bmp7 r d systems  (R&D Systems)

Journal: eLife

Article Title: Altered temporal sequence of transcriptional regulators in the generation of human cerebellar granule cells

doi: 10.7554/elife.67074

Figure Lengend Snippet: Figure 1. Derivation of the human ATOH1 lineage. (A) EN2 expression (log10 fold change of no CHIR99021) in dual SMAD+FGF2-treated human pluripotent stem cells (hPSCs) in the absence and presence of CHIR99021 by RT-qPCR at day in vitro (DIV) 11. (B) ATOH1 expression (fold change of no BMP7) at DIV16 in response to a BMP7 concentration series added at DIV7–15. (C) Dot plot showing the coefficient of variance of mean ATOH1 expression detected by RT-qPCR at DIV16 in cultures grown on regular tissue culture dishes (-BMP7, blue) versus on transwell membranes (-BMP7,

Article Snippet: 67074 15 of 28 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Sequence- based reagent LHX2 This paper PCR primer Forward 5′- GGTCCTC CAGGTCT GGTTC- 3′ Sequence- based reagent LHX2 This paper PCR primer Reverse 5′- TAAGAG GTTGCGC CTGAACT- 3′ Sequence- based reagent LHX9 This paper PCR primer Forward 5′- GCT GGGAGT GGACATCGTCA- 3′ Sequence- based reagent LHX9 This paper PCR primer Reverse 5′- CATG GTCCGGA GCTGGTGAT- 3′ Sequence- based reagent β-ACTIN This paper PCR primer Forward 5′-AAAC TGGAAC GGTGAAGG- 3′ Sequence- based reagent β-ACTIN This paper PCR primer Reverse 5′-AGA GAAGT GGGGTGGCTT- 3′ Sequence- based reagent ATP5O This paper PCR primer Forward 5′- cgcta tgccac agctcttta- 3′ Sequence- based reagent ATP5O This paper PCR primer Reverse 5′- atgg aacgcttc acataggg- 3′ Peptide, recombinant protein Human bFGF Invitrogen Catalog # 13256- 029 Peptide, recombinant protein Human/mouse/ rat BDNF PeproTech Catalog # 450- 02 Peptide, recombinant protein Mouse BMP7 R&D Systems Catalog # 5666BP- 010 Peptide, recombinant protein Human recombinant insulin Tocris Catalog # 3435 Peptide, recombinant protein Human BMP4 R&D Systems Catalog # 314BP- 050 Peptide, recombinant protein Human BMP6 R&D Systems Catalog # 507BP- 020 Peptide, recombinant protein Human/mouse FGF8b R&D Systems Catalog # 423- F8- 025 Commercial assay or kit RNeasy micro kit QIAGEN Catalog # 74004 Commercial assay or kit RNeasy Plus mini kit QIAGEN Catalog # 74134 Commercial assay or kit Transcription First Strand cDNA Synthesis Kit Roche Life Sciences Catalog # 04379012001 Commercial assay or kit HotStarTaq PLUS DNA Polymerase kit QIAGEN Catalog # 203603 Commercial assay or kit Click- iT EdU Cell Proliferation Kit for Imaging Invitrogen Catalog # C10338 Commercial assay or kit SMART- Seq v4 Ultra Low Input RNA Kit TaKaRa Bio Catalog # 634888 Commercial assay or kit Nextera XT DNA library preparation kit Illumina Catalog # FC- 131- 1024 Commercial assay or kit RNA 6000 Pico Kit Agilent Catalog # 5067- 1513 Commercial assay or kit In- fusion HD cloning plus (Clontech) TaKaRa Bio Catalog # 638909 Continued Continued on next page Behesti et al. eLife 2021;10:e67074.

