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human osteosarcoma tumor cell line u2os  (ATCC)


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    ATCC human osteosarcoma tumor cell line u2os
    Human Osteosarcoma Tumor Cell Line U2os, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1347 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cell+lines+human+osteosarcoma+u2os+atcc+htb+96/U-2+OS%3B+Osteosarcoma%3B+Human/pm41617974-205-0-8
    Average 99 stars, based on 1347 article reviews
    human osteosarcoma tumor cell line u2os - by Bioz Stars, 2026-10
    99/100 stars

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    Random Primed:

    Article Title: Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Camptothecin Sigma-Aldrich Cat#208925 Etoposide Sigma-Aldrich Cat#E1383 CD437 Sigma-Aldrich Cat#C5865 Rad51 inhibitor (B02) Sigma-Aldrich Cat#SML0364 Rad52 inhibitor (AICAR) Sigma-Aldrich Cat#A9978 PARP inhibitor (Olaparib) Adooq Bioscience Cat#10111 Aphidicolin Sigma-Aldrich Cat#A4487 Critical commercial assays PureLink Genomic DNA Mini Kit Beckman Coulter Cat#A63881 DNA Clean & Concentrator-5 Thermo Fisher Scientific Cat#10002D RNeasy Mini Kit GeneTex Cat#GTX30920 RNA Clean & Concentrator-5 Polyplus Cat#409-10 Ribo-Zero Gold rRNA Removal Kit (H/M/R) Cat#MRZG12324 Random Primed DNA Labeling Kit Thermo Fisher Scientific Cat#K182001 Qubit dsDNA HS Assay Kit Zymo Research Cat#D4013 SensiFAST SYBR Lo-ROX Kit QIAGEN Cat#74106 Click-iT RNA Alexa Fluor 594 Imaging Kit Zymo Research Cat#R1015 Nextera XT DNA Library Preparation Kit Bioline Cat#BIO-94020 QIAseq Ultralow Input Library Kit Thermo Fisher Scientific Cat#C10330 KAPA RNA HyperPrep Kit with RiboErase (HMR) Sigma-Aldrich Cat#DUO92002 KAPA Library Quantification Kit Sigma-Aldrich Cat#DUO92004 ECL Western Blotting Substrate Sigma-Aldrich Cat#DUO92008 SuperScript III Reverse Transcriptase kit Illumina Cat#FC-131-1024 Deposited data All the datasets generated in this paper This paper GSE136294 BJ GRO-Seq Li et al., 2018 SRX3586216 CTR cells and RNAi of NELFB andNELFEGROSeq Liu et al., 2017 GSE98555 RPE EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 U2OS EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 CAP-Seq HeLa cells Tan-Wong et al., 2019 GSE87607 Ok-Seq RPE h-TERT Chen et al., 2019 GSE114017 Ok-Seq HeLa Petryk et al., 2016 SRP065949 ChIP-Seq ORC1 HeLa Dellino et al., 2013 GSE37583 ChIP-Seq MCM7 HeLa Sugimoto et al., 2018 GSE107248 ChIP-Seq RPA2 HeLa Zhang et al., 2017 GSE76661 ChOR-Seq mouse ES cells Stewart-Morgan et al., 2019 GSE128643 HeLa polyA RNA-Seq Encode Project Consortium ENCFF343WEZ ChIP-Seq 53BP1, RAD51, XRCC4 U2OS Clouaire et al., 2018 E-MTAB-5817 Experimental models: cell lines Human osteosarcoma (U2OS) ATCC HTB-96 Human immortalized fibroblasts (BJ-hTERT) ATCC CRL-4001 Oligonucleotides siGENOME Non-Targeting siRNA Pool #2 Dharmacon Cat#D-001206-14-05 siGENOME Human SUPT5H siRNA Pool Dharmacon Cat#M-016234-01-0005 siGENOME Human NELFA siRNA Pool Dharmacon Cat#M-012156-00-0005 (Continued on next page) e2 Cell Reports 34, 108759, February 16, 2021 Article ll OPEN ACCESS

    DNA Labeling:

    Article Title: Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Camptothecin Sigma-Aldrich Cat#208925 Etoposide Sigma-Aldrich Cat#E1383 CD437 Sigma-Aldrich Cat#C5865 Rad51 inhibitor (B02) Sigma-Aldrich Cat#SML0364 Rad52 inhibitor (AICAR) Sigma-Aldrich Cat#A9978 PARP inhibitor (Olaparib) Adooq Bioscience Cat#10111 Aphidicolin Sigma-Aldrich Cat#A4487 Critical commercial assays PureLink Genomic DNA Mini Kit Beckman Coulter Cat#A63881 DNA Clean & Concentrator-5 Thermo Fisher Scientific Cat#10002D RNeasy Mini Kit GeneTex Cat#GTX30920 RNA Clean & Concentrator-5 Polyplus Cat#409-10 Ribo-Zero Gold rRNA Removal Kit (H/M/R) Cat#MRZG12324 Random Primed DNA Labeling Kit Thermo Fisher Scientific Cat#K182001 Qubit dsDNA HS Assay Kit Zymo Research Cat#D4013 SensiFAST SYBR Lo-ROX Kit QIAGEN Cat#74106 Click-iT RNA Alexa Fluor 594 Imaging Kit Zymo Research Cat#R1015 Nextera XT DNA Library Preparation Kit Bioline Cat#BIO-94020 QIAseq Ultralow Input Library Kit Thermo Fisher Scientific Cat#C10330 KAPA RNA HyperPrep Kit with RiboErase (HMR) Sigma-Aldrich Cat#DUO92002 KAPA Library Quantification Kit Sigma-Aldrich Cat#DUO92004 ECL Western Blotting Substrate Sigma-Aldrich Cat#DUO92008 SuperScript III Reverse Transcriptase kit Illumina Cat#FC-131-1024 Deposited data All the datasets generated in this paper This paper GSE136294 BJ GRO-Seq Li et al., 2018 SRX3586216 CTR cells and RNAi of NELFB andNELFEGROSeq Liu et al., 2017 GSE98555 RPE EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 U2OS EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 CAP-Seq HeLa cells Tan-Wong et al., 2019 GSE87607 Ok-Seq RPE h-TERT Chen et al., 2019 GSE114017 Ok-Seq HeLa Petryk et al., 2016 SRP065949 ChIP-Seq ORC1 HeLa Dellino et al., 2013 GSE37583 ChIP-Seq MCM7 HeLa Sugimoto et al., 2018 GSE107248 ChIP-Seq RPA2 HeLa Zhang et al., 2017 GSE76661 ChOR-Seq mouse ES cells Stewart-Morgan et al., 2019 GSE128643 HeLa polyA RNA-Seq Encode Project Consortium ENCFF343WEZ ChIP-Seq 53BP1, RAD51, XRCC4 U2OS Clouaire et al., 2018 E-MTAB-5817 Experimental models: cell lines Human osteosarcoma (U2OS) ATCC HTB-96 Human immortalized fibroblasts (BJ-hTERT) ATCC CRL-4001 Oligonucleotides siGENOME Non-Targeting siRNA Pool #2 Dharmacon Cat#D-001206-14-05 siGENOME Human SUPT5H siRNA Pool Dharmacon Cat#M-016234-01-0005 siGENOME Human NELFA siRNA Pool Dharmacon Cat#M-012156-00-0005 (Continued on next page) e2 Cell Reports 34, 108759, February 16, 2021 Article ll OPEN ACCESS

    Imaging:

    Article Title: Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Camptothecin Sigma-Aldrich Cat#208925 Etoposide Sigma-Aldrich Cat#E1383 CD437 Sigma-Aldrich Cat#C5865 Rad51 inhibitor (B02) Sigma-Aldrich Cat#SML0364 Rad52 inhibitor (AICAR) Sigma-Aldrich Cat#A9978 PARP inhibitor (Olaparib) Adooq Bioscience Cat#10111 Aphidicolin Sigma-Aldrich Cat#A4487 Critical commercial assays PureLink Genomic DNA Mini Kit Beckman Coulter Cat#A63881 DNA Clean & Concentrator-5 Thermo Fisher Scientific Cat#10002D RNeasy Mini Kit GeneTex Cat#GTX30920 RNA Clean & Concentrator-5 Polyplus Cat#409-10 Ribo-Zero Gold rRNA Removal Kit (H/M/R) Cat#MRZG12324 Random Primed DNA Labeling Kit Thermo Fisher Scientific Cat#K182001 Qubit dsDNA HS Assay Kit Zymo Research Cat#D4013 SensiFAST SYBR Lo-ROX Kit QIAGEN Cat#74106 Click-iT RNA Alexa Fluor 594 Imaging Kit Zymo Research Cat#R1015 Nextera XT DNA Library Preparation Kit Bioline Cat#BIO-94020 QIAseq Ultralow Input Library Kit Thermo Fisher Scientific Cat#C10330 KAPA RNA HyperPrep Kit with RiboErase (HMR) Sigma-Aldrich Cat#DUO92002 KAPA Library Quantification Kit Sigma-Aldrich Cat#DUO92004 ECL Western Blotting Substrate Sigma-Aldrich Cat#DUO92008 SuperScript III Reverse Transcriptase kit Illumina Cat#FC-131-1024 Deposited data All the datasets generated in this paper This paper GSE136294 BJ GRO-Seq Li et al., 2018 SRX3586216 CTR cells and RNAi of NELFB andNELFEGROSeq Liu et al., 2017 GSE98555 RPE EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 U2OS EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 CAP-Seq HeLa cells Tan-Wong et al., 2019 GSE87607 Ok-Seq RPE h-TERT Chen et al., 2019 GSE114017 Ok-Seq HeLa Petryk et al., 2016 SRP065949 ChIP-Seq ORC1 HeLa Dellino et al., 2013 GSE37583 ChIP-Seq MCM7 HeLa Sugimoto et al., 2018 GSE107248 ChIP-Seq RPA2 HeLa Zhang et al., 2017 GSE76661 ChOR-Seq mouse ES cells Stewart-Morgan et al., 2019 GSE128643 HeLa polyA RNA-Seq Encode Project Consortium ENCFF343WEZ ChIP-Seq 53BP1, RAD51, XRCC4 U2OS Clouaire et al., 2018 E-MTAB-5817 Experimental models: cell lines Human osteosarcoma (U2OS) ATCC HTB-96 Human immortalized fibroblasts (BJ-hTERT) ATCC CRL-4001 Oligonucleotides siGENOME Non-Targeting siRNA Pool #2 Dharmacon Cat#D-001206-14-05 siGENOME Human SUPT5H siRNA Pool Dharmacon Cat#M-016234-01-0005 siGENOME Human NELFA siRNA Pool Dharmacon Cat#M-012156-00-0005 (Continued on next page) e2 Cell Reports 34, 108759, February 16, 2021 Article ll OPEN ACCESS

