Review



dynamic array integrated fluidic circuit ifc chips  (fluidigm)


Bioz Verified Symbol fluidigm is a verified supplier
Bioz Manufacturer Symbol fluidigm manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
    • 94
      Buy from Supplier

    Structured Review

    fluidigm dynamic array integrated fluidic circuit ifc chips
    Dynamic Array Integrated Fluidic Circuit Ifc Chips, supplied by fluidigm, used in various techniques. Bioz Stars score: 94/100, based on 313 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip+array+assay/48%2E48+Dynamic+Array+IFC+for+Gene+Expression/pm41866099-141-7-22
    Average 94 stars, based on 313 article reviews
    dynamic array integrated fluidic circuit ifc chips - by Bioz Stars, 2026-09
    94/100 stars

    Images

    Related Articles

    RNA Sequencing:

    Article Title: The 34 th Annual North American Cystic Fibrosis Conference, October 7-23, 2020.
    Article Snippet: .. RNA sequencing and Fluidigm-based protein array analysis (Olink INF/ONC) revealed higher expression and shedding of cytokines and growth factors from CF cells compared to non-CF epithelial cells, including the cytokine CXCL5 and the growth factor PGF, consistent with sterile inflammation and tissue remodeling under basal conditions. ..

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Protein Array:

    Article Title: The 34 th Annual North American Cystic Fibrosis Conference, October 7-23, 2020.
    Article Snippet: .. RNA sequencing and Fluidigm-based protein array analysis (Olink INF/ONC) revealed higher expression and shedding of cytokines and growth factors from CF cells compared to non-CF epithelial cells, including the cytokine CXCL5 and the growth factor PGF, consistent with sterile inflammation and tissue remodeling under basal conditions. ..

    Expressing:

    Article Title: The 34 th Annual North American Cystic Fibrosis Conference, October 7-23, 2020.
    Article Snippet: .. RNA sequencing and Fluidigm-based protein array analysis (Olink INF/ONC) revealed higher expression and shedding of cytokines and growth factors from CF cells compared to non-CF epithelial cells, including the cytokine CXCL5 and the growth factor PGF, consistent with sterile inflammation and tissue remodeling under basal conditions. ..

    Sterility:

    Article Title: The 34 th Annual North American Cystic Fibrosis Conference, October 7-23, 2020.
    Article Snippet: .. RNA sequencing and Fluidigm-based protein array analysis (Olink INF/ONC) revealed higher expression and shedding of cytokines and growth factors from CF cells compared to non-CF epithelial cells, including the cytokine CXCL5 and the growth factor PGF, consistent with sterile inflammation and tissue remodeling under basal conditions. ..

    Single Cell:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: The sorted single cells (a 10:1 mixture of EGFP+E-Cadherin+CD9+KIT-/low and EGFP–E-Cadherin+CD9+KIT-/low Aundiff fractions) were captured individually on a C1 Single-Cell Auto Prep Array for PreAmp (Fluidigm) designed for 10- to 17-um cells using a Fluidigm C1 system (Fluidigm). .. Cell lysis, cDNA synthesis, and preamplification were performed using Single Cell-to-CT Kit (Thermo), C1 Single-Cell Auto Prep Reagent kit, and specific primers for arbitrarily selected target genes (Table S2). qPCR were performed on a 96:96 dynamic array chips (Fluidigm) using GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit (Fluidigm), and SsoFast EvaGreen Supermix with Low ROX (Bio-Rad), in a Biomark HD system (Fluidigm) platform, following the manufacturer’s instructions. .. The Raw data from 60 cells were analyzed in RStudio software (https://www.rstudio. com/).

    Binding Assay:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: The sorted single cells (a 10:1 mixture of EGFP+E-Cadherin+CD9+KIT-/low and EGFP–E-Cadherin+CD9+KIT-/low Aundiff fractions) were captured individually on a C1 Single-Cell Auto Prep Array for PreAmp (Fluidigm) designed for 10- to 17-um cells using a Fluidigm C1 system (Fluidigm). .. Cell lysis, cDNA synthesis, and preamplification were performed using Single Cell-to-CT Kit (Thermo), C1 Single-Cell Auto Prep Reagent kit, and specific primers for arbitrarily selected target genes (Table S2). qPCR were performed on a 96:96 dynamic array chips (Fluidigm) using GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit (Fluidigm), and SsoFast EvaGreen Supermix with Low ROX (Bio-Rad), in a Biomark HD system (Fluidigm) platform, following the manufacturer’s instructions. .. The Raw data from 60 cells were analyzed in RStudio software (https://www.rstudio. com/).