Techniques: Expressing, Quantitative RT-PCR, In Vitro, Concentration Assay

Journal: Cell stem cell

Article Title: LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis.

doi: 10.1016/j.stem.2020.06.017

Figure Lengend Snippet: Figure 1. LEFTY1 Expression Is Restricted to a Subset of Luminal Cells and Rare Basal Cells, while BMP7 Is Secreted Predominantly by Basal Cells (A) Left: representative FACS plot of the mouse mammary epithelial cell subpopulations stained with the indicated cell-surface markers. Different subpopulations are indicated as described in the color key. Right: Principal-component analysis reveals different subpopulations based on single-cell PCR analysis. (B) Hierarchically clustered analysis of single-cell PCR analysis of sorted mouse mammary epithelial populations. (C) Representative images of BMP7 protein staining of mammary glands isolated from 6- to 8-week-old WT mice. Scale bar, 20 mm. (D) Representative images of LEFTY1 protein staining of mammary glands isolated from 6- to 8-week-old WT mice. Scale bar, 20 mm. See also Figure S1.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant EGF Thermo Fisher Scientific Cat# PMG8043 Recombinant Noggin R&D Systems Cat# 6057-NG Growth Factor Reduced Matrigel BD Biociences Cat# 356230 Matrigel BD Biociences Cat# 356234 LEFTY-1 R&D Systems Cat# 994-LF BMP7 R&D Systems Cat# 5666-BP BMP2 R&D Systems Cat# 355-BM BMP4 R&D Systems Cat# 314-BP CRIPTO-1 R&D Systems Cat# 1538-CR NODAL R&D Systems Cat# 1315-ND Recombinant Human TGF-beta 1 Protein R&D Systems Cat#240-B-002 DAPI Sigma-Aldrich Cat# 32670 Dispase StemCell Technologies Cat#07913 Collagenase/Hyaluronidase StemCell Technologies Cat #07912 DNase I solution StemCell Technologies Cat#07900 Lefty Blocking Peptide Santa Cruz Biotechnolgy Cat# sc-365845 P LDN-193189 Selleckchem Cat# S2618 Critical Commercial Assays Dual-Luciferase Reporter Assay System Promega Cat#E1910 DUOLink Sigma Cat#921021 Pierce CO-IP Kit Thermo Fisher Scientific Cat#26147 Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 MDA-MD-157 ATCC Cat# HTB-24, RRID:CVCL_0618 3T3-L1 feeder cells Kindly provided by Dr. Nusse N/A L1-wnt3a feeder cells Kindly provided by Dr. Nusse N/A MDA-MB-231 ATCC Cat# HTB-26, RRID:CVCL_0062 COMMA-D beta cells Kindly provided by Dr. Medina Campbell et al., 1988 Experimental Models: Organisms/Strains C57BL/6 mice Jackson Laboratory Cat# JAX:000664, RRID:IMSR_JAX:000664 NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) Jackson Laboratory Cat# JAX:005557, RRID:IMSR_JAX:005557 pCx-GFP Kind gift of Dr. Irving Weissman N/A Oligonucleotides Cloning primers This paper Table S6 qRT-PCR primers This paper Table S6 Copy number determination primers This paper Table S6 Single cell assay ID This paper Table S3 Recombinant DNA pEIZ-HIV-ZsGreen Kind gift of Dr. Zena Werb N/A HIV-Lefty1-ZsG This paper N/A HIV-Che Shimono et al., 2009 N/A HIV-Bmp7-Che This paper N/A pGL3 BRE-luciferase Kind gift of Martine Roussel and Peter ten Dijike, Addgene #45126 pRL-TK Renilla luciferase vector Promega Cat# E2261 pEGFP-C3 (discontinued) Clontech Clontech Bmp7 cDNA clone Origene Cat# MC201085 clone pSICO-R Addgene Cat#12084 Lefty1 cDNA clone IMAGE Cat# 5221120 plasmid clone (Continued on next page) e2 Cell Stem Cell 27, 1–16.e1–e8, August 6, 2020

Techniques: Expressing, Staining, Isolation

Journal: Cell stem cell

Article Title: LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis.

