterial and virus strains MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A Chemicals, peptides, and recombinant proteins Liberase DL Roche Cat# 5466202001 DNase I, grade II, Roche Cat# 10104159001 Recombinant Murine SCF PeproTech Cat# 250-03 Recombinant Murine IL-3 PeproTech Cat# 213-13 Recombinant Murine IL-6 PeproTech Cat# 216-16 Recombinant Human Flt3-Ligand PeproTech Cat# 300-19 RPMI1640 Nacalai Tesque Cat# 30263-95 Fetal Bovine Serum (Lot# 0001641431) Sigma Cat# 173012 D-MEM FUJIFILM Wako Pure Chemical Cat# 043-30085 PEI MAX Polysciences Cat# 24765-1 Dpn II NEB Cat# R0543M Biotin-14-dATP Thermo Fisher Scientific Cat# 19524016 DNA Polymerase I, Large (Klenow) Fragment NEB Cat# M0210L T4 DNA Ligase NEB Cat# M0202M Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat# 65001 KOD FX Neo polymerase Toyobo Cat# KFX-201 Agarose ME Iwai Chemicals Cat# 50013R Agarose H Nippon gene Cat# 319-01201 Marker 7 GT Nippon gene Cat# 315-03981 Atlas Clear Sight Gold DNA Stain solution BioAtlas Cat# BH40701 Blocking One-P Nacalai Tesque Cat# 05999-84 (Continued on next page) 14 Cell Reports 43, 114107, April 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Lineage Cell Depletion Kit, mouse Miltenyi Biotec Cat# 130-110-470 CD8+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-169 CD4+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-262 RNeasy Micro Kit Qiagen Cat# 74004 SMART-Seq HT Kit Takara Bio Cat# 634437 Nextera XT DNA Library Prep Kit Illumina Cat# FC-131-1096 KAPA HyperPrep Kits Roche Cat# 07962347001 SureSelect XT HS Reagents Agilent Technologies Cat# G9702A SureSelect PostPool Custom Tier2 Agilent Technologies Cat# 5191-6905 PrimeScript RT Reagent kit Takara Bio Cat# RR037B THUNDERBIRD SYBR qPCR Mix Toyobo Cat# QPS-201 Deposited data RNA-seq data for wild-type CDPs, cDC1s and cDC2s Murakami et al.8 GEO: GSE149762 RNA-seq data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 ATAC-seq data for wild-type MDPs and CDPs Murakami et al.8 GEO: GSE149762 ATAC-seq data for wild-type cDC1s Brown et al.43 GEO: GSE130201 ChIP-seq data for wild-type LMPPs and MDPs Murakami et al.8 GEO: GSE149762 Tiled-C data This study DDBJ: DRA016834 H3K27ac CUT&Tag data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 Experimental models: Cell lines 293TN cell line System Biosciences Cat# LV900A-1 Experimental models: Organisms/strains Mouse: C57BL/6 Japan SLC C57BL/6JJmsSlc Mouse: Irf8 / : Irf8tm1Hor Holtschke et al.44 N/A Mouse: +32D/D Murakami et al.8 N/A Mouse: +56D/D Murakami et al.8 N/A Mouse: +32WT/D This study N/A Mouse: +56D/WT This study N/A Mouse: +56D/WT+32WT/D This study N/A Oligonucleotides Oligonucleotides used in this study, see Table S1 This study N/A Recombinant DNA MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A pCL-Eco Naviaux et al.45 N/A Software and algorithms FlowJo (version 10.8.1) BD Life Sciences Cat# 663335 STAR (version 2.7.7a) Dobin et al.46 https://github.com/alexdobin/STAR Picard (version 2.25.0) Broad Institute http://broadinstitute.github.io/picard/ RSEM (version 1.3.3) Li et al.47 https://github.com/deweylab/RSEM R (version 4.0.3) The R Foundation for Statistical Computing https://www.r-project.org/ (Continued on next page) Cell Reports 43, 114107, April 23, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER edgeR (version 3.32.1) Robinson et al.48 https://bioconductor.org/packages/ release/bioc/html/edgeR.html R Stats (version 4.3) R Core Team https://stat.ethz.ch/R-manual/R-devel/ library/stats/html/00Index.html ggplot2 (version 3.2.4) Hadley Wickham, https://ggplot2.tidyverse.org/ authors.html#citation https://ggplot2.tidyverse.org/ Bowtie2 (version 2.3.5.1) Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml HOMER (version 4.11) Heinz et al.50 http://homer.ucsd.edu/homer/index.html GOPHER (version 0.6.0) Hansen et al.51 https://github.com/TheJacksonLaboratory/Gopher Agilent SureDesign tool Agilent Technologies https://earray.chem.agilent.com/suredesign/ Hi-Cpro (version 3.0.0) Servant et al.52 https://github.com/nservant/HiC-Pro Treeview3 (version 3.0 Beta 1) Christopher Keil, https://doi.org/10.5281/ zenodo.1303402 https://bitbucket.org/TreeView3Dev/ treeview3/src/master/ GraphPad Prism 9 GraphPad https://www.graphpad.com GSEA software (version 4.0.3) Broad Institute53 https://www.gsea-msigdb.org/gsea/index.jsp

    Article Title: Potent CTLs can be induced against tumor cells in an environment of lower levels of systemic MFG‐E8
    Article Snippet: .. T, B, and NK-cells were removed from splenocytes by using antibody cocktails which a part of the CD8+ Dendritic Cell Isolation Kit (130-091-169, Miltenyi Biotec, Bergisch Gladbach, MMC for 2 h, and after washing twice with PBS, were cultured overnight, they were used as apoptotic cells. ..

    Article Title: Flt3 ligand augments immune responses to soluble PD1-based DNA vaccine via expansion of type 1 conventional DCs.
    Article Snippet: .. For T cell activation verification, naïve mouse spleens were isolated and treated into single-cell suspensions. cDC1 was obtained using a CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec, Germany) and placed into a 24-well plate at a density of 1 × 105/well. ..

    Article Title: The XCL1-Mediated DNA Vaccine Targeting Type 1 Conventional Dendritic Cells Combined with Gemcitabine and Anti-PD1 Antibody Induces Potent Antitumor Immunity in a Mouse Lung Cancer Model
    Article Snippet: .. For T cell activation verification, naïve mouse spleens were isolated and treated in single-cell suspensions. cDC1 were obtained using a CD8 + Dendritic Cell Isolation Kit (Miltenyi Biotec) and placed into a 24-well plate at a density of 1 × 10 5 /well. ..