    Article Title: Three Types of Functional Regulatory T Cells Control T Cell Responses at the Human Maternal-Fetal Interface.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD3-PerCP; UCHT1 Biolegend RRID:AB_893300; Cat #300427 CD3-LEAF purified; SPV-T3B ThermoFisher RRID:AB_2532975; Cat #07-0303 CD4-PerCp; SK3 Biolegend RRID:AB_2563326; Cat #344624 CD4-Alexa700; SK3 Biolegend RRID:AB_2563150; Cat #344622 CD8-APC; SK1 Biolegend RRID:AB_2616624; Cat #980904 CD8-Alexa700; SK1 Biolegend RRID:AB_2562790; Cat #344724 CD8-Pacific Orange; 3B5 Invitrogen RRID:AB_10372066; Cat #MHCD0830 CD14-PerCp; HCD14 Biolegend RRID:AB_2564058; Cat #301847 CD14-PE-TexasRed; TuK4 Invitrogen RRID:AB_10373552; Cat #MHCD1417 CD25-PE; 2A3 BD Biosciences RRID:AB_2783790; Cat #341011 CD39-FITC; A1 Biolegend RRID:AB_940423; Cat #328205 CD45-Pacific Orange; HI30 Invitrogen RRID:AB_10376143; Cat #MHCD4530 CD45-APC; HI30 Biolegend RRID:AB_2562049; Cat #304037 CD45-PerCp; HI30 Biolegend RRID:AB_893341; Cat #304025 CD45RA-Alexa700; HI100 Biolegend RRID:AB_493762; Cat #304119 CD56-PE; HCD56 Biolegend RRID:AB_604093; Cat #318305 CTLA4-PE-Cy7; BNI3 Biolegend RRID:AB_2632876; Cat #369614 EGFR1-FITC; AY13 Biolegend RRID:AB_11124324; Cat #352907 FOXP3-Pacific Blue; 259D BioLegend RRID:AB_940354; Cat #320215 GITR-APC; DT5D3 Milteny Biotec RRID:AB_2751597; Cat #130-118-997 HELIOS-Alexa488; 22F6 Biolegend RRID:AB_10645334; Cat #137213 HLA-DR-LEAF purified; L243 Biolegend RRID:AB_314680; Cat #307602 HLA-G-PE; MEM/G9 Abcam RRID:AB_448029; Cat #ab24384 HLA-G-LEAF purified; 87G Biolegend RRID:AB_10641840; Cat #335904 IFNg-APC; B27 Biolegend RRID:AB_315443; Cat #506510 IL-10-PE-Cy7; JES3-9D7 Biolegend RRID:AB_2280292; Cat #501419 IL-10R-LEAF purified; 3F9 Biolegend RRID:AB_314737; Cat #308805 IL-2-PE; MQ1-17H12 Biolegend RRID:AB_315093; Cat #500306 ILT2-LEAF purified; GHI/75 Biolegend RRID:AB_1089089; Cat #333702 LRRC32-APC; 7B11 Biolegend RRID:AB_10896059; Cat #352505 PD1-PE-Cy7; EH12.1 BD Biosciences RRID:AB_10611585; Cat #561272 PDL1-LEAF purified; 29E.2A3 Biolegend RRID:AB_940370; Cat #329701 TGFb1-LEAF purified; 19D8 Biolegend RRID:AB_2561694; Cat #521703 TIGIT-APC; MBSA43 eBioscience RRID:AB_2573305; Cat #17-9500-42 TIGIT-PerCp-eFlour710; MBSA43 eBioscience RRID:AB_10853679; Cat #46-9500-42 TIM3-FITC; F38-2E2 Biolegend RRID:AB_2563936; Cat #345021 TNFa- Pacific Blue; MAb11 Biolegend RRID:AB_528965; Cat #502920 Bacterial and Virus Strains HCMV-AD169-GFP (IE-1-GFP) Donald Coen, Harvard Medical School N/A Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Peprotech Cat #200-02 Recombinant human EGF Peprotech Cat #AF-100-15 (Continued on next page) e1 Cell Reports 27, 2537–2547.e1–e5, May 28, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fibronectin Corning Cat #354008 Insulin-Transferrin-Selenium (ITS-G) (100X) GIBCO Cat #41400-045 Human gonadotropic hormone (HcG) Sigma-Aldrich Cat #C1063 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat #P1585 Ionomycin Sigma Cat #I9657 Collagenase type IV Sigma-Aldrich Cat #C5138 DNase I Sigma Cat #DN25 Percoll GE Healthcare Cat #17-5445-02 DNA suspension buffer TEKnova Cat #T0220 Human AB serum Corning Cat #35060CI New Born Calf Serum GIBCO Cat #16010159 Exonuclease I New England BioLabs Cat #M0568S Critical Commercial Assays RosetteSep human CD4+ enrichment cocktail Stem Cell Technologies Cat #15022 Dynabeads Human T-Activator CD3/CD28 Thermofisher Cat #111.31D CytoFix/CytoPermTM Plus kit BD Biosciences Cat #555028 RNAeasy Micro Kit Qiagan Cat #74004 AffinityScript QPCR cDNA Synthesis Kit Agilent Cat #600559 PerfeCTa SYBR Green SuperMix Low ROX QuantaBio Cat #:95056-100 BioMark Fluidigm QPCR 96.96 chip Fluidigm Cat #:BMK-M-96.96 Fluidigm PreAmp Master mix Fluidigm Cat #:100-5580 DNA binding dye sample and assay loading reagent kit Fluidigm Cat #: 100-3415 SsoFast EvaGreen supermix with low ROX BioRad Cat #: 1725210 Oligonucleotides See Table S1 for primers used in this study Software and Algorithms BD FACSDIVA Software BD Biosciences http://www.bdbiosciences.com/us/ instruments/research/software/flowcytometry-acquisition/bd-facsdivasoftware/m/111112/features FlowJo Software FlowJo https://www.flowjo.com/ Prism GraphPad software Prism https://www.graphpad.com/ scientific-software/prism/ Fluidigm BioMark Real-Time PCR analysis software Fluidigm https://www.fluidigm.com/software GenePattern/ Express Cluster V1.3 software GenePattern https://cloud.genepattern.org/gp http://cbdm.hms.harvard.edu/resources.htm Microsoft Excel Microsoft https://products.office.com/en-US/excel ..

    SYBR Green Assay:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Article Title: Three Types of Functional Regulatory T Cells Control T Cell Responses at the Human Maternal-Fetal Interface.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD3-PerCP; UCHT1 Biolegend RRID:AB_893300; Cat #300427 CD3-LEAF purified; SPV-T3B ThermoFisher RRID:AB_2532975; Cat #07-0303 CD4-PerCp; SK3 Biolegend RRID:AB_2563326; Cat #344624 CD4-Alexa700; SK3 Biolegend RRID:AB_2563150; Cat #344622 CD8-APC; SK1 Biolegend RRID:AB_2616624; Cat #980904 CD8-Alexa700; SK1 Biolegend RRID:AB_2562790; Cat #344724 CD8-Pacific Orange; 3B5 Invitrogen RRID:AB_10372066; Cat #MHCD0830 CD14-PerCp; HCD14 Biolegend RRID:AB_2564058; Cat #301847 CD14-PE-TexasRed; TuK4 Invitrogen RRID:AB_10373552; Cat #MHCD1417 CD25-PE; 2A3 BD Biosciences RRID:AB_2783790; Cat #341011 CD39-FITC; A1 Biolegend RRID:AB_940423; Cat #328205 CD45-Pacific Orange; HI30 Invitrogen RRID:AB_10376143; Cat #MHCD4530 CD45-APC; HI30 Biolegend RRID:AB_2562049; Cat #304037 CD45-PerCp; HI30 Biolegend RRID:AB_893341; Cat #304025 CD45RA-Alexa700; HI100 Biolegend RRID:AB_493762; Cat #304119 CD56-PE; HCD56 Biolegend RRID:AB_604093; Cat #318305 CTLA4-PE-Cy7; BNI3 Biolegend RRID:AB_2632876; Cat #369614 EGFR1-FITC; AY13 Biolegend RRID:AB_11124324; Cat #352907 FOXP3-Pacific Blue; 259D BioLegend RRID:AB_940354; Cat #320215 GITR-APC; DT5D3 Milteny Biotec RRID:AB_2751597; Cat #130-118-997 HELIOS-Alexa488; 22F6 Biolegend RRID:AB_10645334; Cat #137213 HLA-DR-LEAF purified; L243 Biolegend RRID:AB_314680; Cat #307602 HLA-G-PE; MEM/G9 Abcam RRID:AB_448029; Cat #ab24384 HLA-G-LEAF purified; 87G Biolegend RRID:AB_10641840; Cat #335904 IFNg-APC; B27 Biolegend RRID:AB_315443; Cat #506510 IL-10-PE-Cy7; JES3-9D7 Biolegend RRID:AB_2280292; Cat #501419 IL-10R-LEAF purified; 3F9 Biolegend RRID:AB_314737; Cat #308805 IL-2-PE; MQ1-17H12 Biolegend RRID:AB_315093; Cat #500306 ILT2-LEAF purified; GHI/75 Biolegend RRID:AB_1089089; Cat #333702 LRRC32-APC; 7B11 Biolegend RRID:AB_10896059; Cat #352505 PD1-PE-Cy7; EH12.1 BD Biosciences RRID:AB_10611585; Cat #561272 PDL1-LEAF purified; 29E.2A3 Biolegend RRID:AB_940370; Cat #329701 TGFb1-LEAF purified; 19D8 Biolegend RRID:AB_2561694; Cat #521703 TIGIT-APC; MBSA43 eBioscience RRID:AB_2573305; Cat #17-9500-42 TIGIT-PerCp-eFlour710; MBSA43 eBioscience RRID:AB_10853679; Cat #46-9500-42 TIM3-FITC; F38-2E2 Biolegend RRID:AB_2563936; Cat #345021 TNFa- Pacific Blue; MAb11 Biolegend RRID:AB_528965; Cat #502920 Bacterial and Virus Strains HCMV-AD169-GFP (IE-1-GFP) Donald Coen, Harvard Medical School N/A Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Peprotech Cat #200-02 Recombinant human EGF Peprotech Cat #AF-100-15 (Continued on next page) e1 Cell Reports 27, 2537–2547.e1–e5, May 28, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fibronectin Corning Cat #354008 Insulin-Transferrin-Selenium (ITS-G) (100X) GIBCO Cat #41400-045 Human gonadotropic hormone (HcG) Sigma-Aldrich Cat #C1063 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat #P1585 Ionomycin Sigma Cat #I9657 Collagenase type IV Sigma-Aldrich Cat #C5138 DNase I Sigma Cat #DN25 Percoll GE Healthcare Cat #17-5445-02 DNA suspension buffer TEKnova Cat #T0220 Human AB serum Corning Cat #35060CI New Born Calf Serum GIBCO Cat #16010159 Exonuclease I New England BioLabs Cat #M0568S Critical Commercial Assays RosetteSep human CD4+ enrichment cocktail Stem Cell Technologies Cat #15022 Dynabeads Human T-Activator CD3/CD28 Thermofisher Cat #111.31D CytoFix/CytoPermTM Plus kit BD Biosciences Cat #555028 RNAeasy Micro Kit Qiagan Cat #74004 AffinityScript QPCR cDNA Synthesis Kit Agilent Cat #600559 PerfeCTa SYBR Green SuperMix Low ROX QuantaBio Cat #:95056-100 BioMark Fluidigm QPCR 96.96 chip Fluidigm Cat #:BMK-M-96.96 Fluidigm PreAmp Master mix Fluidigm Cat #:100-5580 DNA binding dye sample and assay loading reagent kit Fluidigm Cat #: 100-3415 SsoFast EvaGreen supermix with low ROX BioRad Cat #: 1725210 Oligonucleotides See Table S1 for primers used in this study Software and Algorithms BD FACSDIVA Software BD Biosciences http://www.bdbiosciences.com/us/ instruments/research/software/flowcytometry-acquisition/bd-facsdivasoftware/m/111112/features FlowJo Software FlowJo https://www.flowjo.com/ Prism GraphPad software Prism https://www.graphpad.com/ scientific-software/prism/ Fluidigm BioMark Real-Time PCR analysis software Fluidigm https://www.fluidigm.com/software GenePattern/ Express Cluster V1.3 software GenePattern https://cloud.genepattern.org/gp http://cbdm.hms.harvard.edu/resources.htm Microsoft Excel Microsoft https://products.office.com/en-US/excel ..