doi: 10.1016/j.stem.2020.06.017

Figure Lengend Snippet: Figure 2. LEFTY1 Induces and BMP7 Reduces Ductal Branching and the Long-Term Proliferative Potential of Mammary Progenitor Cells (A) Schematic representation of procedure used to inject ligand-secreting L1 fibroblasts into the mammary fat pad followed by analysis of mammary glands. (B) Quantification of branches counted in glands exposed to the LEFTY1 (n = 6) or control (n = 7) group. Statistical analysis, Student’s t test. ***p < 0.001. Data are represented as mean ± SEM. (C) Quantification of branches counted in glands exposed to the BMP7 (n = 6) or control (n = 7) group. Statistical analysis, Student’s t test. *p < 0.05. Data are represented as mean ± SEM. (D) Representative images of the whole-mount staining of the indicated groups of mice. Magnification, 403. (E) Representative images of the organoids grown in the presence of BMP7, LEFTY1, or control (n = 7). Scale bar, 100 mm.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant EGF Thermo Fisher Scientific Cat# PMG8043 Recombinant Noggin R&D Systems Cat# 6057-NG Growth Factor Reduced Matrigel BD Biociences Cat# 356230 Matrigel BD Biociences Cat# 356234 LEFTY-1 R&D Systems Cat# 994-LF BMP7 R&D Systems Cat# 5666-BP BMP2 R&D Systems Cat# 355-BM BMP4 R&D Systems Cat# 314-BP CRIPTO-1 R&D Systems Cat# 1538-CR NODAL R&D Systems Cat# 1315-ND Recombinant Human TGF-beta 1 Protein R&D Systems Cat#240-B-002 DAPI Sigma-Aldrich Cat# 32670 Dispase StemCell Technologies Cat#07913 Collagenase/Hyaluronidase StemCell Technologies Cat #07912 DNase I solution StemCell Technologies Cat#07900 Lefty Blocking Peptide Santa Cruz Biotechnolgy Cat# sc-365845 P LDN-193189 Selleckchem Cat# S2618 Critical Commercial Assays Dual-Luciferase Reporter Assay System Promega Cat#E1910 DUOLink Sigma Cat#921021 Pierce CO-IP Kit Thermo Fisher Scientific Cat#26147 Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 MDA-MD-157 ATCC Cat# HTB-24, RRID:CVCL_0618 3T3-L1 feeder cells Kindly provided by Dr. Nusse N/A L1-wnt3a feeder cells Kindly provided by Dr. Nusse N/A MDA-MB-231 ATCC Cat# HTB-26, RRID:CVCL_0062 COMMA-D beta cells Kindly provided by Dr. Medina Campbell et al., 1988 Experimental Models: Organisms/Strains C57BL/6 mice Jackson Laboratory Cat# JAX:000664, RRID:IMSR_JAX:000664 NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) Jackson Laboratory Cat# JAX:005557, RRID:IMSR_JAX:005557 pCx-GFP Kind gift of Dr. Irving Weissman N/A Oligonucleotides Cloning primers This paper Table S6 qRT-PCR primers This paper Table S6 Copy number determination primers This paper Table S6 Single cell assay ID This paper Table S3 Recombinant DNA pEIZ-HIV-ZsGreen Kind gift of Dr. Zena Werb N/A HIV-Lefty1-ZsG This paper N/A HIV-Che Shimono et al., 2009 N/A HIV-Bmp7-Che This paper N/A pGL3 BRE-luciferase Kind gift of Martine Roussel and Peter ten Dijike, Addgene #45126 pRL-TK Renilla luciferase vector Promega Cat# E2261 pEGFP-C3 (discontinued) Clontech Clontech Bmp7 cDNA clone Origene Cat# MC201085 clone pSICO-R Addgene Cat#12084 Lefty1 cDNA clone IMAGE Cat# 5221120 plasmid clone (Continued on next page) e2 Cell Stem Cell 27, 1–16.e1–e8, August 6, 2020

Techniques: Control, Staining

Journal: Cell stem cell

Article Title: LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis.

