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fish probe 3 plex positive control advanced cell diagnostics ref  (Addgene inc)


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    Addgene inc fish probe 3 plex positive control advanced cell diagnostics ref
    Fish Probe 3 Plex Positive Control Advanced Cell Diagnostics Ref, supplied by Addgene inc, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/fish+probe+3+plex+positive+control+advanced+cell+diagnostics+ref/pWZLFlagMenin(S394A%2C+T397A%2C+S399A)+(Plasmid+%2332086)/pm33476555-240-162-175
    Average 88 stars, based on 1 article reviews
    fish probe 3 plex positive control advanced cell diagnostics ref - by Bioz Stars, 2026-09
    88/100 stars

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    shRNA:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    Plasmid Preparation:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    Mutagenesis:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    SYBR Green Assay:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    Polymerase Chain Reaction:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    RNAscope:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    Multiplex Assay:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    Extraction:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    Fluorescence In Situ Hybridization:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    Negative Control:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    Positive Control:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    Recombinant:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..

    Software:

    Article Title: Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER trypsin-EDTA Gibco Cat#25200072 b-mercaptoethanol Sigma Cat#M7522 hbFGF R&D Systems Cat#100-18B Matrigel Corning Cat#356234 collagenase B Worthington Cat#LS004176 StemPro-34 Invitrogen Cat#10639011 BMP-4 R&D Systems Cat#120-05ET Glutamax Sigma Cat#35050061 monothioglycerol (MTG) Sigma Cat#M1753 ascorbic acid Sigma Cat#A8960 IMDM Gibco Cat#I3390 knockout serum replacement (KSR) Gibco Cat#10828028 human holo transferrin Sigma Cat#T4132 recombinant human insulin Sigma Cat#I6634 Inositol Sigma Cat#I5125 Folic acid Sigma Cat#F7876 Ferric nitrate Sigma Cat#F8508 Ferrous sulfate Sigma Cat#F8633 hSCF PeproTech Cat#300-07 hIL-3 PeproTech Cat#200-03 hIL-6 PeproTech Cat#200-06 hIL-11 PeproTech Cat#200-11 hTPO PeproTech Cat#300-18 hVEGF PeproTech Cat#100-44 hEPO PeproTech Cat#100-64 semisolid medium Stem Cell Technologies Cat#04435 HISTOPAQUE Sigma Cat#10771 BIT Stem Cell Technologies Cat#09500 penicillin and streptomycin Gibco Cat#15140-122 Hydrocortisone Sigma Cat#H2270 StemSpan SFEM Stem Cell Technologies Cat#09650 FLT3 ligand PeproTech Cat#300-19 doxycycline Sigma Cat#9891 dexamethasone Sigma Cat#9891D2915 TRIzol Invitrogen Cat#15596026 Triton X-100 Sigma Cat#A110694 DAPI Sigma Cat#DUO82040 benzidine Sigma Cat#D9143 Protease Inhibitor cocktail Roche Cat#S8830 HNRNPA1 Abcam Cat#ab123212 ECL substrate Millipore Cat#WBKLS0500 SuperScript III Thermo Fisher Cat#18080044 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 Critical commercial assays Anti-PE Multisort Kit MACS Cat#130-090-757 CD235a (Glycophorin A) MicroBeads MACS Cat#130-050-501 EasySep Human CD34 Positive Selection Kit Stem Cell Technologies Cat#17856 Human MTC Panel I TaKaRa Cat#636742 Human MTC Panel II TaKaRa Cat#636743 (Continued on next page) Developmental Cell 56, 478–493.e1–e11, February 22, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER CD34 microbeads Miltenyi Biotec Cat#130-046-702 HNRNPA1 human shRNA plasmid kit Origene Cat#TL312381 QuikChange Site-Directed Mutagenesis Kit Stratagene, Cat#200518 ViraPower Lentiviral Packaging System Invitrogen Cat#K497500 SYBR Green PCR kit Applied Biosystems Cat#A25742 SMARTer RACE 5’/3’ Kit TaKaRa Cat#634858 RNAscope Fluorescent Multiplex Kit Advanced Cell Diagnostics Cat#320293 NE-PER Nuclear and Cytoplasmic extraction Reagents Kit Thermo Fisher Scientific Cat#78835 RiboMAX large scale RNA production systems-T7 Promega Cat#P1300 Pierce RNA 3’ End Desthiobiotinylation Kit Thermo Scientific Cat#20163 Pierce Magnetic RNA-protein Pull-Down Kit Thermo Scientific Cat#20164 Streptavidin agarose beads Invitrogen Cat#65601 Light Shift Chemiluminescent RNA EMSA Kit Pierce Cat#20158 protein A beads Invitrogen Cat#10002D Deposited data Raw and analyzed data This paper GEO: GSE136235 Experimental models: cell lines H1 hESC NIH WA01 HUDEP-2 RIKEN BioResource Research Center N/A Experimental models: organisms/strains NOG mice NOD.Cg-PrkdcscidIl2rgtm1Sug/JicCrl N/A Oligonucleotides FISH Probe Hs-HBBP1 Advanced Cell Diagnostics REF: 496481 FISH Probe Hs-TAL1 Advanced Cell Diagnostics REF: 510091 FISH Probe 3-Plex Negative Control Advanced Cell Diagnostics REF: 320871 FISH Probe 3-Plex Positive Control Advanced Cell Diagnostics REF: 320861 Recombinant DNA pX330-sgRNA Addgene Cat#42230 lentiCRISPR v2 Addgene Cat#52961 pLKO.1 Addgene Cat#10878 Software and algorithms GraphPad Software GraphPad Software, Inc https://www.graphpad.com FlowJo BD Biosciences, San Jose, CA, USAFlowJo https://www.flowjo.com Chromas Technelysium, Inc http://technelysium.com.au/wp/chromas/ STAR Dobin et al., 2013 https://www.elsevier.com/authors/author- resources/research-data/data-base-linking RSEM Li and Dewey, 2011 https://github.com/deweylab/RSEM Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ download.html RSeQC Wang et al., 2012 http://rseqc.sourceforge.net/ #download-rseqc WGCNA Langfelder and Horvath, 2008 http://bioconductor.org/biocLite.R DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ DEGseq Raleigh et al., 2010 http://www.bioconductor.org/packages/ release/bioc/html/DEGseq.html Salmon Patro et al., 2017 https://github.com/COMBINE-lab/salmon/ (Continued on next page) e3 Developmental Cell 56, 478–493.e1–e11, February 22, 2021 ..



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