    DNA Library Preparation:

    Article Title: Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Camptothecin Sigma-Aldrich Cat#208925 Etoposide Sigma-Aldrich Cat#E1383 CD437 Sigma-Aldrich Cat#C5865 Rad51 inhibitor (B02) Sigma-Aldrich Cat#SML0364 Rad52 inhibitor (AICAR) Sigma-Aldrich Cat#A9978 PARP inhibitor (Olaparib) Adooq Bioscience Cat#10111 Aphidicolin Sigma-Aldrich Cat#A4487 Critical commercial assays PureLink Genomic DNA Mini Kit Beckman Coulter Cat#A63881 DNA Clean & Concentrator-5 Thermo Fisher Scientific Cat#10002D RNeasy Mini Kit GeneTex Cat#GTX30920 RNA Clean & Concentrator-5 Polyplus Cat#409-10 Ribo-Zero Gold rRNA Removal Kit (H/M/R) Cat#MRZG12324 Random Primed DNA Labeling Kit Thermo Fisher Scientific Cat#K182001 Qubit dsDNA HS Assay Kit Zymo Research Cat#D4013 SensiFAST SYBR Lo-ROX Kit QIAGEN Cat#74106 Click-iT RNA Alexa Fluor 594 Imaging Kit Zymo Research Cat#R1015 Nextera XT DNA Library Preparation Kit Bioline Cat#BIO-94020 QIAseq Ultralow Input Library Kit Thermo Fisher Scientific Cat#C10330 KAPA RNA HyperPrep Kit with RiboErase (HMR) Sigma-Aldrich Cat#DUO92002 KAPA Library Quantification Kit Sigma-Aldrich Cat#DUO92004 ECL Western Blotting Substrate Sigma-Aldrich Cat#DUO92008 SuperScript III Reverse Transcriptase kit Illumina Cat#FC-131-1024 Deposited data All the datasets generated in this paper This paper GSE136294 BJ GRO-Seq Li et al., 2018 SRX3586216 CTR cells and RNAi of NELFB andNELFEGROSeq Liu et al., 2017 GSE98555 RPE EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 U2OS EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 CAP-Seq HeLa cells Tan-Wong et al., 2019 GSE87607 Ok-Seq RPE h-TERT Chen et al., 2019 GSE114017 Ok-Seq HeLa Petryk et al., 2016 SRP065949 ChIP-Seq ORC1 HeLa Dellino et al., 2013 GSE37583 ChIP-Seq MCM7 HeLa Sugimoto et al., 2018 GSE107248 ChIP-Seq RPA2 HeLa Zhang et al., 2017 GSE76661 ChOR-Seq mouse ES cells Stewart-Morgan et al., 2019 GSE128643 HeLa polyA RNA-Seq Encode Project Consortium ENCFF343WEZ ChIP-Seq 53BP1, RAD51, XRCC4 U2OS Clouaire et al., 2018 E-MTAB-5817 Experimental models: cell lines Human osteosarcoma (U2OS) ATCC HTB-96 Human immortalized fibroblasts (BJ-hTERT) ATCC CRL-4001 Oligonucleotides siGENOME Non-Targeting siRNA Pool #2 Dharmacon Cat#D-001206-14-05 siGENOME Human SUPT5H siRNA Pool Dharmacon Cat#M-016234-01-0005 siGENOME Human NELFA siRNA Pool Dharmacon Cat#M-012156-00-0005 (Continued on next page) e2 Cell Reports 34, 108759, February 16, 2021 Article ll OPEN ACCESS

    Library Quantification:

    Article Title: Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Camptothecin Sigma-Aldrich Cat#208925 Etoposide Sigma-Aldrich Cat#E1383 CD437 Sigma-Aldrich Cat#C5865 Rad51 inhibitor (B02) Sigma-Aldrich Cat#SML0364 Rad52 inhibitor (AICAR) Sigma-Aldrich Cat#A9978 PARP inhibitor (Olaparib) Adooq Bioscience Cat#10111 Aphidicolin Sigma-Aldrich Cat#A4487 Critical commercial assays PureLink Genomic DNA Mini Kit Beckman Coulter Cat#A63881 DNA Clean & Concentrator-5 Thermo Fisher Scientific Cat#10002D RNeasy Mini Kit GeneTex Cat#GTX30920 RNA Clean & Concentrator-5 Polyplus Cat#409-10 Ribo-Zero Gold rRNA Removal Kit (H/M/R) Cat#MRZG12324 Random Primed DNA Labeling Kit Thermo Fisher Scientific Cat#K182001 Qubit dsDNA HS Assay Kit Zymo Research Cat#D4013 SensiFAST SYBR Lo-ROX Kit QIAGEN Cat#74106 Click-iT RNA Alexa Fluor 594 Imaging Kit Zymo Research Cat#R1015 Nextera XT DNA Library Preparation Kit Bioline Cat#BIO-94020 QIAseq Ultralow Input Library Kit Thermo Fisher Scientific Cat#C10330 KAPA RNA HyperPrep Kit with RiboErase (HMR) Sigma-Aldrich Cat#DUO92002 KAPA Library Quantification Kit Sigma-Aldrich Cat#DUO92004 ECL Western Blotting Substrate Sigma-Aldrich Cat#DUO92008 SuperScript III Reverse Transcriptase kit Illumina Cat#FC-131-1024 Deposited data All the datasets generated in this paper This paper GSE136294 BJ GRO-Seq Li et al., 2018 SRX3586216 CTR cells and RNAi of NELFB andNELFEGROSeq Liu et al., 2017 GSE98555 RPE EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 U2OS EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 CAP-Seq HeLa cells Tan-Wong et al., 2019 GSE87607 Ok-Seq RPE h-TERT Chen et al., 2019 GSE114017 Ok-Seq HeLa Petryk et al., 2016 SRP065949 ChIP-Seq ORC1 HeLa Dellino et al., 2013 GSE37583 ChIP-Seq MCM7 HeLa Sugimoto et al., 2018 GSE107248 ChIP-Seq RPA2 HeLa Zhang et al., 2017 GSE76661 ChOR-Seq mouse ES cells Stewart-Morgan et al., 2019 GSE128643 HeLa polyA RNA-Seq Encode Project Consortium ENCFF343WEZ ChIP-Seq 53BP1, RAD51, XRCC4 U2OS Clouaire et al., 2018 E-MTAB-5817 Experimental models: cell lines Human osteosarcoma (U2OS) ATCC HTB-96 Human immortalized fibroblasts (BJ-hTERT) ATCC CRL-4001 Oligonucleotides siGENOME Non-Targeting siRNA Pool #2 Dharmacon Cat#D-001206-14-05 siGENOME Human SUPT5H siRNA Pool Dharmacon Cat#M-016234-01-0005 siGENOME Human NELFA siRNA Pool Dharmacon Cat#M-012156-00-0005 (Continued on next page) e2 Cell Reports 34, 108759, February 16, 2021 Article ll OPEN ACCESS

    Western Blot:

    Article Title: Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Camptothecin Sigma-Aldrich Cat#208925 Etoposide Sigma-Aldrich Cat#E1383 CD437 Sigma-Aldrich Cat#C5865 Rad51 inhibitor (B02) Sigma-Aldrich Cat#SML0364 Rad52 inhibitor (AICAR) Sigma-Aldrich Cat#A9978 PARP inhibitor (Olaparib) Adooq Bioscience Cat#10111 Aphidicolin Sigma-Aldrich Cat#A4487 Critical commercial assays PureLink Genomic DNA Mini Kit Beckman Coulter Cat#A63881 DNA Clean & Concentrator-5 Thermo Fisher Scientific Cat#10002D RNeasy Mini Kit GeneTex Cat#GTX30920 RNA Clean & Concentrator-5 Polyplus Cat#409-10 Ribo-Zero Gold rRNA Removal Kit (H/M/R) Cat#MRZG12324 Random Primed DNA Labeling Kit Thermo Fisher Scientific Cat#K182001 Qubit dsDNA HS Assay Kit Zymo Research Cat#D4013 SensiFAST SYBR Lo-ROX Kit QIAGEN Cat#74106 Click-iT RNA Alexa Fluor 594 Imaging Kit Zymo Research Cat#R1015 Nextera XT DNA Library Preparation Kit Bioline Cat#BIO-94020 QIAseq Ultralow Input Library Kit Thermo Fisher Scientific Cat#C10330 KAPA RNA HyperPrep Kit with RiboErase (HMR) Sigma-Aldrich Cat#DUO92002 KAPA Library Quantification Kit Sigma-Aldrich Cat#DUO92004 ECL Western Blotting Substrate Sigma-Aldrich Cat#DUO92008 SuperScript III Reverse Transcriptase kit Illumina Cat#FC-131-1024 Deposited data All the datasets generated in this paper This paper GSE136294 BJ GRO-Seq Li et al., 2018 SRX3586216 CTR cells and RNAi of NELFB andNELFEGROSeq Liu et al., 2017 GSE98555 RPE EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 U2OS EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 CAP-Seq HeLa cells Tan-Wong et al., 2019 GSE87607 Ok-Seq RPE h-TERT Chen et al., 2019 GSE114017 Ok-Seq HeLa Petryk et al., 2016 SRP065949 ChIP-Seq ORC1 HeLa Dellino et al., 2013 GSE37583 ChIP-Seq MCM7 HeLa Sugimoto et al., 2018 GSE107248 ChIP-Seq RPA2 HeLa Zhang et al., 2017 GSE76661 ChOR-Seq mouse ES cells Stewart-Morgan et al., 2019 GSE128643 HeLa polyA RNA-Seq Encode Project Consortium ENCFF343WEZ ChIP-Seq 53BP1, RAD51, XRCC4 U2OS Clouaire et al., 2018 E-MTAB-5817 Experimental models: cell lines Human osteosarcoma (U2OS) ATCC HTB-96 Human immortalized fibroblasts (BJ-hTERT) ATCC CRL-4001 Oligonucleotides siGENOME Non-Targeting siRNA Pool #2 Dharmacon Cat#D-001206-14-05 siGENOME Human SUPT5H siRNA Pool Dharmacon Cat#M-016234-01-0005 siGENOME Human NELFA siRNA Pool Dharmacon Cat#M-012156-00-0005 (Continued on next page) e2 Cell Reports 34, 108759, February 16, 2021 Article ll OPEN ACCESS