    Polymerase Chain Reaction:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Real-time Polymerase Chain Reaction:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: The sorted single cells (a 10:1 mixture of EGFP+E-Cadherin+CD9+KIT-/low and EGFP–E-Cadherin+CD9+KIT-/low Aundiff fractions) were captured individually on a C1 Single-Cell Auto Prep Array for PreAmp (Fluidigm) designed for 10- to 17-um cells using a Fluidigm C1 system (Fluidigm). .. Cell lysis, cDNA synthesis, and preamplification were performed using Single Cell-to-CT Kit (Thermo), C1 Single-Cell Auto Prep Reagent kit, and specific primers for arbitrarily selected target genes (Table S2). qPCR were performed on a 96:96 dynamic array chips (Fluidigm) using GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit (Fluidigm), and SsoFast EvaGreen Supermix with Low ROX (Bio-Rad), in a Biomark HD system (Fluidigm) platform, following the manufacturer’s instructions. .. The Raw data from 60 cells were analyzed in RStudio software (https://www.rstudio. com/).

    Article Title: Three Types of Functional Regulatory T Cells Control T Cell Responses at the Human Maternal-Fetal Interface.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD3-PerCP; UCHT1 Biolegend RRID:AB_893300; Cat #300427 CD3-LEAF purified; SPV-T3B ThermoFisher RRID:AB_2532975; Cat #07-0303 CD4-PerCp; SK3 Biolegend RRID:AB_2563326; Cat #344624 CD4-Alexa700; SK3 Biolegend RRID:AB_2563150; Cat #344622 CD8-APC; SK1 Biolegend RRID:AB_2616624; Cat #980904 CD8-Alexa700; SK1 Biolegend RRID:AB_2562790; Cat #344724 CD8-Pacific Orange; 3B5 Invitrogen RRID:AB_10372066; Cat #MHCD0830 CD14-PerCp; HCD14 Biolegend RRID:AB_2564058; Cat #301847 CD14-PE-TexasRed; TuK4 Invitrogen RRID:AB_10373552; Cat #MHCD1417 CD25-PE; 2A3 BD Biosciences RRID:AB_2783790; Cat #341011 CD39-FITC; A1 Biolegend RRID:AB_940423; Cat #328205 CD45-Pacific Orange; HI30 Invitrogen RRID:AB_10376143; Cat #MHCD4530 CD45-APC; HI30 Biolegend RRID:AB_2562049; Cat #304037 CD45-PerCp; HI30 Biolegend RRID:AB_893341; Cat #304025 CD45RA-Alexa700; HI100 Biolegend RRID:AB_493762; Cat #304119 CD56-PE; HCD56 Biolegend RRID:AB_604093; Cat #318305 CTLA4-PE-Cy7; BNI3 Biolegend RRID:AB_2632876; Cat #369614 EGFR1-FITC; AY13 Biolegend RRID:AB_11124324; Cat #352907 FOXP3-Pacific Blue; 259D BioLegend RRID:AB_940354; Cat #320215 GITR-APC; DT5D3 Milteny Biotec RRID:AB_2751597; Cat #130-118-997 HELIOS-Alexa488; 22F6 Biolegend RRID:AB_10645334; Cat #137213 HLA-DR-LEAF purified; L243 Biolegend RRID:AB_314680; Cat #307602 HLA-G-PE; MEM/G9 Abcam RRID:AB_448029; Cat #ab24384 HLA-G-LEAF purified; 87G Biolegend RRID:AB_10641840; Cat #335904 IFNg-APC; B27 Biolegend RRID:AB_315443; Cat #506510 IL-10-PE-Cy7; JES3-9D7 Biolegend RRID:AB_2280292; Cat #501419 IL-10R-LEAF purified; 3F9 Biolegend RRID:AB_314737; Cat #308805 IL-2-PE; MQ1-17H12 Biolegend RRID:AB_315093; Cat #500306 ILT2-LEAF purified; GHI/75 Biolegend RRID:AB_1089089; Cat #333702 LRRC32-APC; 7B11 Biolegend RRID:AB_10896059; Cat #352505 PD1-PE-Cy7; EH12.1 BD Biosciences RRID:AB_10611585; Cat #561272 PDL1-LEAF purified; 29E.2A3 Biolegend RRID:AB_940370; Cat #329701 TGFb1-LEAF purified; 19D8 Biolegend RRID:AB_2561694; Cat #521703 TIGIT-APC; MBSA43 eBioscience RRID:AB_2573305; Cat #17-9500-42 TIGIT-PerCp-eFlour710; MBSA43 eBioscience RRID:AB_10853679; Cat #46-9500-42 TIM3-FITC; F38-2E2 Biolegend RRID:AB_2563936; Cat #345021 TNFa- Pacific Blue; MAb11 Biolegend RRID:AB_528965; Cat #502920 Bacterial and Virus Strains HCMV-AD169-GFP (IE-1-GFP) Donald Coen, Harvard Medical School N/A Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Peprotech Cat #200-02 Recombinant human EGF Peprotech Cat #AF-100-15 (Continued on next page) e1 Cell Reports 27, 2537–2547.e1–e5, May 28, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fibronectin Corning Cat #354008 Insulin-Transferrin-Selenium (ITS-G) (100X) GIBCO Cat #41400-045 Human gonadotropic hormone (HcG) Sigma-Aldrich Cat #C1063 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat #P1585 Ionomycin Sigma Cat #I9657 Collagenase type IV Sigma-Aldrich Cat #C5138 DNase I Sigma Cat #DN25 Percoll GE Healthcare Cat #17-5445-02 DNA suspension buffer TEKnova Cat #T0220 Human AB serum Corning Cat #35060CI New Born Calf Serum GIBCO Cat #16010159 Exonuclease I New England BioLabs Cat #M0568S Critical Commercial Assays RosetteSep human CD4+ enrichment cocktail Stem Cell Technologies Cat #15022 Dynabeads Human T-Activator CD3/CD28 Thermofisher Cat #111.31D CytoFix/CytoPermTM Plus kit BD Biosciences Cat #555028 RNAeasy Micro Kit Qiagan Cat #74004 AffinityScript QPCR cDNA Synthesis Kit Agilent Cat #600559 PerfeCTa SYBR Green SuperMix Low ROX QuantaBio Cat #:95056-100 BioMark Fluidigm QPCR 96.96 chip Fluidigm Cat #:BMK-M-96.96 Fluidigm PreAmp Master mix Fluidigm Cat #:100-5580 DNA binding dye sample and assay loading reagent kit Fluidigm Cat #: 100-3415 SsoFast EvaGreen supermix with low ROX BioRad Cat #: 1725210 Oligonucleotides See Table S1 for primers used in this study Software and Algorithms BD FACSDIVA Software BD Biosciences http://www.bdbiosciences.com/us/ instruments/research/software/flowcytometry-acquisition/bd-facsdivasoftware/m/111112/features FlowJo Software FlowJo https://www.flowjo.com/ Prism GraphPad software Prism https://www.graphpad.com/ scientific-software/prism/ Fluidigm BioMark Real-Time PCR analysis software Fluidigm https://www.fluidigm.com/software GenePattern/ Express Cluster V1.3 software GenePattern https://cloud.genepattern.org/gp http://cbdm.hms.harvard.edu/resources.htm Microsoft Excel Microsoft https://products.office.com/en-US/excel ..

