| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Biotin anti-mouse CD9 Antibody (Clone MZ3; 1 μg/106 cells) | Biolegend | Cat# 124804 |
| Biotin Rat IgG2a, κ Isotype Ctrl Antibody (Clone RTK2758; 1μg/106 cells) | Biolegend | Cat# 400504 |
| Streptavidin-APC (0.5μg/106 cells) | Biolegend | Cat# 405207 |
| APC Anti-Human HLA-ABC (Clone G46–2.6; 20μl/106 cells) | BD Biosciences | Cat# 562006 |
| APC Mouse IgG1 κ Isotype Control (Clone MOPC-21; 20μl/106 cells) | BD Biosciences | Cat# 555751 |
| APC anti-human CD49e Antibody (Clone NKI-SAM-1; 20μl/106 cells) | Biolegend | Cat# 328011 |
| APC Mouse IgG2b, κ Isotype Ctrl Antibody (Clone MPC-11; 10μl/106 cells) | Biolegend | Cat# 400321 |
| Biotin Mouse Anti-Human CD90 (Clone 5E10, 1μg/106 cells) | BD PharMingen | Cat# 555594 |
| Biotin Mouse IgG1 κ Isotype Control (Clone MOPC-21; 2μl/106 cells) | BD PharMingen | Cat# 555747 |
| PE/Cy7 Streptavidin (2.5μl/106 cells) | Biolegend | Cat# 405206 |
| Pacific Blue anti-human/mouse CD49f Antibody (Clone GoH3; 20μl/106 cells) | Biolegend | Cat# 313619 |
| Pacific Blue Rat IgG2a, κ Isotype Ctrl Antibody (Clone RTK2758; 8μl/106 cells) | Biolegend | Cat# 400527 |
| PE anti-human CD326 (EpCAM) Antibody (Clone 9C4; 20μl/106 cells) | Biolegend | Cat# 324205 |
| PE Mouse IgG2b, κ Isotype Ctrl Antibody (Clone MPC-11; 2.5μl/106 cells) | Biolegend | Cat# 400313 |
| Alexa Fluor 488 anti-human SSEA-4 Antibody (Clone MC813–70; 5μl/106 cells) | Biolegend | Cat# 330412 |
| Alexa Fluor 488 Mouse IgG3, κ Isotype Ctrl Antibody (Clone MG3–35; 4μl/106 cells) | Biolegend | Cat# 401324 |
| Rabbit anti-KCTD9 antibody [EPR13909], 0.142 μg/ml | Abcam | Cat# ab180937 |
| Donkey Anti-Rabbit IgG H&L (Alexa Fluor 555) preadsorbed, 1:500; Figure S1I & NDRG4 (Figure 6L) | Abcam | Cat# ab150062 |
| Rat anti-Germ cell-specific antigen antibody [TRA98], 1 Rabbit anti-KCTD9 antibody μg/ml; Figure S1I | Abcam | Cat# ab82527 |
| Donkey Anti-Rat Alexa Fluor 647 (IgG H&L) preadsorbed; 1:500; Figure S1I | Abcam | Cat# ab150155 |
| Goat anti-GATA4 antibody (C-20), 2 μg/ml; Figures 6K and S1H | Santa Cruz | Cat# sc-1237 |
| Donkey anti-Goat IgG (H+L) Cross-Adsorbed, Alexa Fluor 555; 1:500; Figures 6K (GFRA1), S1H (GATA4), and S6C (GATA4) | ThermoFisher Scientific | Cat# A21432 |
| Rabbit anti-DDX4/MVH antibody (1 μg/ml); Figures S1J and S2Q | Abcam | Cat# ab13840 |
| Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed, Alexa Fluor 647; 1:500; Figures S1J and S2Q | ThermoFisher Scientific | Cat# A31573 |
| Goat anti-GFRA1 antibody, 0.25 μg/ml; Figure 6K | R&D Systems | Cat# AF560 |
| Rabbit anti-NDRG4 antibody; Figure 6L | Proteintech | Cat# 12184–1-AP |
| Goat anti-Human VASA antibody (diluted to 2μg/ml); Figure S2N | R&D Systems | Cat# AF2030 |
| Donkey anti-Goat IgG (H+L) Cross-Adsorbed, Alexa Fluor 568 (diluted 1:200); Figure S2N | ThermoFisher Scientific | Cat# A11057 |
| Rabbit anti-SOX9 antibody (diluted to 4μg/ml); Figure S2N | EMD Millipore | Cat# AB5535 |
| Donkey anti-Rabbit IgG (H+L) Cross-Adsorbed, Alexa Fluor 488 (diluted 1:200); Figure S2N | ThermoFisher Scientific | Cat# A21206 |
| Rabbit Anti-DUSP6 antibody [EPR129Y] (diluted to 2.5μg/ml); Figure S3I | Abcam | Cat# 76310 |
| chicken anti-rabbit IgG-Biotin; Figure S3I | Santa Cruz Biotechnology | Cat# sc-2986 |
| Streptavidin HRP; Figure S3I | Sigma-Aldrich | Cat# S5512 |
| Rabbit Anti-RHCG antibody (diluted to 4μg/ml); Figure S4J | GeneTex | Cat# GTX60193 |
| Goat anti-Rabbit IgG (H+L) Cross-Adsorbed, Alexa Fluor 488 (diluted 1:200); Figure S4J | ThermoFisher Scientific | Cat# A11108 |
| Rabbit anti-ACTL7B antibody (diluted 1:750); Figures S5I and S5J. | Proteintech Group | Cat#13537–1-AP |
| Biological Samples | ||
| Human testicular tissue biopsies | Infertility Center of St. Louis | Table S5 |
| Human testicular tissue from organ donors | University of Texas Transplant Center & Texas Organ Sharing Alliance | Table S5 |