    Reverse Transcription:

    Article Title: Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Camptothecin Sigma-Aldrich Cat#208925 Etoposide Sigma-Aldrich Cat#E1383 CD437 Sigma-Aldrich Cat#C5865 Rad51 inhibitor (B02) Sigma-Aldrich Cat#SML0364 Rad52 inhibitor (AICAR) Sigma-Aldrich Cat#A9978 PARP inhibitor (Olaparib) Adooq Bioscience Cat#10111 Aphidicolin Sigma-Aldrich Cat#A4487 Critical commercial assays PureLink Genomic DNA Mini Kit Beckman Coulter Cat#A63881 DNA Clean & Concentrator-5 Thermo Fisher Scientific Cat#10002D RNeasy Mini Kit GeneTex Cat#GTX30920 RNA Clean & Concentrator-5 Polyplus Cat#409-10 Ribo-Zero Gold rRNA Removal Kit (H/M/R) Cat#MRZG12324 Random Primed DNA Labeling Kit Thermo Fisher Scientific Cat#K182001 Qubit dsDNA HS Assay Kit Zymo Research Cat#D4013 SensiFAST SYBR Lo-ROX Kit QIAGEN Cat#74106 Click-iT RNA Alexa Fluor 594 Imaging Kit Zymo Research Cat#R1015 Nextera XT DNA Library Preparation Kit Bioline Cat#BIO-94020 QIAseq Ultralow Input Library Kit Thermo Fisher Scientific Cat#C10330 KAPA RNA HyperPrep Kit with RiboErase (HMR) Sigma-Aldrich Cat#DUO92002 KAPA Library Quantification Kit Sigma-Aldrich Cat#DUO92004 ECL Western Blotting Substrate Sigma-Aldrich Cat#DUO92008 SuperScript III Reverse Transcriptase kit Illumina Cat#FC-131-1024 Deposited data All the datasets generated in this paper This paper GSE136294 BJ GRO-Seq Li et al., 2018 SRX3586216 CTR cells and RNAi of NELFB andNELFEGROSeq Liu et al., 2017 GSE98555 RPE EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 U2OS EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 CAP-Seq HeLa cells Tan-Wong et al., 2019 GSE87607 Ok-Seq RPE h-TERT Chen et al., 2019 GSE114017 Ok-Seq HeLa Petryk et al., 2016 SRP065949 ChIP-Seq ORC1 HeLa Dellino et al., 2013 GSE37583 ChIP-Seq MCM7 HeLa Sugimoto et al., 2018 GSE107248 ChIP-Seq RPA2 HeLa Zhang et al., 2017 GSE76661 ChOR-Seq mouse ES cells Stewart-Morgan et al., 2019 GSE128643 HeLa polyA RNA-Seq Encode Project Consortium ENCFF343WEZ ChIP-Seq 53BP1, RAD51, XRCC4 U2OS Clouaire et al., 2018 E-MTAB-5817 Experimental models: cell lines Human osteosarcoma (U2OS) ATCC HTB-96 Human immortalized fibroblasts (BJ-hTERT) ATCC CRL-4001 Oligonucleotides siGENOME Non-Targeting siRNA Pool #2 Dharmacon Cat#D-001206-14-05 siGENOME Human SUPT5H siRNA Pool Dharmacon Cat#M-016234-01-0005 siGENOME Human NELFA siRNA Pool Dharmacon Cat#M-012156-00-0005 (Continued on next page) e2 Cell Reports 34, 108759, February 16, 2021 Article ll OPEN ACCESS

    Generated:

    Article Title: Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Camptothecin Sigma-Aldrich Cat#208925 Etoposide Sigma-Aldrich Cat#E1383 CD437 Sigma-Aldrich Cat#C5865 Rad51 inhibitor (B02) Sigma-Aldrich Cat#SML0364 Rad52 inhibitor (AICAR) Sigma-Aldrich Cat#A9978 PARP inhibitor (Olaparib) Adooq Bioscience Cat#10111 Aphidicolin Sigma-Aldrich Cat#A4487 Critical commercial assays PureLink Genomic DNA Mini Kit Beckman Coulter Cat#A63881 DNA Clean & Concentrator-5 Thermo Fisher Scientific Cat#10002D RNeasy Mini Kit GeneTex Cat#GTX30920 RNA Clean & Concentrator-5 Polyplus Cat#409-10 Ribo-Zero Gold rRNA Removal Kit (H/M/R) Cat#MRZG12324 Random Primed DNA Labeling Kit Thermo Fisher Scientific Cat#K182001 Qubit dsDNA HS Assay Kit Zymo Research Cat#D4013 SensiFAST SYBR Lo-ROX Kit QIAGEN Cat#74106 Click-iT RNA Alexa Fluor 594 Imaging Kit Zymo Research Cat#R1015 Nextera XT DNA Library Preparation Kit Bioline Cat#BIO-94020 QIAseq Ultralow Input Library Kit Thermo Fisher Scientific Cat#C10330 KAPA RNA HyperPrep Kit with RiboErase (HMR) Sigma-Aldrich Cat#DUO92002 KAPA Library Quantification Kit Sigma-Aldrich Cat#DUO92004 ECL Western Blotting Substrate Sigma-Aldrich Cat#DUO92008 SuperScript III Reverse Transcriptase kit Illumina Cat#FC-131-1024 Deposited data All the datasets generated in this paper This paper GSE136294 BJ GRO-Seq Li et al., 2018 SRX3586216 CTR cells and RNAi of NELFB andNELFEGROSeq Liu et al., 2017 GSE98555 RPE EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 U2OS EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 CAP-Seq HeLa cells Tan-Wong et al., 2019 GSE87607 Ok-Seq RPE h-TERT Chen et al., 2019 GSE114017 Ok-Seq HeLa Petryk et al., 2016 SRP065949 ChIP-Seq ORC1 HeLa Dellino et al., 2013 GSE37583 ChIP-Seq MCM7 HeLa Sugimoto et al., 2018 GSE107248 ChIP-Seq RPA2 HeLa Zhang et al., 2017 GSE76661 ChOR-Seq mouse ES cells Stewart-Morgan et al., 2019 GSE128643 HeLa polyA RNA-Seq Encode Project Consortium ENCFF343WEZ ChIP-Seq 53BP1, RAD51, XRCC4 U2OS Clouaire et al., 2018 E-MTAB-5817 Experimental models: cell lines Human osteosarcoma (U2OS) ATCC HTB-96 Human immortalized fibroblasts (BJ-hTERT) ATCC CRL-4001 Oligonucleotides siGENOME Non-Targeting siRNA Pool #2 Dharmacon Cat#D-001206-14-05 siGENOME Human SUPT5H siRNA Pool Dharmacon Cat#M-016234-01-0005 siGENOME Human NELFA siRNA Pool Dharmacon Cat#M-012156-00-0005 (Continued on next page) e2 Cell Reports 34, 108759, February 16, 2021 Article ll OPEN ACCESS

    Chromatin Immunoprecipitation:

    Article Title: Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Camptothecin Sigma-Aldrich Cat#208925 Etoposide Sigma-Aldrich Cat#E1383 CD437 Sigma-Aldrich Cat#C5865 Rad51 inhibitor (B02) Sigma-Aldrich Cat#SML0364 Rad52 inhibitor (AICAR) Sigma-Aldrich Cat#A9978 PARP inhibitor (Olaparib) Adooq Bioscience Cat#10111 Aphidicolin Sigma-Aldrich Cat#A4487 Critical commercial assays PureLink Genomic DNA Mini Kit Beckman Coulter Cat#A63881 DNA Clean & Concentrator-5 Thermo Fisher Scientific Cat#10002D RNeasy Mini Kit GeneTex Cat#GTX30920 RNA Clean & Concentrator-5 Polyplus Cat#409-10 Ribo-Zero Gold rRNA Removal Kit (H/M/R) Cat#MRZG12324 Random Primed DNA Labeling Kit Thermo Fisher Scientific Cat#K182001 Qubit dsDNA HS Assay Kit Zymo Research Cat#D4013 SensiFAST SYBR Lo-ROX Kit QIAGEN Cat#74106 Click-iT RNA Alexa Fluor 594 Imaging Kit Zymo Research Cat#R1015 Nextera XT DNA Library Preparation Kit Bioline Cat#BIO-94020 QIAseq Ultralow Input Library Kit Thermo Fisher Scientific Cat#C10330 KAPA RNA HyperPrep Kit with RiboErase (HMR) Sigma-Aldrich Cat#DUO92002 KAPA Library Quantification Kit Sigma-Aldrich Cat#DUO92004 ECL Western Blotting Substrate Sigma-Aldrich Cat#DUO92008 SuperScript III Reverse Transcriptase kit Illumina Cat#FC-131-1024 Deposited data All the datasets generated in this paper This paper GSE136294 BJ GRO-Seq Li et al., 2018 SRX3586216 CTR cells and RNAi of NELFB andNELFEGROSeq Liu et al., 2017 GSE98555 RPE EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 U2OS EdU-Seq Macheret and Halazonetis, 2018 PRJNA397123 CAP-Seq HeLa cells Tan-Wong et al., 2019 GSE87607 Ok-Seq RPE h-TERT Chen et al., 2019 GSE114017 Ok-Seq HeLa Petryk et al., 2016 SRP065949 ChIP-Seq ORC1 HeLa Dellino et al., 2013 GSE37583 ChIP-Seq MCM7 HeLa Sugimoto et al., 2018 GSE107248 ChIP-Seq RPA2 HeLa Zhang et al., 2017 GSE76661 ChOR-Seq mouse ES cells Stewart-Morgan et al., 2019 GSE128643 HeLa polyA RNA-Seq Encode Project Consortium ENCFF343WEZ ChIP-Seq 53BP1, RAD51, XRCC4 U2OS Clouaire et al., 2018 E-MTAB-5817 Experimental models: cell lines Human osteosarcoma (U2OS) ATCC HTB-96 Human immortalized fibroblasts (BJ-hTERT) ATCC CRL-4001 Oligonucleotides siGENOME Non-Targeting siRNA Pool #2 Dharmacon Cat#D-001206-14-05 siGENOME Human SUPT5H siRNA Pool Dharmacon Cat#M-016234-01-0005 siGENOME Human NELFA siRNA Pool Dharmacon Cat#M-012156-00-0005 (Continued on next page) e2 Cell Reports 34, 108759, February 16, 2021 Article ll OPEN ACCESS