    Recombinant:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Sequencing:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Software:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Article Title: Three Types of Functional Regulatory T Cells Control T Cell Responses at the Human Maternal-Fetal Interface.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD3-PerCP; UCHT1 Biolegend RRID:AB_893300; Cat #300427 CD3-LEAF purified; SPV-T3B ThermoFisher RRID:AB_2532975; Cat #07-0303 CD4-PerCp; SK3 Biolegend RRID:AB_2563326; Cat #344624 CD4-Alexa700; SK3 Biolegend RRID:AB_2563150; Cat #344622 CD8-APC; SK1 Biolegend RRID:AB_2616624; Cat #980904 CD8-Alexa700; SK1 Biolegend RRID:AB_2562790; Cat #344724 CD8-Pacific Orange; 3B5 Invitrogen RRID:AB_10372066; Cat #MHCD0830 CD14-PerCp; HCD14 Biolegend RRID:AB_2564058; Cat #301847 CD14-PE-TexasRed; TuK4 Invitrogen RRID:AB_10373552; Cat #MHCD1417 CD25-PE; 2A3 BD Biosciences RRID:AB_2783790; Cat #341011 CD39-FITC; A1 Biolegend RRID:AB_940423; Cat #328205 CD45-Pacific Orange; HI30 Invitrogen RRID:AB_10376143; Cat #MHCD4530 CD45-APC; HI30 Biolegend RRID:AB_2562049; Cat #304037 CD45-PerCp; HI30 Biolegend RRID:AB_893341; Cat #304025 CD45RA-Alexa700; HI100 Biolegend RRID:AB_493762; Cat #304119 CD56-PE; HCD56 Biolegend RRID:AB_604093; Cat #318305 CTLA4-PE-Cy7; BNI3 Biolegend RRID:AB_2632876; Cat #369614 EGFR1-FITC; AY13 Biolegend RRID:AB_11124324; Cat #352907 FOXP3-Pacific Blue; 259D BioLegend RRID:AB_940354; Cat #320215 GITR-APC; DT5D3 Milteny Biotec RRID:AB_2751597; Cat #130-118-997 HELIOS-Alexa488; 22F6 Biolegend RRID:AB_10645334; Cat #137213 HLA-DR-LEAF purified; L243 Biolegend RRID:AB_314680; Cat #307602 HLA-G-PE; MEM/G9 Abcam RRID:AB_448029; Cat #ab24384 HLA-G-LEAF purified; 87G Biolegend RRID:AB_10641840; Cat #335904 IFNg-APC; B27 Biolegend RRID:AB_315443; Cat #506510 IL-10-PE-Cy7; JES3-9D7 Biolegend RRID:AB_2280292; Cat #501419 IL-10R-LEAF purified; 3F9 Biolegend RRID:AB_314737; Cat #308805 IL-2-PE; MQ1-17H12 Biolegend RRID:AB_315093; Cat #500306 ILT2-LEAF purified; GHI/75 Biolegend RRID:AB_1089089; Cat #333702 LRRC32-APC; 7B11 Biolegend RRID:AB_10896059; Cat #352505 PD1-PE-Cy7; EH12.1 BD Biosciences RRID:AB_10611585; Cat #561272 PDL1-LEAF purified; 29E.2A3 Biolegend RRID:AB_940370; Cat #329701 TGFb1-LEAF purified; 19D8 Biolegend RRID:AB_2561694; Cat #521703 TIGIT-APC; MBSA43 eBioscience RRID:AB_2573305; Cat #17-9500-42 TIGIT-PerCp-eFlour710; MBSA43 eBioscience RRID:AB_10853679; Cat #46-9500-42 TIM3-FITC; F38-2E2 Biolegend RRID:AB_2563936; Cat #345021 TNFa- Pacific Blue; MAb11 Biolegend RRID:AB_528965; Cat #502920 Bacterial and Virus Strains HCMV-AD169-GFP (IE-1-GFP) Donald Coen, Harvard Medical School N/A Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Peprotech Cat #200-02 Recombinant human EGF Peprotech Cat #AF-100-15 (Continued on next page) e1 Cell Reports 27, 2537–2547.e1–e5, May 28, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fibronectin Corning Cat #354008 Insulin-Transferrin-Selenium (ITS-G) (100X) GIBCO Cat #41400-045 Human gonadotropic hormone (HcG) Sigma-Aldrich Cat #C1063 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat #P1585 Ionomycin Sigma Cat #I9657 Collagenase type IV Sigma-Aldrich Cat #C5138 DNase I Sigma Cat #DN25 Percoll GE Healthcare Cat #17-5445-02 DNA suspension buffer TEKnova Cat #T0220 Human AB serum Corning Cat #35060CI New Born Calf Serum GIBCO Cat #16010159 Exonuclease I New England BioLabs Cat #M0568S Critical Commercial Assays RosetteSep human CD4+ enrichment cocktail Stem Cell Technologies Cat #15022 Dynabeads Human T-Activator CD3/CD28 Thermofisher Cat #111.31D CytoFix/CytoPermTM Plus kit BD Biosciences Cat #555028 RNAeasy Micro Kit Qiagan Cat #74004 AffinityScript QPCR cDNA Synthesis Kit Agilent Cat #600559 PerfeCTa SYBR Green SuperMix Low ROX QuantaBio Cat #:95056-100 BioMark Fluidigm QPCR 96.96 chip Fluidigm Cat #:BMK-M-96.96 Fluidigm PreAmp Master mix Fluidigm Cat #:100-5580 DNA binding dye sample and assay loading reagent kit Fluidigm Cat #: 100-3415 SsoFast EvaGreen supermix with low ROX BioRad Cat #: 1725210 Oligonucleotides See Table S1 for primers used in this study Software and Algorithms BD FACSDIVA Software BD Biosciences http://www.bdbiosciences.com/us/ instruments/research/software/flowcytometry-acquisition/bd-facsdivasoftware/m/111112/features FlowJo Software FlowJo https://www.flowjo.com/ Prism GraphPad software Prism https://www.graphpad.com/ scientific-software/prism/ Fluidigm BioMark Real-Time PCR analysis software Fluidigm https://www.fluidigm.com/software GenePattern/ Express Cluster V1.3 software GenePattern https://cloud.genepattern.org/gp http://cbdm.hms.harvard.edu/resources.htm Microsoft Excel Microsoft https://products.office.com/en-US/excel ..