doi: 10.1016/j.stem.2020.06.017

Figure Lengend Snippet: Figure 3. LEFTY1 Simultaneously Suppresses SMAD2 and SMAD5 in Basal Cells (A) Quantification of pSMAD2-positive cells within the luminal and basal compartments of endogenous ductal structures exposed to LEFTY1-secreting fibro- blasts. Data are represented as mean ± SD. Statistical analysis, Student’s t test. ****p < 0.0001. (B) Quantification of pSMAD2-positive cells within the luminal and basal compartments of endogenous ductal structures exposed to BMP7-secreting fibroblasts. Data are represented as mean ± SD. Statistical analysis, Student’s t test. n.s., non-significant. (C) Quantification of pSMAD5-positive cells within the luminal and basal compartments of endogenous ductal structures exposed to LEFTY1-secreting fibro- blasts. Data are represented as mean ± SD. Statistical analysis, Student’s t test. *p < 0.05; ****p < 0.0001. (D) Quantification of pSMAD5-positive cells within the luminal and basal compartments of endogenous ductal structures exposed to BMP7-secreting fibroblasts. Data are represented as mean ± SD. Statistical analysis, Student’s t test. *p < 0.05; n.s., non-significant. (E) Representative images of the quantified sections for pSMAD2 analysis of mammary glands exposed to LEFTY1-secreting fibroblasts. (F) Representative images of the quantified sections for pSMAD5 analysis of mammary glands exposed to LEFTY1-secreting fibroblasts. (G) Representative images of the quantified sections for pSMAD2 analysis of mammary glands exposed to BMP7-secreting fibroblasts. (H) Representative images of the quantified sections for pSMAD5 analysis of mammary glands exposed to BMP7-secreting fibroblasts. (I) Western blot for pSMAD2, pSMAD5, total SMAD2/3, or SMAD1/5/8 proteins in COMMA-D cells blocked with LEFTY1 and stimulated with BMP7 and Nodal (n = 3). (J) Quantification of the pSMAD5 signal detected by western blot in the indicated conditions. (K) Quantification of the pSMAD2 signal detected by western blot in the indicated conditions. Scale bar, 20 mm. See also Figure S5.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant EGF Thermo Fisher Scientific Cat# PMG8043 Recombinant Noggin R&D Systems Cat# 6057-NG Growth Factor Reduced Matrigel BD Biociences Cat# 356230 Matrigel BD Biociences Cat# 356234 LEFTY-1 R&D Systems Cat# 994-LF BMP7 R&D Systems Cat# 5666-BP BMP2 R&D Systems Cat# 355-BM BMP4 R&D Systems Cat# 314-BP CRIPTO-1 R&D Systems Cat# 1538-CR NODAL R&D Systems Cat# 1315-ND Recombinant Human TGF-beta 1 Protein R&D Systems Cat#240-B-002 DAPI Sigma-Aldrich Cat# 32670 Dispase StemCell Technologies Cat#07913 Collagenase/Hyaluronidase StemCell Technologies Cat #07912 DNase I solution StemCell Technologies Cat#07900 Lefty Blocking Peptide Santa Cruz Biotechnolgy Cat# sc-365845 P LDN-193189 Selleckchem Cat# S2618 Critical Commercial Assays Dual-Luciferase Reporter Assay System Promega Cat#E1910 DUOLink Sigma Cat#921021 Pierce CO-IP Kit Thermo Fisher Scientific Cat#26147 Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 MDA-MD-157 ATCC Cat# HTB-24, RRID:CVCL_0618 3T3-L1 feeder cells Kindly provided by Dr. Nusse N/A L1-wnt3a feeder cells Kindly provided by Dr. Nusse N/A MDA-MB-231 ATCC Cat# HTB-26, RRID:CVCL_0062 COMMA-D beta cells Kindly provided by Dr. Medina Campbell et al., 1988 Experimental Models: Organisms/Strains C57BL/6 mice Jackson Laboratory Cat# JAX:000664, RRID:IMSR_JAX:000664 NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) Jackson Laboratory Cat# JAX:005557, RRID:IMSR_JAX:005557 pCx-GFP Kind gift of Dr. Irving Weissman N/A Oligonucleotides Cloning primers This paper Table S6 qRT-PCR primers This paper Table S6 Copy number determination primers This paper Table S6 Single cell assay ID This paper Table S3 Recombinant DNA pEIZ-HIV-ZsGreen Kind gift of Dr. Zena Werb N/A HIV-Lefty1-ZsG This paper N/A HIV-Che Shimono et al., 2009 N/A HIV-Bmp7-Che This paper N/A pGL3 BRE-luciferase Kind gift of Martine Roussel and Peter ten Dijike, Addgene #45126 pRL-TK Renilla luciferase vector Promega Cat# E2261 pEGFP-C3 (discontinued) Clontech Clontech Bmp7 cDNA clone Origene Cat# MC201085 clone pSICO-R Addgene Cat#12084 Lefty1 cDNA clone IMAGE Cat# 5221120 plasmid clone (Continued on next page) e2 Cell Stem Cell 27, 1–16.e1–e8, August 6, 2020