    FACS:

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: FlowJo software (version 10.8.1, BD Life Sciences Cat# 663335) was used for data analysis. .. Cell sorting was performed using FACSAria II (BD Biosciences). cDC1s and cDC2s from mice for RNA-seq, CUT&Tag, or Tiled-C experiments were isolated from splenocytes using a CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec Cat# 130-091-169) or a CD4+ Dendritic Cell Isolation Kit (Miltenyi Biotec Cat# 130-091-262), respectively. ..

    RNA Sequencing:

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: FlowJo software (version 10.8.1, BD Life Sciences Cat# 663335) was used for data analysis. .. Cell sorting was performed using FACSAria II (BD Biosciences). cDC1s and cDC2s from mice for RNA-seq, CUT&Tag, or Tiled-C experiments were isolated from splenocytes using a CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec Cat# 130-091-169) or a CD4+ Dendritic Cell Isolation Kit (Miltenyi Biotec Cat# 130-091-262), respectively. ..

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-conjugated Armenian Hamster Anti-Mouse CD3ε (clone 145-2C11) BioLegend Cat# 100304 Biotin-conjugated Rat Anti-Mouse F4/80 (clone BM8) BioLegend Cat# 123106 Biotin-conjugated Rat Anti-mouse IL-7R (clone A7R34) BioLegend Cat# 135006 Biotin-conjugated Rat Anti-mouse Ly-6G (clone 1A8) BioLegend Cat# 127604 Biotin-conjugated Mouse Anti-Mouse NK1.1 (clone PK136) BD Biosciences Cat# 553163 Biotin-conjugated Rat Anti-Mouse Ter119 (clone TER-119) BioLegend Cat# 116204 Purified Rat anti-mouse CD16/32 (clone 93) BioLegend Cat# 101302 Rabbit Polyclonal Anti-Mouse Histone H3 (acetyl K27) Antibody Abcam Cat# ab4729 Guinea Pig Polyclonal Anti-Rabbit IgG (Heavy & Light Chain) Antibody Antibodies online Cat# ABIN101961 Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (PE Conjugate) Cell Signaling Cat# 15562S Rabbit (DA1E) mAb IgG XP Isotype Control (PE Conjugate) Cell Signaling Cat# 5742S Bacterial and virus strains MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A Chemicals, peptides, and recombinant proteins Liberase DL Roche Cat# 5466202001 DNase I, grade II, Roche Cat# 10104159001 Recombinant Murine SCF PeproTech Cat# 250-03 Recombinant Murine IL-3 PeproTech Cat# 213-13 Recombinant Murine IL-6 PeproTech Cat# 216-16 Recombinant Human Flt3-Ligand PeproTech Cat# 300-19 RPMI1640 Nacalai Tesque Cat# 30263-95 Fetal Bovine Serum (Lot# 0001641431) Sigma Cat# 173012 D-MEM FUJIFILM Wako Pure Chemical Cat# 043-30085 PEI MAX Polysciences Cat# 24765-1 Dpn II NEB Cat# R0543M Biotin-14-dATP Thermo Fisher Scientific Cat# 19524016 DNA Polymerase I, Large (Klenow) Fragment NEB Cat# M0210L T4 DNA Ligase NEB Cat# M0202M Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat# 65001 KOD FX Neo polymerase Toyobo Cat# KFX-201 Agarose ME Iwai Chemicals Cat# 50013R Agarose H Nippon gene Cat# 319-01201 Marker 7 GT Nippon gene Cat# 315-03981 Atlas Clear Sight Gold DNA Stain solution BioAtlas Cat# BH40701 Blocking One-P Nacalai Tesque Cat# 05999-84 (Continued on next page) 14 Cell Reports 43, 114107, April 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Lineage Cell Depletion Kit, mouse Miltenyi Biotec Cat# 130-110-470 CD8+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-169 CD4+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-262 RNeasy Micro Kit Qiagen Cat# 74004 SMART-Seq HT Kit Takara Bio Cat# 634437 Nextera XT DNA Library Prep Kit Illumina Cat# FC-131-1096 KAPA HyperPrep Kits Roche Cat# 07962347001 SureSelect XT HS Reagents Agilent Technologies Cat# G9702A SureSelect PostPool Custom Tier2 Agilent Technologies Cat# 5191-6905 PrimeScript RT Reagent kit Takara Bio Cat# RR037B THUNDERBIRD SYBR qPCR Mix Toyobo Cat# QPS-201 Deposited data RNA-seq data for wild-type CDPs, cDC1s and cDC2s Murakami et al.8 GEO: GSE149762 RNA-seq data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 ATAC-seq data for wild-type MDPs and CDPs Murakami et al.8 GEO: GSE149762 ATAC-seq data for wild-type cDC1s Brown et al.43 GEO: GSE130201 ChIP-seq data for wild-type LMPPs and MDPs Murakami et al.8 GEO: GSE149762 Tiled-C data This study DDBJ: DRA016834 H3K27ac CUT&Tag data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 Experimental models: Cell lines 293TN cell line System Biosciences Cat# LV900A-1 Experimental models: Organisms/strains Mouse: C57BL/6 Japan SLC C57BL/6JJmsSlc Mouse: Irf8 / : Irf8tm1Hor Holtschke et al.44 N/A Mouse: +32D/D Murakami et al.8 N/A Mouse: +56D/D Murakami et al.8 N/A Mouse: +32WT/D This study N/A Mouse: +56D/WT This study N/A Mouse: +56D/WT+32WT/D This study N/A Oligonucleotides Oligonucleotides used in this study, see Table S1 This study N/A Recombinant DNA MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A pCL-Eco Naviaux et al.45 N/A Software and algorithms FlowJo (version 10.8.1) BD Life Sciences Cat# 663335 STAR (version 2.7.7a) Dobin et al.46 https://github.com/alexdobin/STAR Picard (version 2.25.0) Broad Institute http://broadinstitute.github.io/picard/ RSEM (version 1.3.3) Li et al.47 https://github.com/deweylab/RSEM R (version 4.0.3) The R Foundation for Statistical Computing https://www.r-project.org/ (Continued on next page) Cell Reports 43, 114107, April 23, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER edgeR (version 3.32.1) Robinson et al.48 https://bioconductor.org/packages/ release/bioc/html/edgeR.html R Stats (version 4.3) R Core Team https://stat.ethz.ch/R-manual/R-devel/ library/stats/html/00Index.html ggplot2 (version 3.2.4) Hadley Wickham, https://ggplot2.tidyverse.org/ authors.html#citation https://ggplot2.tidyverse.org/ Bowtie2 (version 2.3.5.1) Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml HOMER (version 4.11) Heinz et al.50 http://homer.ucsd.edu/homer/index.html GOPHER (version 0.6.0) Hansen et al.51 https://github.com/TheJacksonLaboratory/Gopher Agilent SureDesign tool Agilent Technologies https://earray.chem.agilent.com/suredesign/ Hi-Cpro (version 3.0.0) Servant et al.52 https://github.com/nservant/HiC-Pro Treeview3 (version 3.0 Beta 1) Christopher Keil, https://doi.org/10.5281/ zenodo.1303402 https://bitbucket.org/TreeView3Dev/ treeview3/src/master/ GraphPad Prism 9 GraphPad https://www.graphpad.com GSEA software (version 4.0.3) Broad Institute53 https://www.gsea-msigdb.org/gsea/index.jsp