    FACS:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Cytometry:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    BAC Assay:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: Reagent or resource Source Identifier Antibodies Rat anti-PLVAP Biolegend Cat#120502; RRID: AB_493302 Biotin-conjugated rat anti-PLVAP Biolegend Cat#120504; RRID:AB_493304 Goat anti-GFRa1 R&D Cat#AF560; RRID:AB_2110307 Rabbit anti-SOX3 GeneTex Cat#GTX129235; RRID:AB_2885934 Goat anti-SOX3 R&D Cat#AF2569; RRID:AB_2239933 Goat anti-PDX1 R&D Cat#AF2419; RRID:AB_355257 Rabbit anti-CRE CST Cat#15036S; RRID:AB_2798694 Rat anti-E-Cadherin Takara Cat#M108 Alexa Fluor 488-conjugated rabbit anti-GFP Thermo Fisher Cat#A-21311; RRID:AB_221477 Goat anti-GFP Abcam ab6673; RRID:AB_305643 Alexa Fluor 488-conjugated mouse anti-BrdU Thermo Fisher Cat#B35139; RRID:AB_2536439 PECy7-conjugated rat anti-KIT Biolegend Cat#105814; RRID:AB_313223 Alexa Fluor 647-conjugated rat anti-CD9 Biolegend Cat#124810; RRID:AB_2076037 Donkey polyclonal anti-rat IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#712-546-153; RRID:AB_2340686 Donkey polyclonal anti-rat IgG (Alexa Fluor 647) Jackson ImmunoResearch Cat#712-606-153; RRID:AB_2340696 Donkey polyclonal anti-rabbit IgG (Alexa Fluor 488) Jackson ImmunoResearch Cat#711-546-152; RRID:AB_2340619 Donkey polyclonal anti-rabbit IgG (Cy3) Jackson ImmunoResearch Cat#711-166-152; RRID:AB_2313568 Donkey polyclonal anti-goat IgG (Alexa Fluor 594) Thermo Fisher Cat#A32758; RID:AB_2762828 PE-conjugated goat anti-rat IgG BD Cat#550767; RRID:AB_393876 Biotin-conjugated rat IgG Biolegend Cat#400403; RRID:AB_326509 Control Alexa Fluor 647-conjugated goat IgG Bioss antibodies Cat#bs-0294P-A647 Chemicals, peptides, and recombinant proteins Alexa Fluor 488 NHS Ester Thermo Cat#A20181 Alexa Fluor 647 NHS Ester Thermo Cat#A20186 DyLight 488-conjugated streptavidin Vector Cat#SA-5488; RRID:AB_2336405 Brilliant Violet 421-conjugated streptavidin Biolegend Cat#405225 4OH-Tamoxifen Sigma Cat#H6278 Tamoxifen Tronto Research Chemicals Cat#T006000 EdU Tokyo Kasei Cat#E1057 BrdU Tokyo Kasei Cat#B1575 CF405M azide Biotium Cat#92092 Trypsin SIGMA Cat #59427C Blocking One Histo Nacalai Tesque Cat #06349-64 Can Get Signal Solution 1&2 Toyobo Cat#NKB-101 Type 1 collagenase Worthington Cat#CLS1 ISOGEN Nippon Gene Cat#311-02501 Recombinant human FGF2 PeproTech Cat#100-18B Recombinant human FGF5 R&D Cat#237-F5 Recombinant rat GDNF PeproTech Cat#076-06121 Critical commercial assays Click-iT EdU Alexa Fluor 647 imaging Kit Thermo Fisher Cat#C10340 Single Cell-to-CT Kit Thermo Fisher Cat#4458237 (Continued on next page) e1 Cell Reports 37, 109875, October 19, 2021 .. Reagent or resource Source Identifier C1 Single-Cell Auto Prep Reagent kit Fluidigm Cat100-6201 GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit Fluidigm Cat#100-3415 SuperScript VILO Thermo Fisher Cat#11755050 Power SYBR Green PCR Master mix Thermo Fisher Cat#4367659 THUNDERBIRD SYBR qPCR Mix Toyobo Cat#QPS-201 SsoFast EvaGreen Supermix with Low ROX Bio-Rad Cat#172-5212 Deposited data Single cell RNA sequencing data (La et al., 2018) accession number GSE107256 Experimental models: Organisms/strains PlvapCreERT2 mice This study N/A Sox3-CreERT2 mice This study N/A Ngn3-CreERTM mice (Yoshida et al., 2006) N/A CAG-CAT-EGFP mice (Kawamoto et al., 2000) N/A CAG-EGFP mice (Okabe et al., 1997) N/A GFRa1-GFP mice (Uesaka et al., 2007) N/A Ngn3-EGFP mice (Yoshida et al., 2004) N/A TnEGFP-CreERt2 mice (Imuta et al., 2013) N/A Flipper mice The Jackson Laboratory JAX 003946 C57BL/6J mice CLEA Japan, Japan SLC N/A DBA/2 mice CLEA Japan N/A Recombinant DNA IRES sequence from pEF1a-IRES-AcGFP1 vector Takara Cat #631971 Software and algorithms BD FACS Diva 6.1 and 8.0 BD https://www.bdbiosciences.com/ja-jp/products/software/ instrument-software/bd-facsdiva-software Flowlogic 7 Milteny https://www.miltenyibiotec.com/products/macs-flow- cytometry/software/macsquantify.html PhotoshopCC 17.0.0 Adobe https://www.adobe.com/jp/products/photoshop.html Illustrator 20.0.0 Adobe https://www.adobe.com/jp/products/illustrator.html Affinity designer 1.8.4 AFFINITY https://affinity.serif.com/ja-jp/ Microsoft Excel for Mac 15.32 and 16.46 Microsoft https://www.office.com/ R (v4.0.3) R Foundation for Statistical Computing https://www.r-project.org/ scran (v1.12.1) (Lun et al., 2016) https://bioconductor.org/packages/release/bioc/ html/scran.html scater (1.18.6) (McCarthy et al., 2017) https://bioconductor.org/packages/release/bioc/ html/scater.html Seurat (v3.0.2) (Stuart et al., 2019) https://satijalab.org/seurat/ igraph (v1.2.4.1) Gábor Csárdi https://igraph.org/r/ pheatmap (v1.0.12) Raivo Kolde https://cran.r-project.org/web/packages/pheatmap/ slingshot (v1.9.1) (Street et al., 2018) https://github.com/kstreet13/slingshot bluster (v1.0.0) Aaron Lun http://www.bioconductor.org/packages/release/bioc/ html/bluster.html Codes for clonal simulations This study https://doi.org/10.5281/zenodo.5515900 Other BAC Clone Thermo Fisher RP23-150I6 C1 Single-Cell Auto Prep Array for PreAmp Fluidigm Cat#100-5480 96:96 dynamic array chips Fluidigm Cat#BMK-M10-96.96-EG Cell Reports 37, 109875, October 19, 2021 e2 ..