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    ATCC cell lines human osteosarcoma cells u2os atcc htb 96
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    human osteosarcoma u2os cell line  (ATCC)
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    ATCC human osteosarcoma u2os cell line
    ( A and B ) Agarose gel electrophoresis (images show Cy5 fluorophore emission) revealed consistent mobility when 8HB structures were incubated at 37°C in (A) cell culture media or (B) cytoplasmic (C) or nuclear (N) extract from <t>U2OS</t> cells, verifying structural stability and fluorophore attachment integrity up to 24 hours. ( C ) TEM imaging also confirmed that structures remain intact, shown for the 24-hour nuclear extract condition (Scale bar, 30 nm). ( D ) Agarose gel electrophoresis also revealed no changes in mobility in electroporation buffer (R buffer) and after being subjected to electroporation for structures alone or for structures with one or two antibodies (Ab) attached. The ethidium bromide stain is shown on top, and Cy5 emission channel at the bottom. ( E ) TEM imaging also confirmed that structures remain intact and antibodies remain attached in R buffer and after electroporation. Insets show zoomed-in views of a single 8HB structure with one or two antibodies attached (Scale bars, 30 nm). ( F and G ) 8HB double-labeled with Cy3 and Cy5 electroporated into U2OS cells exhibit colocalization of both fluorophores in the cytoplasm (F) and the nucleus (G). Scale bars are indicated in the panels and insets.
    Human Osteosarcoma U2os Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ( A and B ) Agarose gel electrophoresis (images show Cy5 fluorophore emission) revealed consistent mobility when 8HB structures were incubated at 37°C in (A) cell culture media or (B) cytoplasmic (C) or nuclear (N) extract from U2OS cells, verifying structural stability and fluorophore attachment integrity up to 24 hours. ( C ) TEM imaging also confirmed that structures remain intact, shown for the 24-hour nuclear extract condition (Scale bar, 30 nm). ( D ) Agarose gel electrophoresis also revealed no changes in mobility in electroporation buffer (R buffer) and after being subjected to electroporation for structures alone or for structures with one or two antibodies (Ab) attached. The ethidium bromide stain is shown on top, and Cy5 emission channel at the bottom. ( E ) TEM imaging also confirmed that structures remain intact and antibodies remain attached in R buffer and after electroporation. Insets show zoomed-in views of a single 8HB structure with one or two antibodies attached (Scale bars, 30 nm). ( F and G ) 8HB double-labeled with Cy3 and Cy5 electroporated into U2OS cells exhibit colocalization of both fluorophores in the cytoplasm (F) and the nucleus (G). Scale bars are indicated in the panels and insets.

    Journal: Science Advances

    Article Title: Piggybacking functionalized DNA nanostructures into live-cell nuclei

    doi: 10.1126/sciadv.adn9423

    Figure Lengend Snippet: ( A and B ) Agarose gel electrophoresis (images show Cy5 fluorophore emission) revealed consistent mobility when 8HB structures were incubated at 37°C in (A) cell culture media or (B) cytoplasmic (C) or nuclear (N) extract from U2OS cells, verifying structural stability and fluorophore attachment integrity up to 24 hours. ( C ) TEM imaging also confirmed that structures remain intact, shown for the 24-hour nuclear extract condition (Scale bar, 30 nm). ( D ) Agarose gel electrophoresis also revealed no changes in mobility in electroporation buffer (R buffer) and after being subjected to electroporation for structures alone or for structures with one or two antibodies (Ab) attached. The ethidium bromide stain is shown on top, and Cy5 emission channel at the bottom. ( E ) TEM imaging also confirmed that structures remain intact and antibodies remain attached in R buffer and after electroporation. Insets show zoomed-in views of a single 8HB structure with one or two antibodies attached (Scale bars, 30 nm). ( F and G ) 8HB double-labeled with Cy3 and Cy5 electroporated into U2OS cells exhibit colocalization of both fluorophores in the cytoplasm (F) and the nucleus (G). Scale bars are indicated in the panels and insets.

    Article Snippet: A human osteosarcoma U2OS cell line (ATCC HTB-96) was obtained from the American Type Culture Collection (Manassas, VA).

    Techniques: Agarose Gel Electrophoresis, Incubation, Cell Culture, Imaging, Electroporation, Staining, Labeling

    ( A ) HILO imaging at the mid-plane of U2OS cells illustrates DO structures inside cells for 8HB-8Cy5 with zero antibodies (left, 8HB-8Cy5), one Pol II antibody (middle, anti–Pol II 8HB-8Cy5 1 Ab), or two Pol II antibodies (right, anti–Pol II 8HB-8Cy5 2 Ab). A clear increase in Cy5 fluorescence emission in cell nuclei is evident when 8HB-8Cy5 are labeled with one or two Pol II antibodies. Upper images show zoomed-in views of the nucleus and the cytoplasm for each condition. Scale bars, 10 μm. ( B ) The number of observed particles in the nuclei was quantified for each condition, showing that some 8HB-8Cy5 enter the nucleus even without antibodies, and there is a significant increase in nuclear localization with one or two antibodies on 8HB-8Cy5 structures. **** P ≤ 0.0001; ns, not significant.