Techniques: Western Blot

Journal: Cell stem cell

Article Title: LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis.

doi: 10.1016/j.stem.2020.06.017

Figure Lengend Snippet: Figure 4. LEFTY1 Directly Binds to the BMP Receptor BMPR2 (A) Relative mRNA levels of Bmpr2 in basal cell populations (CD49fhiCD24med and CD49flowCD24low) and luminal ones (CD49flowCD24hi and CD49flow/-CD24med). Statistical analysis is one-way ANOVA with Dunnett’s adjustment. (B) Representative images of proximity ligation assay show the interaction between LEFTY1 and BMPR2. Red puncta indicate positive interactions. Scale bar, 10 mm. (C) Quantification of the positive interaction between BMP7 or LEFTY1 with BMPR2 (n = 3). Statistical analysis is one-way ANOVA with Dunnett’s adjustment. ****p < 0.0001. (D) Western blot on co-immunoprecipitated beads of LEFTY1 and BMPR2. (E) Schematic representation of the mechanism by which LEFTY1 inhibits SMAD5 and SMAD2 phosphorylation. See also Figure S5.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant EGF Thermo Fisher Scientific Cat# PMG8043 Recombinant Noggin R&D Systems Cat# 6057-NG Growth Factor Reduced Matrigel BD Biociences Cat# 356230 Matrigel BD Biociences Cat# 356234 LEFTY-1 R&D Systems Cat# 994-LF BMP7 R&D Systems Cat# 5666-BP BMP2 R&D Systems Cat# 355-BM BMP4 R&D Systems Cat# 314-BP CRIPTO-1 R&D Systems Cat# 1538-CR NODAL R&D Systems Cat# 1315-ND Recombinant Human TGF-beta 1 Protein R&D Systems Cat#240-B-002 DAPI Sigma-Aldrich Cat# 32670 Dispase StemCell Technologies Cat#07913 Collagenase/Hyaluronidase StemCell Technologies Cat #07912 DNase I solution StemCell Technologies Cat#07900 Lefty Blocking Peptide Santa Cruz Biotechnolgy Cat# sc-365845 P LDN-193189 Selleckchem Cat# S2618 Critical Commercial Assays Dual-Luciferase Reporter Assay System Promega Cat#E1910 DUOLink Sigma Cat#921021 Pierce CO-IP Kit Thermo Fisher Scientific Cat#26147 Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 MDA-MD-157 ATCC Cat# HTB-24, RRID:CVCL_0618 3T3-L1 feeder cells Kindly provided by Dr. Nusse N/A L1-wnt3a feeder cells Kindly provided by Dr. Nusse N/A MDA-MB-231 ATCC Cat# HTB-26, RRID:CVCL_0062 COMMA-D beta cells Kindly provided by Dr. Medina Campbell et al., 1988 Experimental Models: Organisms/Strains C57BL/6 mice Jackson Laboratory Cat# JAX:000664, RRID:IMSR_JAX:000664 NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) Jackson Laboratory Cat# JAX:005557, RRID:IMSR_JAX:005557 pCx-GFP Kind gift of Dr. Irving Weissman N/A Oligonucleotides Cloning primers This paper Table S6 qRT-PCR primers This paper Table S6 Copy number determination primers This paper Table S6 Single cell assay ID This paper Table S3 Recombinant DNA pEIZ-HIV-ZsGreen Kind gift of Dr. Zena Werb N/A HIV-Lefty1-ZsG This paper N/A HIV-Che Shimono et al., 2009 N/A HIV-Bmp7-Che This paper N/A pGL3 BRE-luciferase Kind gift of Martine Roussel and Peter ten Dijike, Addgene #45126 pRL-TK Renilla luciferase vector Promega Cat# E2261 pEGFP-C3 (discontinued) Clontech Clontech Bmp7 cDNA clone Origene Cat# MC201085 clone pSICO-R Addgene Cat#12084 Lefty1 cDNA clone IMAGE Cat# 5221120 plasmid clone (Continued on next page) e2 Cell Stem Cell 27, 1–16.e1–e8, August 6, 2020