    Lysis:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: The sorted single cells (a 10:1 mixture of EGFP+E-Cadherin+CD9+KIT-/low and EGFP–E-Cadherin+CD9+KIT-/low Aundiff fractions) were captured individually on a C1 Single-Cell Auto Prep Array for PreAmp (Fluidigm) designed for 10- to 17-um cells using a Fluidigm C1 system (Fluidigm). .. Cell lysis, cDNA synthesis, and preamplification were performed using Single Cell-to-CT Kit (Thermo), C1 Single-Cell Auto Prep Reagent kit, and specific primers for arbitrarily selected target genes (Table S2). qPCR were performed on a 96:96 dynamic array chips (Fluidigm) using GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit (Fluidigm), and SsoFast EvaGreen Supermix with Low ROX (Bio-Rad), in a Biomark HD system (Fluidigm) platform, following the manufacturer’s instructions. .. The Raw data from 60 cells were analyzed in RStudio software (https://www.rstudio. com/).

    cDNA Synthesis:

    Article Title: A multistate stem cell dynamics maintains homeostasis in mouse spermatogenesis.
    Article Snippet: The sorted single cells (a 10:1 mixture of EGFP+E-Cadherin+CD9+KIT-/low and EGFP–E-Cadherin+CD9+KIT-/low Aundiff fractions) were captured individually on a C1 Single-Cell Auto Prep Array for PreAmp (Fluidigm) designed for 10- to 17-um cells using a Fluidigm C1 system (Fluidigm). .. Cell lysis, cDNA synthesis, and preamplification were performed using Single Cell-to-CT Kit (Thermo), C1 Single-Cell Auto Prep Reagent kit, and specific primers for arbitrarily selected target genes (Table S2). qPCR were performed on a 96:96 dynamic array chips (Fluidigm) using GE 96.96 Dynamic Array DNA Binding Dye Sample & Loading Reagent Kit (Fluidigm), and SsoFast EvaGreen Supermix with Low ROX (Bio-Rad), in a Biomark HD system (Fluidigm) platform, following the manufacturer’s instructions. .. The Raw data from 60 cells were analyzed in RStudio software (https://www.rstudio. com/).