    Journal: Science Advances

    Article Title: Piggybacking functionalized DNA nanostructures into live-cell nuclei

    doi: 10.1126/sciadv.adn9423

    Figure Lengend Snippet: ( A ) HILO imaging at the mid-plane of U2OS cells illustrates DO structures inside cells for 8HB-8Cy5 with zero antibodies (left, 8HB-8Cy5), one Pol II antibody (middle, anti–Pol II 8HB-8Cy5 1 Ab), or two Pol II antibodies (right, anti–Pol II 8HB-8Cy5 2 Ab). A clear increase in Cy5 fluorescence emission in cell nuclei is evident when 8HB-8Cy5 are labeled with one or two Pol II antibodies. Upper images show zoomed-in views of the nucleus and the cytoplasm for each condition. Scale bars, 10 μm. ( B ) The number of observed particles in the nuclei was quantified for each condition, showing that some 8HB-8Cy5 enter the nucleus even without antibodies, and there is a significant increase in nuclear localization with one or two antibodies on 8HB-8Cy5 structures. **** P ≤ 0.0001; ns, not significant.

    Article Snippet: A human osteosarcoma U2OS cell line (ATCC HTB-96) was obtained from the American Type Culture Collection (Manassas, VA).

    Techniques: Imaging, Fluorescence, Labeling

    ( A ) Representative images of live U2OS cells 24 hours after electroporation with nonfunctionalized 8HB DO structures (right, 8HB No Cy5) or 8HB-8Cy5 DO structures functionalized with either one anti–Pol II antibody (anti–Pol II 8HB-8Cy5; left), one anti-MBP antibody (anti-MBP 8HB-8Cy5; second from left), or 8HB-8Cy5 with no antibodies (8HB-8Cy5; second from right). White arrowheads point to nuclear particles representing single DO structures. Color bars indicate the fluorescence intensity range of the Cy5 signal (scale is ×1000). Nuclear Hoechst staining is shown in blue. Scale bars, 5 μm. ( B ) Combined violin, box, and jitter plots showing the quantification of nuclear particles. A significantly higher number of particles per nuclear area were detected in cells that were electroporated with anti–Pol II 8HB-8Cy5 compared to the other three conditions ( H = 22.6447, P = 4.789 × 10 −5 , Kruskal-Wallis test). P values for pairwise comparisons using Dunn post hoc analyses are shown. n = 10. ( C ) Traces of tracked particles for anti–Pol II 8HB-8Cy5 within the nucleus depicted in (A). ( D ) Average MSD data measured from each of the eight nuclei analyzed and power-law fit over the entire data showing anomalous diffusion with an exponent of 0.4 (95% CI 0.2 to 0.6). ( E ) Average MSD data for Alexa 647–labeled anti–Pol II antibody–Pol II complex (anti–Pol II alone), without DO, from eight nuclei as in (D), showing anomalous diffusion with exponent 0.5 (95% CI 0.2 to 0.8).

    Journal: Science Advances

    Article Title: Piggybacking functionalized DNA nanostructures into live-cell nuclei

    doi: 10.1126/sciadv.adn9423

    Figure Lengend Snippet: ( A ) Representative images of live U2OS cells 24 hours after electroporation with nonfunctionalized 8HB DO structures (right, 8HB No Cy5) or 8HB-8Cy5 DO structures functionalized with either one anti–Pol II antibody (anti–Pol II 8HB-8Cy5; left), one anti-MBP antibody (anti-MBP 8HB-8Cy5; second from left), or 8HB-8Cy5 with no antibodies (8HB-8Cy5; second from right). White arrowheads point to nuclear particles representing single DO structures. Color bars indicate the fluorescence intensity range of the Cy5 signal (scale is ×1000). Nuclear Hoechst staining is shown in blue. Scale bars, 5 μm. ( B ) Combined violin, box, and jitter plots showing the quantification of nuclear particles. A significantly higher number of particles per nuclear area were detected in cells that were electroporated with anti–Pol II 8HB-8Cy5 compared to the other three conditions ( H = 22.6447, P = 4.789 × 10 −5 , Kruskal-Wallis test). P values for pairwise comparisons using Dunn post hoc analyses are shown. n = 10. ( C ) Traces of tracked particles for anti–Pol II 8HB-8Cy5 within the nucleus depicted in (A). ( D ) Average MSD data measured from each of the eight nuclei analyzed and power-law fit over the entire data showing anomalous diffusion with an exponent of 0.4 (95% CI 0.2 to 0.6). ( E ) Average MSD data for Alexa 647–labeled anti–Pol II antibody–Pol II complex (anti–Pol II alone), without DO, from eight nuclei as in (D), showing anomalous diffusion with exponent 0.5 (95% CI 0.2 to 0.8).

    Article Snippet: A human osteosarcoma U2OS cell line (ATCC HTB-96) was obtained from the American Type Culture Collection (Manassas, VA).

    Techniques: Electroporation, Fluorescence, Staining, Diffusion-based Assay, Labeling