Techniques: Proximity Ligation Assay, Western Blot, Immunoprecipitation, Phospho-proteomics

Journal: Cell stem cell

Article Title: LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis.

doi: 10.1016/j.stem.2020.06.017

Figure Lengend Snippet: Figure 7. LEFTY1 Binds to BMPR2 and Is a Concomitant SMAD2 and SMAD5 Inhibitor in Tumor-Initiating Cells (A) Representative pictures of cells from isolated tumorigenic (TG) and non-TG (NTG) cells to assess LEFTY1-BMPR2 and BMP7-BMRP2 interaction. Scale bar, 20 mm. (B) Quantification by proximity ligation assay of LEFTY1-BMPR2 or BMP7-BMPR2 interaction in TG cells or NTG sorted cells. (C) Representative images of cells from isolated TG and NTG cells stained to assess pSMAD5 staining. Scale bar, 100 mm.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant EGF Thermo Fisher Scientific Cat# PMG8043 Recombinant Noggin R&D Systems Cat# 6057-NG Growth Factor Reduced Matrigel BD Biociences Cat# 356230 Matrigel BD Biociences Cat# 356234 LEFTY-1 R&D Systems Cat# 994-LF BMP7 R&D Systems Cat# 5666-BP BMP2 R&D Systems Cat# 355-BM BMP4 R&D Systems Cat# 314-BP CRIPTO-1 R&D Systems Cat# 1538-CR NODAL R&D Systems Cat# 1315-ND Recombinant Human TGF-beta 1 Protein R&D Systems Cat#240-B-002 DAPI Sigma-Aldrich Cat# 32670 Dispase StemCell Technologies Cat#07913 Collagenase/Hyaluronidase StemCell Technologies Cat #07912 DNase I solution StemCell Technologies Cat#07900 Lefty Blocking Peptide Santa Cruz Biotechnolgy Cat# sc-365845 P LDN-193189 Selleckchem Cat# S2618 Critical Commercial Assays Dual-Luciferase Reporter Assay System Promega Cat#E1910 DUOLink Sigma Cat#921021 Pierce CO-IP Kit Thermo Fisher Scientific Cat#26147 Experimental Models: Cell Lines HEK293T ATCC Cat# CRL-3216, RRID:CVCL_0063 MDA-MD-157 ATCC Cat# HTB-24, RRID:CVCL_0618 3T3-L1 feeder cells Kindly provided by Dr. Nusse N/A L1-wnt3a feeder cells Kindly provided by Dr. Nusse N/A MDA-MB-231 ATCC Cat# HTB-26, RRID:CVCL_0062 COMMA-D beta cells Kindly provided by Dr. Medina Campbell et al., 1988 Experimental Models: Organisms/Strains C57BL/6 mice Jackson Laboratory Cat# JAX:000664, RRID:IMSR_JAX:000664 NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) Jackson Laboratory Cat# JAX:005557, RRID:IMSR_JAX:005557 pCx-GFP Kind gift of Dr. Irving Weissman N/A Oligonucleotides Cloning primers This paper Table S6 qRT-PCR primers This paper Table S6 Copy number determination primers This paper Table S6 Single cell assay ID This paper Table S3 Recombinant DNA pEIZ-HIV-ZsGreen Kind gift of Dr. Zena Werb N/A HIV-Lefty1-ZsG This paper N/A HIV-Che Shimono et al., 2009 N/A HIV-Bmp7-Che This paper N/A pGL3 BRE-luciferase Kind gift of Martine Roussel and Peter ten Dijike, Addgene #45126 pRL-TK Renilla luciferase vector Promega Cat# E2261 pEGFP-C3 (discontinued) Clontech Clontech Bmp7 cDNA clone Origene Cat# MC201085 clone pSICO-R Addgene Cat#12084 Lefty1 cDNA clone IMAGE Cat# 5221120 plasmid clone (Continued on next page) e2 Cell Stem Cell 27, 1–16.e1–e8, August 6, 2020

Techniques: Isolation, Proximity Ligation Assay, Staining