    Article Title: Three Types of Functional Regulatory T Cells Control T Cell Responses at the Human Maternal-Fetal Interface.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD3-PerCP; UCHT1 Biolegend RRID:AB_893300; Cat #300427 CD3-LEAF purified; SPV-T3B ThermoFisher RRID:AB_2532975; Cat #07-0303 CD4-PerCp; SK3 Biolegend RRID:AB_2563326; Cat #344624 CD4-Alexa700; SK3 Biolegend RRID:AB_2563150; Cat #344622 CD8-APC; SK1 Biolegend RRID:AB_2616624; Cat #980904 CD8-Alexa700; SK1 Biolegend RRID:AB_2562790; Cat #344724 CD8-Pacific Orange; 3B5 Invitrogen RRID:AB_10372066; Cat #MHCD0830 CD14-PerCp; HCD14 Biolegend RRID:AB_2564058; Cat #301847 CD14-PE-TexasRed; TuK4 Invitrogen RRID:AB_10373552; Cat #MHCD1417 CD25-PE; 2A3 BD Biosciences RRID:AB_2783790; Cat #341011 CD39-FITC; A1 Biolegend RRID:AB_940423; Cat #328205 CD45-Pacific Orange; HI30 Invitrogen RRID:AB_10376143; Cat #MHCD4530 CD45-APC; HI30 Biolegend RRID:AB_2562049; Cat #304037 CD45-PerCp; HI30 Biolegend RRID:AB_893341; Cat #304025 CD45RA-Alexa700; HI100 Biolegend RRID:AB_493762; Cat #304119 CD56-PE; HCD56 Biolegend RRID:AB_604093; Cat #318305 CTLA4-PE-Cy7; BNI3 Biolegend RRID:AB_2632876; Cat #369614 EGFR1-FITC; AY13 Biolegend RRID:AB_11124324; Cat #352907 FOXP3-Pacific Blue; 259D BioLegend RRID:AB_940354; Cat #320215 GITR-APC; DT5D3 Milteny Biotec RRID:AB_2751597; Cat #130-118-997 HELIOS-Alexa488; 22F6 Biolegend RRID:AB_10645334; Cat #137213 HLA-DR-LEAF purified; L243 Biolegend RRID:AB_314680; Cat #307602 HLA-G-PE; MEM/G9 Abcam RRID:AB_448029; Cat #ab24384 HLA-G-LEAF purified; 87G Biolegend RRID:AB_10641840; Cat #335904 IFNg-APC; B27 Biolegend RRID:AB_315443; Cat #506510 IL-10-PE-Cy7; JES3-9D7 Biolegend RRID:AB_2280292; Cat #501419 IL-10R-LEAF purified; 3F9 Biolegend RRID:AB_314737; Cat #308805 IL-2-PE; MQ1-17H12 Biolegend RRID:AB_315093; Cat #500306 ILT2-LEAF purified; GHI/75 Biolegend RRID:AB_1089089; Cat #333702 LRRC32-APC; 7B11 Biolegend RRID:AB_10896059; Cat #352505 PD1-PE-Cy7; EH12.1 BD Biosciences RRID:AB_10611585; Cat #561272 PDL1-LEAF purified; 29E.2A3 Biolegend RRID:AB_940370; Cat #329701 TGFb1-LEAF purified; 19D8 Biolegend RRID:AB_2561694; Cat #521703 TIGIT-APC; MBSA43 eBioscience RRID:AB_2573305; Cat #17-9500-42 TIGIT-PerCp-eFlour710; MBSA43 eBioscience RRID:AB_10853679; Cat #46-9500-42 TIM3-FITC; F38-2E2 Biolegend RRID:AB_2563936; Cat #345021 TNFa- Pacific Blue; MAb11 Biolegend RRID:AB_528965; Cat #502920 Bacterial and Virus Strains HCMV-AD169-GFP (IE-1-GFP) Donald Coen, Harvard Medical School N/A Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Peprotech Cat #200-02 Recombinant human EGF Peprotech Cat #AF-100-15 (Continued on next page) e1 Cell Reports 27, 2537–2547.e1–e5, May 28, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fibronectin Corning Cat #354008 Insulin-Transferrin-Selenium (ITS-G) (100X) GIBCO Cat #41400-045 Human gonadotropic hormone (HcG) Sigma-Aldrich Cat #C1063 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat #P1585 Ionomycin Sigma Cat #I9657 Collagenase type IV Sigma-Aldrich Cat #C5138 DNase I Sigma Cat #DN25 Percoll GE Healthcare Cat #17-5445-02 DNA suspension buffer TEKnova Cat #T0220 Human AB serum Corning Cat #35060CI New Born Calf Serum GIBCO Cat #16010159 Exonuclease I New England BioLabs Cat #M0568S Critical Commercial Assays RosetteSep human CD4+ enrichment cocktail Stem Cell Technologies Cat #15022 Dynabeads Human T-Activator CD3/CD28 Thermofisher Cat #111.31D CytoFix/CytoPermTM Plus kit BD Biosciences Cat #555028 RNAeasy Micro Kit Qiagan Cat #74004 AffinityScript QPCR cDNA Synthesis Kit Agilent Cat #600559 PerfeCTa SYBR Green SuperMix Low ROX QuantaBio Cat #:95056-100 BioMark Fluidigm QPCR 96.96 chip Fluidigm Cat #:BMK-M-96.96 Fluidigm PreAmp Master mix Fluidigm Cat #:100-5580 DNA binding dye sample and assay loading reagent kit Fluidigm Cat #: 100-3415 SsoFast EvaGreen supermix with low ROX BioRad Cat #: 1725210 Oligonucleotides See Table S1 for primers used in this study Software and Algorithms BD FACSDIVA Software BD Biosciences http://www.bdbiosciences.com/us/ instruments/research/software/flowcytometry-acquisition/bd-facsdivasoftware/m/111112/features FlowJo Software FlowJo https://www.flowjo.com/ Prism GraphPad software Prism https://www.graphpad.com/ scientific-software/prism/ Fluidigm BioMark Real-Time PCR analysis software Fluidigm https://www.fluidigm.com/software GenePattern/ Express Cluster V1.3 software GenePattern https://cloud.genepattern.org/gp http://cbdm.hms.harvard.edu/resources.htm Microsoft Excel Microsoft https://products.office.com/en-US/excel ..

    other:

    Article Title: CFTR Correctors and Antioxidants Partially Normalize Lipid Imbalance but not Abnormal Basal Inflammatory Cytokine Profile in CF Bronchial Epithelial Cells
    Article Snippet: Fluidigm-based protein array analysis (Olink 96x96 IMMUNO/ONCOLOGY) was applied to basal medium 24 h after changing the medium (BEGM-EGF) (see methods).

    High Throughput Screening Assay:

    Article Title: Transversal gene expression panel to evaluate intestinal health in broiler chickens in different challenging conditions
    Article Snippet: .. High throughput RT-qPCR was performed in a 48.48 microfluidic dynamic array IFC chip in a BioMark HD System (Fluidigm Corporation) . ..

    Quantitative RT-PCR:

    Article Title: Transversal gene expression panel to evaluate intestinal health in broiler chickens in different challenging conditions
    Article Snippet: .. High throughput RT-qPCR was performed in a 48.48 microfluidic dynamic array IFC chip in a BioMark HD System (Fluidigm Corporation) . ..

    Suspension:

    Article Title: Three Types of Functional Regulatory T Cells Control T Cell Responses at the Human Maternal-Fetal Interface.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD3-PerCP; UCHT1 Biolegend RRID:AB_893300; Cat #300427 CD3-LEAF purified; SPV-T3B ThermoFisher RRID:AB_2532975; Cat #07-0303 CD4-PerCp; SK3 Biolegend RRID:AB_2563326; Cat #344624 CD4-Alexa700; SK3 Biolegend RRID:AB_2563150; Cat #344622 CD8-APC; SK1 Biolegend RRID:AB_2616624; Cat #980904 CD8-Alexa700; SK1 Biolegend RRID:AB_2562790; Cat #344724 CD8-Pacific Orange; 3B5 Invitrogen RRID:AB_10372066; Cat #MHCD0830 CD14-PerCp; HCD14 Biolegend RRID:AB_2564058; Cat #301847 CD14-PE-TexasRed; TuK4 Invitrogen RRID:AB_10373552; Cat #MHCD1417 CD25-PE; 2A3 BD Biosciences RRID:AB_2783790; Cat #341011 CD39-FITC; A1 Biolegend RRID:AB_940423; Cat #328205 CD45-Pacific Orange; HI30 Invitrogen RRID:AB_10376143; Cat #MHCD4530 CD45-APC; HI30 Biolegend RRID:AB_2562049; Cat #304037 CD45-PerCp; HI30 Biolegend RRID:AB_893341; Cat #304025 CD45RA-Alexa700; HI100 Biolegend RRID:AB_493762; Cat #304119 CD56-PE; HCD56 Biolegend RRID:AB_604093; Cat #318305 CTLA4-PE-Cy7; BNI3 Biolegend RRID:AB_2632876; Cat #369614 EGFR1-FITC; AY13 Biolegend RRID:AB_11124324; Cat #352907 FOXP3-Pacific Blue; 259D BioLegend RRID:AB_940354; Cat #320215 GITR-APC; DT5D3 Milteny Biotec RRID:AB_2751597; Cat #130-118-997 HELIOS-Alexa488; 22F6 Biolegend RRID:AB_10645334; Cat #137213 HLA-DR-LEAF purified; L243 Biolegend RRID:AB_314680; Cat #307602 HLA-G-PE; MEM/G9 Abcam RRID:AB_448029; Cat #ab24384 HLA-G-LEAF purified; 87G Biolegend RRID:AB_10641840; Cat #335904 IFNg-APC; B27 Biolegend RRID:AB_315443; Cat #506510 IL-10-PE-Cy7; JES3-9D7 Biolegend RRID:AB_2280292; Cat #501419 IL-10R-LEAF purified; 3F9 Biolegend RRID:AB_314737; Cat #308805 IL-2-PE; MQ1-17H12 Biolegend RRID:AB_315093; Cat #500306 ILT2-LEAF purified; GHI/75 Biolegend RRID:AB_1089089; Cat #333702 LRRC32-APC; 7B11 Biolegend RRID:AB_10896059; Cat #352505 PD1-PE-Cy7; EH12.1 BD Biosciences RRID:AB_10611585; Cat #561272 PDL1-LEAF purified; 29E.2A3 Biolegend RRID:AB_940370; Cat #329701 TGFb1-LEAF purified; 19D8 Biolegend RRID:AB_2561694; Cat #521703 TIGIT-APC; MBSA43 eBioscience RRID:AB_2573305; Cat #17-9500-42 TIGIT-PerCp-eFlour710; MBSA43 eBioscience RRID:AB_10853679; Cat #46-9500-42 TIM3-FITC; F38-2E2 Biolegend RRID:AB_2563936; Cat #345021 TNFa- Pacific Blue; MAb11 Biolegend RRID:AB_528965; Cat #502920 Bacterial and Virus Strains HCMV-AD169-GFP (IE-1-GFP) Donald Coen, Harvard Medical School N/A Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Peprotech Cat #200-02 Recombinant human EGF Peprotech Cat #AF-100-15 (Continued on next page) e1 Cell Reports 27, 2537–2547.e1–e5, May 28, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fibronectin Corning Cat #354008 Insulin-Transferrin-Selenium (ITS-G) (100X) GIBCO Cat #41400-045 Human gonadotropic hormone (HcG) Sigma-Aldrich Cat #C1063 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat #P1585 Ionomycin Sigma Cat #I9657 Collagenase type IV Sigma-Aldrich Cat #C5138 DNase I Sigma Cat #DN25 Percoll GE Healthcare Cat #17-5445-02 DNA suspension buffer TEKnova Cat #T0220 Human AB serum Corning Cat #35060CI New Born Calf Serum GIBCO Cat #16010159 Exonuclease I New England BioLabs Cat #M0568S Critical Commercial Assays RosetteSep human CD4+ enrichment cocktail Stem Cell Technologies Cat #15022 Dynabeads Human T-Activator CD3/CD28 Thermofisher Cat #111.31D CytoFix/CytoPermTM Plus kit BD Biosciences Cat #555028 RNAeasy Micro Kit Qiagan Cat #74004 AffinityScript QPCR cDNA Synthesis Kit Agilent Cat #600559 PerfeCTa SYBR Green SuperMix Low ROX QuantaBio Cat #:95056-100 BioMark Fluidigm QPCR 96.96 chip Fluidigm Cat #:BMK-M-96.96 Fluidigm PreAmp Master mix Fluidigm Cat #:100-5580 DNA binding dye sample and assay loading reagent kit Fluidigm Cat #: 100-3415 SsoFast EvaGreen supermix with low ROX BioRad Cat #: 1725210 Oligonucleotides See Table S1 for primers used in this study Software and Algorithms BD FACSDIVA Software BD Biosciences http://www.bdbiosciences.com/us/ instruments/research/software/flowcytometry-acquisition/bd-facsdivasoftware/m/111112/features FlowJo Software FlowJo https://www.flowjo.com/ Prism GraphPad software Prism https://www.graphpad.com/ scientific-software/prism/ Fluidigm BioMark Real-Time PCR analysis software Fluidigm https://www.fluidigm.com/software GenePattern/ Express Cluster V1.3 software GenePattern https://cloud.genepattern.org/gp http://cbdm.hms.harvard.edu/resources.htm Microsoft Excel Microsoft https://products.office.com/en-US/excel ..



    Similar Products

    renal chip array  (Mimetas Inc)
    86
    Mimetas Inc renal chip array
    Renal Chip Array, supplied by Mimetas Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip+array+assay/array+chip+renal/pmc12805313-461-3-9
    Average 86 stars, based on 1 article reviews
    renal chip array - by Bioz Stars, 2026-09
    86/100 stars
    		  Buy from Supplier
    cytokine chip array kit  (Randox)
    95
    Randox cytokine chip array kit
    Cytokine Chip Array Kit, supplied by Randox, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip+array+assay/CYTOKINE+ARRAY/pm41974355-96-19-25
    Average 95 stars, based on 1 article reviews
    cytokine chip array kit - by Bioz Stars, 2026-09
    95/100 stars
    		  Buy from Supplier
    dynamic array integrated fluidic circuit ifc chips  (fluidigm)
    94
    fluidigm dynamic array integrated fluidic circuit ifc chips
    Dynamic Array Integrated Fluidic Circuit Ifc Chips, supplied by fluidigm, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip+array+assay/48%2E48+Dynamic+Array+IFC+for+Gene+Expression/pm41866099-141-7-22
    Average 94 stars, based on 1 article reviews
    dynamic array integrated fluidic circuit ifc chips - by Bioz Stars, 2026-09
    94/100 stars
    		  Buy from Supplier
    array ifc chip  (fluidigm)
    94
    fluidigm array ifc chip
    Array Ifc Chip, supplied by fluidigm, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip+array+assay/48%2E48+Dynamic+Array+IFC+for+Gene+Expression/pmc12858333-209-35-38
    Average 94 stars, based on 1 article reviews
    array ifc chip - by Bioz Stars, 2026-09
    94/100 stars
    		  Buy from Supplier
    dynamicarray 96 96 chips  (fluidigm)
    95
    fluidigm dynamicarray 96 96 chips
    Dynamicarray 96 96 Chips, supplied by fluidigm, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip+array+assay/96%2E96+Dynamic+Array+IFC+for+Gene+Expression/pm41326455-110-26-29
    Average 95 stars, based on 1 article reviews
    dynamicarray 96 96 chips - by Bioz Stars, 2026-09
    95/100 stars
    		  Buy from Supplier
    array ifc chip format  (fluidigm)
    95
    fluidigm array ifc chip format
    Array Ifc Chip Format, supplied by fluidigm, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip+array+assay/96%2E96+Dynamic+Array+IFC+for+Gene+Expression/pmc12691114-83-19-23
    Average 95 stars, based on 1 article reviews
    array ifc chip format - by Bioz Stars, 2026-09
    95/100 stars
    		  Buy from Supplier
    dynamic array chips  (fluidigm)
    95
    fluidigm dynamic array chips
    Dynamic Array Chips, supplied by fluidigm, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip+array+assay/96%2E96+Dynamic+Array+IFC+for+Gene+Expression/pmc12615833__41467_2025_64998_MOESM1_ESM-68-0-5
    Average 95 stars, based on 1 article reviews
    dynamic array chips - by Bioz Stars, 2026-09
    95/100 stars
    		  Buy from Supplier
    access array ifc chip  (fluidigm)
    93
    fluidigm access array ifc chip
    Access Array Ifc Chip, supplied by fluidigm, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip+array+assay/Access+Array/pmc12676078-90-4-3
    Average 93 stars, based on 1 article reviews
    access array ifc chip - by Bioz Stars, 2026-09
    93/100 stars
    		  Buy from Supplier

    Image Search Results