| Critical Commercial Assays | ||
| Chromium Single Cell 3’ v2 Reagent Kits & Chip Kits | 10X Genomics | Cat#s 120237,120267, 1000009, 120236 |
| SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (v2) | Takara/Clontech | Cat#s 634832, 634833 |
| Deposited Data | ||
| Raw and analyzed P6 ID4-EGFP spermatogonia C1 scRNA-seq data | This paper | GEO: GSE108970 |
| Raw and analyzed Adult ID4-EGFP spermatogonia C1 scRNA-seq data | This paper | GEO: GSE108974 |
| Raw and analyzed Adult Human Spermatogonia C1 scRNA-seq data | This paper | GEO: GSE108977 |
| Raw and analyzed P6 ID4-EGFP testis and spermatogonia 10X Genomics Drop-Seq data | This paper | GEO: GSE109049 |
| Raw and analyzed Adult Mouse spermatogenic cell 10X Genomics Drop-Seq data | This paper | GEO: GSE109033 |
| Raw and analyzed Adult Human spermatogenic cell 10X Genomics Drop-Seq data | This paper | GEO: GSE109037 |
| Mendeley Data - Queryable single-cell RNA-seq (Drop-Seq) datasets of Human and Mouse spermatogenic cells; Loupe Cell Browser files (from 9 datasets) for easy retrieval and interrogation of the resource data in this manuscript. | This paper | Mendeley Data: https://doi.org/10.17632/kxd5f8vpt4.1 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | JAX:000664 |
| Mouse: C57BL/6NTac | Taconic Farms | TAC:b6 |
| Mouse: B6-Cg-Id4-Egfp(LT-11) | Chan et al., 2014 | N/A |
| Mouse: B6;129S-Gt(ROSA)26Sor/J | Friedrich and Soriano, 1991 | JAX:002073 |
| Mouse: 129S1/SvImJ | The Jackson Laboratory | JAX:002448 |
| Oligonucleotides | ||
| Primers for qRT-PCR (Figure 7) | This paper | Table S7 |
| Software and Algorithms | ||
| FlowJo v9 | FlowJo, LLC | N/A |
| AxioVision 4.8.2 | Zeiss | N/A |
| Galaxy | Giardine et al., 2005; https://usegalaxy.org | SCR_006281 |
| TopHat (Galaxy v0.9) | Trapnell et al., 2012 | SCR_013035 |
| Cufflinks/Cuffnorm (Galaxy v.2.2.1.0) | Trapnell et al., 2012 | SCR_014597 |
| Picard tools (Collectrnaseqmetrics) | Broad Institute, http://broadinstitute.github.io/picard | SCR_007073 |
| SINGuLar analysis toolset 3.1 | Fluidigm | SCR_015685 |
| Seurat2.3.0 | Butler, 2018. https://github.com/satijalab/seurat | N/A |
| Monocle2 | Trapnell et al., 2014 and Qiu et al., 2017. http://cole-trapnelllab.github.io/monocle-release/ | N/A |
| Ingenuity Pathway Analysis, Build 477929M, Content versions 43605602 (3/2018) and 44691306 (6/2018) | QIAGEN | SCR_008653 |
| Cell Ranger v1.3.0 and v2.0.1 | 10X Genomics, https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest | N/A |
| Loupe Cell Browser v2.0.0 | 10X Genomics, https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest | N/A |
| Cell Ranger R kit v2.0.0 | 10X Genomics, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/rkit | N/A |
| Real-time PCR Analysis Software | Fluidigm | SCR_015686 |
| Other | ||
| Human reference genome NCBI build 37, GRCh37 (hg19) | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/ |
| Mouse reference genome NCBI build 38, GRCm38 (mm10) | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/ |
| Human reference GRCh38 dataset required for Cell Ranger, v1.2.0 | 10X Genomics, https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest | N/A |
| Mouse reference GRCm38 (mm10) dataset required for Cell Ranger, v1.2.0 | 10X Genomics, https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest | N/A |
| Human GRCh37 (hg19) and Mouse GRCm38 (mm10) reference dataset required for Cell Ranger, v1.2.0 | 10X Genomics, https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest | N/A |
Official websites use .gov
A
.gov website belongs to an official
government organization in the United States.
Secure .gov websites use HTTPS
A lock (
) or https:// means you've safely
connected to the .gov website. Share sensitive
information only on official, secure websites.