SRX23801545 GSM8121373_r1 SRP492698 PRJNA1082387 SRS20624527 GSM8121373 GSM8121373 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801546 GSM8121374_r1 SRP492698 PRJNA1082387 SRS20624528 GSM8121374 GSM8121374 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801547 GSM8121375_r1 SRP492698 PRJNA1082387 SRS20624529 GSM8121375 GSM8121375 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801548 GSM8121376_r1 SRP492698 PRJNA1082387 SRS20624530 GSM8121376 GSM8121376 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801549 GSM8121377_r1 SRP492698 PRJNA1082387 SRS20624531 GSM8121377 GSM8121377 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801550 GSM8121378_r1 SRP492698 PRJNA1082387 SRS20624532 GSM8121378 GSM8121378 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801551 GSM8121379_r1 SRP492698 PRJNA1082387 SRS20624533 GSM8121379 GSM8121379 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801552 GSM8121380_r1 SRP492698 PRJNA1082387 SRS20624534 GSM8121380 GSM8121380 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801553 GSM8121381_r1 SRP492698 PRJNA1082387 SRS20624535 GSM8121381 GSM8121381 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801554 GSM8121382_r1 SRP492698 PRJNA1082387 SRS20624536 GSM8121382 GSM8121382 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801555 GSM8121383_r1 SRP492698 PRJNA1082387 SRS20624537 GSM8121383 GSM8121383 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801556 GSM8121384_r1 SRP492698 PRJNA1082387 SRS20624538 GSM8121384 GSM8121384 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801557 GSM8121385_r1 SRP492698 PRJNA1082387 SRS20624539 GSM8121385 GSM8121385 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801558 GSM8121386_r1 SRP492698 PRJNA1082387 SRS20624540 GSM8121386 GSM8121386 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801559 GSM8121387_r1 SRP492698 PRJNA1082387 SRS20624541 GSM8121387 GSM8121387 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000 SRX23801560 GSM8121388_r1 SRP492698 PRJNA1082387 SRS20624542 GSM8121388 GSM8121388 RNA-Seq TRANSCRIPTOMIC cDNA To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760). Illumina NovaSeq 6000