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nuclear isolation buffer  (TaKaRa)


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    TaKaRa nuclear isolation buffer
    Nuclear Isolation Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/nuclear+isolation+buffer/NucleoSpin+96+Virus/pmc11148166-401-10-49
    Average 93 stars, based on 9 article reviews
    nuclear isolation buffer - by Bioz Stars, 2026-11
    93/100 stars

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    Related Articles

    Gene Expression:

    Article Title: Application of a recombinant replicase to localize the Trionyx sinensis hemorrhagic syndrome virus and evaluate its effects on antiviral genes of T. sinensis
    Article Snippet: The PCR amplification products were analyzed by elec‐ trophoresis on 1.2% (0.012 g/mL) agarose gels, and the target segment (TSHSV-661) was extracted using a DNA gel extraction kit (TIANGEN Biotech, China). .. 2.2.2 Construction of TSHSV-HP4 gene expression vector The purified TSHSV-661 segment was digested using BamHI and XhoII restriction enzymes at 37 °C for 3 h and the digested products were inserted into the pET-30a vector (TaKaRa, China) via a ligase en‐ zyme, and the recombinant plasmid was named as pET30a-TSHSV-661. .. The recombinant plasmid was 296 J Zhejiang Univ-Sci B (Biomed & Biotechnol) 2021 22(4):295-304 | transformed directly into Escherichia coli BL21 (DE3) cells (TaKaRa, Japan).

    Purification:

    Article Title: Application of a recombinant replicase to localize the Trionyx sinensis hemorrhagic syndrome virus and evaluate its effects on antiviral genes of T. sinensis
    Article Snippet: The PCR amplification products were analyzed by elec‐ trophoresis on 1.2% (0.012 g/mL) agarose gels, and the target segment (TSHSV-661) was extracted using a DNA gel extraction kit (TIANGEN Biotech, China). .. 2.2.2 Construction of TSHSV-HP4 gene expression vector The purified TSHSV-661 segment was digested using BamHI and XhoII restriction enzymes at 37 °C for 3 h and the digested products were inserted into the pET-30a vector (TaKaRa, China) via a ligase en‐ zyme, and the recombinant plasmid was named as pET30a-TSHSV-661. .. The recombinant plasmid was 296 J Zhejiang Univ-Sci B (Biomed & Biotechnol) 2021 22(4):295-304 | transformed directly into Escherichia coli BL21 (DE3) cells (TaKaRa, Japan).

    Recombinant:

    Article Title: Application of a recombinant replicase to localize the Trionyx sinensis hemorrhagic syndrome virus and evaluate its effects on antiviral genes of T. sinensis
    Article Snippet: The PCR amplification products were analyzed by elec‐ trophoresis on 1.2% (0.012 g/mL) agarose gels, and the target segment (TSHSV-661) was extracted using a DNA gel extraction kit (TIANGEN Biotech, China). .. 2.2.2 Construction of TSHSV-HP4 gene expression vector The purified TSHSV-661 segment was digested using BamHI and XhoII restriction enzymes at 37 °C for 3 h and the digested products were inserted into the pET-30a vector (TaKaRa, China) via a ligase en‐ zyme, and the recombinant plasmid was named as pET30a-TSHSV-661. .. The recombinant plasmid was 296 J Zhejiang Univ-Sci B (Biomed & Biotechnol) 2021 22(4):295-304 | transformed directly into Escherichia coli BL21 (DE3) cells (TaKaRa, Japan).

    Article Title: Development of an Immunotoxin Incorporating the Australian Jumper Ant Toxin, Pilosulin 1
    Article Snippet: .. 2.2.2.12 Generation of recombinant virus The recombinant baculovirus was generated according to the protocols described in the BacPAKTM Baculovirus Expression system manual (Clontech, Palo Alto, CA, USA) by co-transfecting St21 insect cells with recombinant BacPAK9 transfer vector and pre- digested BacPAK6 viral DNA. ..

    Article Title: Dynamic control of gene expression by ISGF3 and IRF1 during IFNβ and IFNγ signaling
    Article Snippet: .. The supernatant was removed and cells resuspended in 1 ml nuclear isolation buffer (NIB; 0.32 M sucrose, 3 mM CaCl 2 , 2 mM magnesium acetate, 0.1 mM EDTA, 10 mM Tris-HCl pH 8, 0.6% NP-40 and freshly added 1 mM DTT) supplemented with 0.2 U/μl recombinant RNase Inhibitor (Takara, Catalog # 2313B) and incubated for 5 min on ice. ..