    Isolation:

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: FlowJo software (version 10.8.1, BD Life Sciences Cat# 663335) was used for data analysis. .. Cell sorting was performed using FACSAria II (BD Biosciences). cDC1s and cDC2s from mice for RNA-seq, CUT&Tag, or Tiled-C experiments were isolated from splenocytes using a CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec Cat# 130-091-169) or a CD4+ Dendritic Cell Isolation Kit (Miltenyi Biotec Cat# 130-091-262), respectively. ..

    Article Title: Flt3 ligand augments immune responses to soluble PD1-based DNA vaccine via expansion of type 1 conventional DCs.
    Article Snippet: .. For T cell activation verification, naïve mouse spleens were isolated and treated into single-cell suspensions. cDC1 was obtained using a CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec, Germany) and placed into a 24-well plate at a density of 1 × 105/well. ..

    Article Title: The XCL1-Mediated DNA Vaccine Targeting Type 1 Conventional Dendritic Cells Combined with Gemcitabine and Anti-PD1 Antibody Induces Potent Antitumor Immunity in a Mouse Lung Cancer Model
    Article Snippet: .. For T cell activation verification, naïve mouse spleens were isolated and treated in single-cell suspensions. cDC1 were obtained using a CD8 + Dendritic Cell Isolation Kit (Miltenyi Biotec) and placed into a 24-well plate at a density of 1 × 10 5 /well. ..

    Magnetic Cell Separation:

    Article Title: Differential Activation of Splenic cDC1 and cDC2 Cell Subsets following Poxvirus Infection of BALB/c and C57BL/6 Mice
    Article Snippet: .. In some experiments, freshly obtained splenocytes were subjected to the magnetic cell separation system (MACS) for the positive selection of the cDC1 (CD8α + ) population using CD8 + Dendritic Cell Isolation Kit (Miltenyi Biotec), in accordance with the manufacturer’s instructions. .. During the first step of separation, the splenocytes were depleted of T, B, and NK cells using a cocktail of biotinylated antibodies against CD90.2, CD45R, and CD49b, followed by incubation with anti-biotin MicroBeads.

    Article Title: Differential Activation of Splenic cDC1 and cDC2 Cell Subsets following Poxvirus Infection of BALB/c and C57BL/6 Mice.
    Article Snippet: .. In some experiments, freshly obtained splenocytes were subjected to the magnetic cell separation system (MACS) for the positive selection of the cDC1 (CD8α+) population using CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec), in accordance with the manufacturer’s instructions. .. During the first step of separation, the splenocytes were depleted of T, B, and NK cells using a cocktail of biotinylated antibodies against CD90.2, CD45R, and CD49b, followed by incubation with anti-biotin MicroBeads.

    Real-time Polymerase Chain Reaction:

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-conjugated Armenian Hamster Anti-Mouse CD3ε (clone 145-2C11) BioLegend Cat# 100304 Biotin-conjugated Rat Anti-Mouse F4/80 (clone BM8) BioLegend Cat# 123106 Biotin-conjugated Rat Anti-mouse IL-7R (clone A7R34) BioLegend Cat# 135006 Biotin-conjugated Rat Anti-mouse Ly-6G (clone 1A8) BioLegend Cat# 127604 Biotin-conjugated Mouse Anti-Mouse NK1.1 (clone PK136) BD Biosciences Cat# 553163 Biotin-conjugated Rat Anti-Mouse Ter119 (clone TER-119) BioLegend Cat# 116204 Purified Rat anti-mouse CD16/32 (clone 93) BioLegend Cat# 101302 Rabbit Polyclonal Anti-Mouse Histone H3 (acetyl K27) Antibody Abcam Cat# ab4729 Guinea Pig Polyclonal Anti-Rabbit IgG (Heavy & Light Chain) Antibody Antibodies online Cat# ABIN101961 Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (PE Conjugate) Cell Signaling Cat# 15562S Rabbit (DA1E) mAb IgG XP Isotype Control (PE Conjugate) Cell Signaling Cat# 5742S Bacterial and virus strains MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A Chemicals, peptides, and recombinant proteins Liberase DL Roche Cat# 5466202001 DNase I, grade II, Roche Cat# 10104159001 Recombinant Murine SCF PeproTech Cat# 250-03 Recombinant Murine IL-3 PeproTech Cat# 213-13 Recombinant Murine IL-6 PeproTech Cat# 216-16 Recombinant Human Flt3-Ligand PeproTech Cat# 300-19 RPMI1640 Nacalai Tesque Cat# 30263-95 Fetal Bovine Serum (Lot# 0001641431) Sigma Cat# 173012 D-MEM FUJIFILM Wako Pure Chemical Cat# 043-30085 PEI MAX Polysciences Cat# 24765-1 Dpn II NEB Cat# R0543M Biotin-14-dATP Thermo Fisher Scientific Cat# 19524016 DNA Polymerase I, Large (Klenow) Fragment NEB Cat# M0210L T4 DNA Ligase NEB Cat# M0202M Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat# 65001 KOD FX Neo polymerase Toyobo Cat# KFX-201 Agarose ME Iwai Chemicals Cat# 50013R Agarose H Nippon gene Cat# 319-01201 Marker 7 GT Nippon gene Cat# 315-03981 Atlas Clear Sight Gold DNA Stain solution BioAtlas Cat# BH40701 Blocking One-P Nacalai Tesque Cat# 05999-84 (Continued on next page) 14 Cell Reports 43, 114107, April 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Lineage Cell Depletion Kit, mouse Miltenyi Biotec Cat# 130-110-470 CD8+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-169 CD4+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-262 RNeasy Micro Kit Qiagen Cat# 74004 SMART-Seq HT Kit Takara Bio Cat# 634437 Nextera XT DNA Library Prep Kit Illumina Cat# FC-131-1096 KAPA HyperPrep Kits Roche Cat# 07962347001 SureSelect XT HS Reagents Agilent Technologies Cat# G9702A SureSelect PostPool Custom Tier2 Agilent Technologies Cat# 5191-6905 PrimeScript RT Reagent kit Takara Bio Cat# RR037B THUNDERBIRD SYBR qPCR Mix Toyobo Cat# QPS-201 Deposited data RNA-seq data for wild-type CDPs, cDC1s and cDC2s Murakami et al.8 GEO: GSE149762 RNA-seq data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 ATAC-seq data for wild-type MDPs and CDPs Murakami et al.8 GEO: GSE149762 ATAC-seq data for wild-type cDC1s Brown et al.43 GEO: GSE130201 ChIP-seq data for wild-type LMPPs and MDPs Murakami et al.8 GEO: GSE149762 Tiled-C data This study DDBJ: DRA016834 H3K27ac CUT&Tag data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 Experimental models: Cell lines 293TN cell line System Biosciences Cat# LV900A-1 Experimental models: Organisms/strains Mouse: C57BL/6 Japan SLC C57BL/6JJmsSlc Mouse: Irf8 / : Irf8tm1Hor Holtschke et al.44 N/A Mouse: +32D/D Murakami et al.8 N/A Mouse: +56D/D Murakami et al.8 N/A Mouse: +32WT/D This study N/A Mouse: +56D/WT This study N/A Mouse: +56D/WT+32WT/D This study N/A Oligonucleotides Oligonucleotides used in this study, see Table S1 This study N/A Recombinant DNA MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A pCL-Eco Naviaux et al.45 N/A Software and algorithms FlowJo (version 10.8.1) BD Life Sciences Cat# 663335 STAR (version 2.7.7a) Dobin et al.46 https://github.com/alexdobin/STAR Picard (version 2.25.0) Broad Institute http://broadinstitute.github.io/picard/ RSEM (version 1.3.3) Li et al.47 https://github.com/deweylab/RSEM R (version 4.0.3) The R Foundation for Statistical Computing https://www.r-project.org/ (Continued on next page) Cell Reports 43, 114107, April 23, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER edgeR (version 3.32.1) Robinson et al.48 https://bioconductor.org/packages/ release/bioc/html/edgeR.html R Stats (version 4.3) R Core Team https://stat.ethz.ch/R-manual/R-devel/ library/stats/html/00Index.html ggplot2 (version 3.2.4) Hadley Wickham, https://ggplot2.tidyverse.org/ authors.html#citation https://ggplot2.tidyverse.org/ Bowtie2 (version 2.3.5.1) Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml HOMER (version 4.11) Heinz et al.50 http://homer.ucsd.edu/homer/index.html GOPHER (version 0.6.0) Hansen et al.51 https://github.com/TheJacksonLaboratory/Gopher Agilent SureDesign tool Agilent Technologies https://earray.chem.agilent.com/suredesign/ Hi-Cpro (version 3.0.0) Servant et al.52 https://github.com/nservant/HiC-Pro Treeview3 (version 3.0 Beta 1) Christopher Keil, https://doi.org/10.5281/ zenodo.1303402 https://bitbucket.org/TreeView3Dev/ treeview3/src/master/ GraphPad Prism 9 GraphPad https://www.graphpad.com GSEA software (version 4.0.3) Broad Institute53 https://www.gsea-msigdb.org/gsea/index.jsp

    In Vitro:

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-conjugated Armenian Hamster Anti-Mouse CD3ε (clone 145-2C11) BioLegend Cat# 100304 Biotin-conjugated Rat Anti-Mouse F4/80 (clone BM8) BioLegend Cat# 123106 Biotin-conjugated Rat Anti-mouse IL-7R (clone A7R34) BioLegend Cat# 135006 Biotin-conjugated Rat Anti-mouse Ly-6G (clone 1A8) BioLegend Cat# 127604 Biotin-conjugated Mouse Anti-Mouse NK1.1 (clone PK136) BD Biosciences Cat# 553163 Biotin-conjugated Rat Anti-Mouse Ter119 (clone TER-119) BioLegend Cat# 116204 Purified Rat anti-mouse CD16/32 (clone 93) BioLegend Cat# 101302 Rabbit Polyclonal Anti-Mouse Histone H3 (acetyl K27) Antibody Abcam Cat# ab4729 Guinea Pig Polyclonal Anti-Rabbit IgG (Heavy & Light Chain) Antibody Antibodies online Cat# ABIN101961 Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (PE Conjugate) Cell Signaling Cat# 15562S Rabbit (DA1E) mAb IgG XP Isotype Control (PE Conjugate) Cell Signaling Cat# 5742S Bacterial and virus strains MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A Chemicals, peptides, and recombinant proteins Liberase DL Roche Cat# 5466202001 DNase I, grade II, Roche Cat# 10104159001 Recombinant Murine SCF PeproTech Cat# 250-03 Recombinant Murine IL-3 PeproTech Cat# 213-13 Recombinant Murine IL-6 PeproTech Cat# 216-16 Recombinant Human Flt3-Ligand PeproTech Cat# 300-19 RPMI1640 Nacalai Tesque Cat# 30263-95 Fetal Bovine Serum (Lot# 0001641431) Sigma Cat# 173012 D-MEM FUJIFILM Wako Pure Chemical Cat# 043-30085 PEI MAX Polysciences Cat# 24765-1 Dpn II NEB Cat# R0543M Biotin-14-dATP Thermo Fisher Scientific Cat# 19524016 DNA Polymerase I, Large (Klenow) Fragment NEB Cat# M0210L T4 DNA Ligase NEB Cat# M0202M Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat# 65001 KOD FX Neo polymerase Toyobo Cat# KFX-201 Agarose ME Iwai Chemicals Cat# 50013R Agarose H Nippon gene Cat# 319-01201 Marker 7 GT Nippon gene Cat# 315-03981 Atlas Clear Sight Gold DNA Stain solution BioAtlas Cat# BH40701 Blocking One-P Nacalai Tesque Cat# 05999-84 (Continued on next page) 14 Cell Reports 43, 114107, April 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Lineage Cell Depletion Kit, mouse Miltenyi Biotec Cat# 130-110-470 CD8+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-169 CD4+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-262 RNeasy Micro Kit Qiagen Cat# 74004 SMART-Seq HT Kit Takara Bio Cat# 634437 Nextera XT DNA Library Prep Kit Illumina Cat# FC-131-1096 KAPA HyperPrep Kits Roche Cat# 07962347001 SureSelect XT HS Reagents Agilent Technologies Cat# G9702A SureSelect PostPool Custom Tier2 Agilent Technologies Cat# 5191-6905 PrimeScript RT Reagent kit Takara Bio Cat# RR037B THUNDERBIRD SYBR qPCR Mix Toyobo Cat# QPS-201 Deposited data RNA-seq data for wild-type CDPs, cDC1s and cDC2s Murakami et al.8 GEO: GSE149762 RNA-seq data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 ATAC-seq data for wild-type MDPs and CDPs Murakami et al.8 GEO: GSE149762 ATAC-seq data for wild-type cDC1s Brown et al.43 GEO: GSE130201 ChIP-seq data for wild-type LMPPs and MDPs Murakami et al.8 GEO: GSE149762 Tiled-C data This study DDBJ: DRA016834 H3K27ac CUT&Tag data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 Experimental models: Cell lines 293TN cell line System Biosciences Cat# LV900A-1 Experimental models: Organisms/strains Mouse: C57BL/6 Japan SLC C57BL/6JJmsSlc Mouse: Irf8 / : Irf8tm1Hor Holtschke et al.44 N/A Mouse: +32D/D Murakami et al.8 N/A Mouse: +56D/D Murakami et al.8 N/A Mouse: +32WT/D This study N/A Mouse: +56D/WT This study N/A Mouse: +56D/WT+32WT/D This study N/A Oligonucleotides Oligonucleotides used in this study, see Table S1 This study N/A Recombinant DNA MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A pCL-Eco Naviaux et al.45 N/A Software and algorithms FlowJo (version 10.8.1) BD Life Sciences Cat# 663335 STAR (version 2.7.7a) Dobin et al.46 https://github.com/alexdobin/STAR Picard (version 2.25.0) Broad Institute http://broadinstitute.github.io/picard/ RSEM (version 1.3.3) Li et al.47 https://github.com/deweylab/RSEM R (version 4.0.3) The R Foundation for Statistical Computing https://www.r-project.org/ (Continued on next page) Cell Reports 43, 114107, April 23, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER edgeR (version 3.32.1) Robinson et al.48 https://bioconductor.org/packages/ release/bioc/html/edgeR.html R Stats (version 4.3) R Core Team https://stat.ethz.ch/R-manual/R-devel/ library/stats/html/00Index.html ggplot2 (version 3.2.4) Hadley Wickham, https://ggplot2.tidyverse.org/ authors.html#citation https://ggplot2.tidyverse.org/ Bowtie2 (version 2.3.5.1) Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml HOMER (version 4.11) Heinz et al.50 http://homer.ucsd.edu/homer/index.html GOPHER (version 0.6.0) Hansen et al.51 https://github.com/TheJacksonLaboratory/Gopher Agilent SureDesign tool Agilent Technologies https://earray.chem.agilent.com/suredesign/ Hi-Cpro (version 3.0.0) Servant et al.52 https://github.com/nservant/HiC-Pro Treeview3 (version 3.0 Beta 1) Christopher Keil, https://doi.org/10.5281/ zenodo.1303402 https://bitbucket.org/TreeView3Dev/ treeview3/src/master/ GraphPad Prism 9 GraphPad https://www.graphpad.com GSEA software (version 4.0.3) Broad Institute53 https://www.gsea-msigdb.org/gsea/index.jsp

    Chromatin Immunoprecipitation:

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-conjugated Armenian Hamster Anti-Mouse CD3ε (clone 145-2C11) BioLegend Cat# 100304 Biotin-conjugated Rat Anti-Mouse F4/80 (clone BM8) BioLegend Cat# 123106 Biotin-conjugated Rat Anti-mouse IL-7R (clone A7R34) BioLegend Cat# 135006 Biotin-conjugated Rat Anti-mouse Ly-6G (clone 1A8) BioLegend Cat# 127604 Biotin-conjugated Mouse Anti-Mouse NK1.1 (clone PK136) BD Biosciences Cat# 553163 Biotin-conjugated Rat Anti-Mouse Ter119 (clone TER-119) BioLegend Cat# 116204 Purified Rat anti-mouse CD16/32 (clone 93) BioLegend Cat# 101302 Rabbit Polyclonal Anti-Mouse Histone H3 (acetyl K27) Antibody Abcam Cat# ab4729 Guinea Pig Polyclonal Anti-Rabbit IgG (Heavy & Light Chain) Antibody Antibodies online Cat# ABIN101961 Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (PE Conjugate) Cell Signaling Cat# 15562S Rabbit (DA1E) mAb IgG XP Isotype Control (PE Conjugate) Cell Signaling Cat# 5742S Bacterial and virus strains MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A Chemicals, peptides, and recombinant proteins Liberase DL Roche Cat# 5466202001 DNase I, grade II, Roche Cat# 10104159001 Recombinant Murine SCF PeproTech Cat# 250-03 Recombinant Murine IL-3 PeproTech Cat# 213-13 Recombinant Murine IL-6 PeproTech Cat# 216-16 Recombinant Human Flt3-Ligand PeproTech Cat# 300-19 RPMI1640 Nacalai Tesque Cat# 30263-95 Fetal Bovine Serum (Lot# 0001641431) Sigma Cat# 173012 D-MEM FUJIFILM Wako Pure Chemical Cat# 043-30085 PEI MAX Polysciences Cat# 24765-1 Dpn II NEB Cat# R0543M Biotin-14-dATP Thermo Fisher Scientific Cat# 19524016 DNA Polymerase I, Large (Klenow) Fragment NEB Cat# M0210L T4 DNA Ligase NEB Cat# M0202M Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat# 65001 KOD FX Neo polymerase Toyobo Cat# KFX-201 Agarose ME Iwai Chemicals Cat# 50013R Agarose H Nippon gene Cat# 319-01201 Marker 7 GT Nippon gene Cat# 315-03981 Atlas Clear Sight Gold DNA Stain solution BioAtlas Cat# BH40701 Blocking One-P Nacalai Tesque Cat# 05999-84 (Continued on next page) 14 Cell Reports 43, 114107, April 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Lineage Cell Depletion Kit, mouse Miltenyi Biotec Cat# 130-110-470 CD8+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-169 CD4+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-262 RNeasy Micro Kit Qiagen Cat# 74004 SMART-Seq HT Kit Takara Bio Cat# 634437 Nextera XT DNA Library Prep Kit Illumina Cat# FC-131-1096 KAPA HyperPrep Kits Roche Cat# 07962347001 SureSelect XT HS Reagents Agilent Technologies Cat# G9702A SureSelect PostPool Custom Tier2 Agilent Technologies Cat# 5191-6905 PrimeScript RT Reagent kit Takara Bio Cat# RR037B THUNDERBIRD SYBR qPCR Mix Toyobo Cat# QPS-201 Deposited data RNA-seq data for wild-type CDPs, cDC1s and cDC2s Murakami et al.8 GEO: GSE149762 RNA-seq data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 ATAC-seq data for wild-type MDPs and CDPs Murakami et al.8 GEO: GSE149762 ATAC-seq data for wild-type cDC1s Brown et al.43 GEO: GSE130201 ChIP-seq data for wild-type LMPPs and MDPs Murakami et al.8 GEO: GSE149762 Tiled-C data This study DDBJ: DRA016834 H3K27ac CUT&Tag data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 Experimental models: Cell lines 293TN cell line System Biosciences Cat# LV900A-1 Experimental models: Organisms/strains Mouse: C57BL/6 Japan SLC C57BL/6JJmsSlc Mouse: Irf8 / : Irf8tm1Hor Holtschke et al.44 N/A Mouse: +32D/D Murakami et al.8 N/A Mouse: +56D/D Murakami et al.8 N/A Mouse: +32WT/D This study N/A Mouse: +56D/WT This study N/A Mouse: +56D/WT+32WT/D This study N/A Oligonucleotides Oligonucleotides used in this study, see Table S1 This study N/A Recombinant DNA MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A pCL-Eco Naviaux et al.45 N/A Software and algorithms FlowJo (version 10.8.1) BD Life Sciences Cat# 663335 STAR (version 2.7.7a) Dobin et al.46 https://github.com/alexdobin/STAR Picard (version 2.25.0) Broad Institute http://broadinstitute.github.io/picard/ RSEM (version 1.3.3) Li et al.47 https://github.com/deweylab/RSEM R (version 4.0.3) The R Foundation for Statistical Computing https://www.r-project.org/ (Continued on next page) Cell Reports 43, 114107, April 23, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER edgeR (version 3.32.1) Robinson et al.48 https://bioconductor.org/packages/ release/bioc/html/edgeR.html R Stats (version 4.3) R Core Team https://stat.ethz.ch/R-manual/R-devel/ library/stats/html/00Index.html ggplot2 (version 3.2.4) Hadley Wickham, https://ggplot2.tidyverse.org/ authors.html#citation https://ggplot2.tidyverse.org/ Bowtie2 (version 2.3.5.1) Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml HOMER (version 4.11) Heinz et al.50 http://homer.ucsd.edu/homer/index.html GOPHER (version 0.6.0) Hansen et al.51 https://github.com/TheJacksonLaboratory/Gopher Agilent SureDesign tool Agilent Technologies https://earray.chem.agilent.com/suredesign/ Hi-Cpro (version 3.0.0) Servant et al.52 https://github.com/nservant/HiC-Pro Treeview3 (version 3.0 Beta 1) Christopher Keil, https://doi.org/10.5281/ zenodo.1303402 https://bitbucket.org/TreeView3Dev/ treeview3/src/master/ GraphPad Prism 9 GraphPad https://www.graphpad.com GSEA software (version 4.0.3) Broad Institute53 https://www.gsea-msigdb.org/gsea/index.jsp

    Recombinant:

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-conjugated Armenian Hamster Anti-Mouse CD3ε (clone 145-2C11) BioLegend Cat# 100304 Biotin-conjugated Rat Anti-Mouse F4/80 (clone BM8) BioLegend Cat# 123106 Biotin-conjugated Rat Anti-mouse IL-7R (clone A7R34) BioLegend Cat# 135006 Biotin-conjugated Rat Anti-mouse Ly-6G (clone 1A8) BioLegend Cat# 127604 Biotin-conjugated Mouse Anti-Mouse NK1.1 (clone PK136) BD Biosciences Cat# 553163 Biotin-conjugated Rat Anti-Mouse Ter119 (clone TER-119) BioLegend Cat# 116204 Purified Rat anti-mouse CD16/32 (clone 93) BioLegend Cat# 101302 Rabbit Polyclonal Anti-Mouse Histone H3 (acetyl K27) Antibody Abcam Cat# ab4729 Guinea Pig Polyclonal Anti-Rabbit IgG (Heavy & Light Chain) Antibody Antibodies online Cat# ABIN101961 Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (PE Conjugate) Cell Signaling Cat# 15562S Rabbit (DA1E) mAb IgG XP Isotype Control (PE Conjugate) Cell Signaling Cat# 5742S Bacterial and virus strains MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A Chemicals, peptides, and recombinant proteins Liberase DL Roche Cat# 5466202001 DNase I, grade II, Roche Cat# 10104159001 Recombinant Murine SCF PeproTech Cat# 250-03 Recombinant Murine IL-3 PeproTech Cat# 213-13 Recombinant Murine IL-6 PeproTech Cat# 216-16 Recombinant Human Flt3-Ligand PeproTech Cat# 300-19 RPMI1640 Nacalai Tesque Cat# 30263-95 Fetal Bovine Serum (Lot# 0001641431) Sigma Cat# 173012 D-MEM FUJIFILM Wako Pure Chemical Cat# 043-30085 PEI MAX Polysciences Cat# 24765-1 Dpn II NEB Cat# R0543M Biotin-14-dATP Thermo Fisher Scientific Cat# 19524016 DNA Polymerase I, Large (Klenow) Fragment NEB Cat# M0210L T4 DNA Ligase NEB Cat# M0202M Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat# 65001 KOD FX Neo polymerase Toyobo Cat# KFX-201 Agarose ME Iwai Chemicals Cat# 50013R Agarose H Nippon gene Cat# 319-01201 Marker 7 GT Nippon gene Cat# 315-03981 Atlas Clear Sight Gold DNA Stain solution BioAtlas Cat# BH40701 Blocking One-P Nacalai Tesque Cat# 05999-84 (Continued on next page) 14 Cell Reports 43, 114107, April 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Lineage Cell Depletion Kit, mouse Miltenyi Biotec Cat# 130-110-470 CD8+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-169 CD4+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-262 RNeasy Micro Kit Qiagen Cat# 74004 SMART-Seq HT Kit Takara Bio Cat# 634437 Nextera XT DNA Library Prep Kit Illumina Cat# FC-131-1096 KAPA HyperPrep Kits Roche Cat# 07962347001 SureSelect XT HS Reagents Agilent Technologies Cat# G9702A SureSelect PostPool Custom Tier2 Agilent Technologies Cat# 5191-6905 PrimeScript RT Reagent kit Takara Bio Cat# RR037B THUNDERBIRD SYBR qPCR Mix Toyobo Cat# QPS-201 Deposited data RNA-seq data for wild-type CDPs, cDC1s and cDC2s Murakami et al.8 GEO: GSE149762 RNA-seq data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 ATAC-seq data for wild-type MDPs and CDPs Murakami et al.8 GEO: GSE149762 ATAC-seq data for wild-type cDC1s Brown et al.43 GEO: GSE130201 ChIP-seq data for wild-type LMPPs and MDPs Murakami et al.8 GEO: GSE149762 Tiled-C data This study DDBJ: DRA016834 H3K27ac CUT&Tag data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 Experimental models: Cell lines 293TN cell line System Biosciences Cat# LV900A-1 Experimental models: Organisms/strains Mouse: C57BL/6 Japan SLC C57BL/6JJmsSlc Mouse: Irf8 / : Irf8tm1Hor Holtschke et al.44 N/A Mouse: +32D/D Murakami et al.8 N/A Mouse: +56D/D Murakami et al.8 N/A Mouse: +32WT/D This study N/A Mouse: +56D/WT This study N/A Mouse: +56D/WT+32WT/D This study N/A Oligonucleotides Oligonucleotides used in this study, see Table S1 This study N/A Recombinant DNA MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A pCL-Eco Naviaux et al.45 N/A Software and algorithms FlowJo (version 10.8.1) BD Life Sciences Cat# 663335 STAR (version 2.7.7a) Dobin et al.46 https://github.com/alexdobin/STAR Picard (version 2.25.0) Broad Institute http://broadinstitute.github.io/picard/ RSEM (version 1.3.3) Li et al.47 https://github.com/deweylab/RSEM R (version 4.0.3) The R Foundation for Statistical Computing https://www.r-project.org/ (Continued on next page) Cell Reports 43, 114107, April 23, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER edgeR (version 3.32.1) Robinson et al.48 https://bioconductor.org/packages/ release/bioc/html/edgeR.html R Stats (version 4.3) R Core Team https://stat.ethz.ch/R-manual/R-devel/ library/stats/html/00Index.html ggplot2 (version 3.2.4) Hadley Wickham, https://ggplot2.tidyverse.org/ authors.html#citation https://ggplot2.tidyverse.org/ Bowtie2 (version 2.3.5.1) Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml HOMER (version 4.11) Heinz et al.50 http://homer.ucsd.edu/homer/index.html GOPHER (version 0.6.0) Hansen et al.51 https://github.com/TheJacksonLaboratory/Gopher Agilent SureDesign tool Agilent Technologies https://earray.chem.agilent.com/suredesign/ Hi-Cpro (version 3.0.0) Servant et al.52 https://github.com/nservant/HiC-Pro Treeview3 (version 3.0 Beta 1) Christopher Keil, https://doi.org/10.5281/ zenodo.1303402 https://bitbucket.org/TreeView3Dev/ treeview3/src/master/ GraphPad Prism 9 GraphPad https://www.graphpad.com GSEA software (version 4.0.3) Broad Institute53 https://www.gsea-msigdb.org/gsea/index.jsp

    Software:

    Article Title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-conjugated Armenian Hamster Anti-Mouse CD3ε (clone 145-2C11) BioLegend Cat# 100304 Biotin-conjugated Rat Anti-Mouse F4/80 (clone BM8) BioLegend Cat# 123106 Biotin-conjugated Rat Anti-mouse IL-7R (clone A7R34) BioLegend Cat# 135006 Biotin-conjugated Rat Anti-mouse Ly-6G (clone 1A8) BioLegend Cat# 127604 Biotin-conjugated Mouse Anti-Mouse NK1.1 (clone PK136) BD Biosciences Cat# 553163 Biotin-conjugated Rat Anti-Mouse Ter119 (clone TER-119) BioLegend Cat# 116204 Purified Rat anti-mouse CD16/32 (clone 93) BioLegend Cat# 101302 Rabbit Polyclonal Anti-Mouse Histone H3 (acetyl K27) Antibody Abcam Cat# ab4729 Guinea Pig Polyclonal Anti-Rabbit IgG (Heavy & Light Chain) Antibody Antibodies online Cat# ABIN101961 Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (PE Conjugate) Cell Signaling Cat# 15562S Rabbit (DA1E) mAb IgG XP Isotype Control (PE Conjugate) Cell Signaling Cat# 5742S Bacterial and virus strains MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A Chemicals, peptides, and recombinant proteins Liberase DL Roche Cat# 5466202001 DNase I, grade II, Roche Cat# 10104159001 Recombinant Murine SCF PeproTech Cat# 250-03 Recombinant Murine IL-3 PeproTech Cat# 213-13 Recombinant Murine IL-6 PeproTech Cat# 216-16 Recombinant Human Flt3-Ligand PeproTech Cat# 300-19 RPMI1640 Nacalai Tesque Cat# 30263-95 Fetal Bovine Serum (Lot# 0001641431) Sigma Cat# 173012 D-MEM FUJIFILM Wako Pure Chemical Cat# 043-30085 PEI MAX Polysciences Cat# 24765-1 Dpn II NEB Cat# R0543M Biotin-14-dATP Thermo Fisher Scientific Cat# 19524016 DNA Polymerase I, Large (Klenow) Fragment NEB Cat# M0210L T4 DNA Ligase NEB Cat# M0202M Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat# 65001 KOD FX Neo polymerase Toyobo Cat# KFX-201 Agarose ME Iwai Chemicals Cat# 50013R Agarose H Nippon gene Cat# 319-01201 Marker 7 GT Nippon gene Cat# 315-03981 Atlas Clear Sight Gold DNA Stain solution BioAtlas Cat# BH40701 Blocking One-P Nacalai Tesque Cat# 05999-84 (Continued on next page) 14 Cell Reports 43, 114107, April 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Lineage Cell Depletion Kit, mouse Miltenyi Biotec Cat# 130-110-470 CD8+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-169 CD4+ Dendritic Cell Isolation Kit, mouse Miltenyi Biotec Cat# 130-091-262 RNeasy Micro Kit Qiagen Cat# 74004 SMART-Seq HT Kit Takara Bio Cat# 634437 Nextera XT DNA Library Prep Kit Illumina Cat# FC-131-1096 KAPA HyperPrep Kits Roche Cat# 07962347001 SureSelect XT HS Reagents Agilent Technologies Cat# G9702A SureSelect PostPool Custom Tier2 Agilent Technologies Cat# 5191-6905 PrimeScript RT Reagent kit Takara Bio Cat# RR037B THUNDERBIRD SYBR qPCR Mix Toyobo Cat# QPS-201 Deposited data RNA-seq data for wild-type CDPs, cDC1s and cDC2s Murakami et al.8 GEO: GSE149762 RNA-seq data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 ATAC-seq data for wild-type MDPs and CDPs Murakami et al.8 GEO: GSE149762 ATAC-seq data for wild-type cDC1s Brown et al.43 GEO: GSE130201 ChIP-seq data for wild-type LMPPs and MDPs Murakami et al.8 GEO: GSE149762 Tiled-C data This study DDBJ: DRA016834 H3K27ac CUT&Tag data for progenitors and cDCs from mice and in vitro culture This study GEO: GSE239952 Experimental models: Cell lines 293TN cell line System Biosciences Cat# LV900A-1 Experimental models: Organisms/strains Mouse: C57BL/6 Japan SLC C57BL/6JJmsSlc Mouse: Irf8 / : Irf8tm1Hor Holtschke et al.44 N/A Mouse: +32D/D Murakami et al.8 N/A Mouse: +56D/D Murakami et al.8 N/A Mouse: +32WT/D This study N/A Mouse: +56D/WT This study N/A Mouse: +56D/WT+32WT/D This study N/A Oligonucleotides Oligonucleotides used in this study, see Table S1 This study N/A Recombinant DNA MSCV-EGFP DeKoter et al.41 N/A MSCV-IRF8-EGFP Tsujimura et al.42 N/A pCL-Eco Naviaux et al.45 N/A Software and algorithms FlowJo (version 10.8.1) BD Life Sciences Cat# 663335 STAR (version 2.7.7a) Dobin et al.46 https://github.com/alexdobin/STAR Picard (version 2.25.0) Broad Institute http://broadinstitute.github.io/picard/ RSEM (version 1.3.3) Li et al.47 https://github.com/deweylab/RSEM R (version 4.0.3) The R Foundation for Statistical Computing https://www.r-project.org/ (Continued on next page) Cell Reports 43, 114107, April 23, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER edgeR (version 3.32.1) Robinson et al.48 https://bioconductor.org/packages/ release/bioc/html/edgeR.html R Stats (version 4.3) R Core Team https://stat.ethz.ch/R-manual/R-devel/ library/stats/html/00Index.html ggplot2 (version 3.2.4) Hadley Wickham, https://ggplot2.tidyverse.org/ authors.html#citation https://ggplot2.tidyverse.org/ Bowtie2 (version 2.3.5.1) Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml HOMER (version 4.11) Heinz et al.50 http://homer.ucsd.edu/homer/index.html GOPHER (version 0.6.0) Hansen et al.51 https://github.com/TheJacksonLaboratory/Gopher Agilent SureDesign tool Agilent Technologies https://earray.chem.agilent.com/suredesign/ Hi-Cpro (version 3.0.0) Servant et al.52 https://github.com/nservant/HiC-Pro Treeview3 (version 3.0 Beta 1) Christopher Keil, https://doi.org/10.5281/ zenodo.1303402 https://bitbucket.org/TreeView3Dev/ treeview3/src/master/ GraphPad Prism 9 GraphPad https://www.graphpad.com GSEA software (version 4.0.3) Broad Institute53 https://www.gsea-msigdb.org/gsea/index.jsp

    Cell Culture:

    Article Title: Potent CTLs can be induced against tumor cells in an environment of lower levels of systemic MFG‐E8
    Article Snippet: .. T, B, and NK-cells were removed from splenocytes by using antibody cocktails which a part of the CD8+ Dendritic Cell Isolation Kit (130-091-169, Miltenyi Biotec, Bergisch Gladbach, MMC for 2 h, and after washing twice with PBS, were cultured overnight, they were used as apoptotic cells. ..

    Activation Assay:

    Article Title: Flt3 ligand augments immune responses to soluble PD1-based DNA vaccine via expansion of type 1 conventional DCs.
    Article Snippet: .. For T cell activation verification, naïve mouse spleens were isolated and treated into single-cell suspensions. cDC1 was obtained using a CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec, Germany) and placed into a 24-well plate at a density of 1 × 105/well. ..

    Article Title: The XCL1-Mediated DNA Vaccine Targeting Type 1 Conventional Dendritic Cells Combined with Gemcitabine and Anti-PD1 Antibody Induces Potent Antitumor Immunity in a Mouse Lung Cancer Model
    Article Snippet: .. For T cell activation verification, naïve mouse spleens were isolated and treated in single-cell suspensions. cDC1 were obtained using a CD8 + Dendritic Cell Isolation Kit (Miltenyi Biotec) and placed into a 24-well plate at a density of 1 × 10 5 /well. ..

    Single Cell:

    Article Title: Flt3 ligand augments immune responses to soluble PD1-based DNA vaccine via expansion of type 1 conventional DCs.
    Article Snippet: .. For T cell activation verification, naïve mouse spleens were isolated and treated into single-cell suspensions. cDC1 was obtained using a CD8+ Dendritic Cell Isolation Kit (Miltenyi Biotec, Germany) and placed into a 24-well plate at a density of 1 × 105/well. ..

    Article Title: The XCL1-Mediated DNA Vaccine Targeting Type 1 Conventional Dendritic Cells Combined with Gemcitabine and Anti-PD1 Antibody Induces Potent Antitumor Immunity in a Mouse Lung Cancer Model
    Article Snippet: .. For T cell activation verification, naïve mouse spleens were isolated and treated in single-cell suspensions. cDC1 were obtained using a CD8 + Dendritic Cell Isolation Kit (Miltenyi Biotec) and placed into a 24-well plate at a density of 1 × 10 5 /well. ..



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