    Article Title: STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4-thiouridine (s4U) Alfa Aesar AAJ60679-MC Methane thiosulfonate biotin-XX (MTSEA-biotin-XX) Biotium 91022 Dynabeads MyOne Streptavidin C1 beads Thermo Fisher Scientific 65002 meta-chloroperoxybenzoic acid (mCPBA) Alfa Aesar AAAL00286-14 2,2,2-trifluoroethylamine (TFEA) Thermo Fisher Scientific AC303500010 Flavopiridol Sigma Aldrich F3055-1MG Triptolide Invivogen Ant-tpl Agencourt RNAClean XP beads Beckman Coulter A63987 SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Takara Bio USA 634413 Deposited data S2 Start-seq Krebs et al., 2017; Elrod et al., 2019 GEO: GSE77369 Kc167 ChIP-nexus pausing half-lives Shao and Zeitlinger, 2017 https://github.com/zeitlingerlab/Shao_NG_2017 S2 PRO-seq Elrod et al., 2019 GEO: GSE114467 S2 H3K4me3, H3K4me1, H3K27ac ChIP-seq Henriques et al., 2018 GEO: GSE85191 S2 H3K36me3 Chen et al., 2012 GEO: GSE27679 S2 ATAC-seq Elrod et al., 2019 GEO: GSE114467 S2 STARR-seq Arnold et al., 2013; Zabidi et al., 2015 GEO: GSE57876 HEK293T TT-TL-seq Rosa-Mercado et al., 2021 GEO: GSE152063 Raw and analyzed S2 STL-seq data This paper GEO: GSE166202 Raw and analyzed 293T STL-seq data This paper GEO: GSE166202 Raw and analyzed S2 TT-TL-seq data This paper GEO: GSE166202 Experimental models: Cell lines HEK293T cells Steitz Lab NA S2 cells Simon Lab NA Oligonucleotides STL-seq custom 30 DNA adaptor Table S1 NA STL-seq custom 50 RNA adaptor Table S1 NA STL-seq custom RT primer Table S1 NA STL-seq custom indexing primers Table S1 NA Software and algorithms SAMtools Li et al., 2009 NA BEDTools Quinlan and Hall, 2010 NA FastUniq Xu et al., 2012 NA Cutadapt Martin, 2011 NA Bismark Krueger and Andrews, 2011 NA Bowtie2 Langmead and Salzberg, 2012 NA HISAT2 Kim et al., 2019 NA HTSeq Anders et al., 2015 NA edgeR Robinson et al., 2010 NA deepTools Ramı́rez et al., 2016 NA Stan Carpenter et al., 2017 NA (Continued on next page) Molecular Cell 81, 4398–4412.e1–e7, November 4, 2021 e1 ..

    Plasmid Preparation:

    Article Title: Application of a recombinant replicase to localize the Trionyx sinensis hemorrhagic syndrome virus and evaluate its effects on antiviral genes of T. sinensis
    Article Snippet: The PCR amplification products were analyzed by elec‐ trophoresis on 1.2% (0.012 g/mL) agarose gels, and the target segment (TSHSV-661) was extracted using a DNA gel extraction kit (TIANGEN Biotech, China). .. 2.2.2 Construction of TSHSV-HP4 gene expression vector The purified TSHSV-661 segment was digested using BamHI and XhoII restriction enzymes at 37 °C for 3 h and the digested products were inserted into the pET-30a vector (TaKaRa, China) via a ligase en‐ zyme, and the recombinant plasmid was named as pET30a-TSHSV-661. .. The recombinant plasmid was 296 J Zhejiang Univ-Sci B (Biomed & Biotechnol) 2021 22(4):295-304 | transformed directly into Escherichia coli BL21 (DE3) cells (TaKaRa, Japan).

    Article Title: Expression of bcl-X(L) restores cell survival, but not proliferation off effector differentiation, in CD28-deficient T lymphocytes.
    Article Snippet: .. The murine stem cell virus (MSCV) 2.2 vector (13) modified to contain an internal ribosomal binding site, IRES (Novagen), and the cDNA of green fluorescent protein (GFP) 1 (hGFP S65T; CLONTECH Laboratories, Inc.) were gifts of Dr. Bill Sha (University of California at Berkeley, Berkeley, CA; 14). ..

    Virus:

    Article Title: Development of an Immunotoxin Incorporating the Australian Jumper Ant Toxin, Pilosulin 1
    Article Snippet: .. 2.2.2.12 Generation of recombinant virus The recombinant baculovirus was generated according to the protocols described in the BacPAKTM Baculovirus Expression system manual (Clontech, Palo Alto, CA, USA) by co-transfecting St21 insect cells with recombinant BacPAK9 transfer vector and pre- digested BacPAK6 viral DNA. ..

    Article Title: Expression of bcl-X(L) restores cell survival, but not proliferation off effector differentiation, in CD28-deficient T lymphocytes.
    Article Snippet: .. The murine stem cell virus (MSCV) 2.2 vector (13) modified to contain an internal ribosomal binding site, IRES (Novagen), and the cDNA of green fluorescent protein (GFP) 1 (hGFP S65T; CLONTECH Laboratories, Inc.) were gifts of Dr. Bill Sha (University of California at Berkeley, Berkeley, CA; 14). ..

    Generated:

    Article Title: Development of an Immunotoxin Incorporating the Australian Jumper Ant Toxin, Pilosulin 1
    Article Snippet: .. 2.2.2.12 Generation of recombinant virus The recombinant baculovirus was generated according to the protocols described in the BacPAKTM Baculovirus Expression system manual (Clontech, Palo Alto, CA, USA) by co-transfecting St21 insect cells with recombinant BacPAK9 transfer vector and pre- digested BacPAK6 viral DNA. ..

    Article Title: Molecular characterization of SrSTP14, a sugar transporter from thermogenic skunk cabbage, and its possible role in developing pollen.
    Article Snippet: .. See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.2 | Isolation and sequencing of SrSTP1a, SrSTP1b, and SrSTP14 cDNAs To isolate SrSTP1 and SrSTP14 transcripts, total RNA was first extracted from the petals of female-stage spadices using the RNeasy Mini Kit (QIAGEN), and cDNAs were generated using a PrimeScript RT Reagent Kit (Takara). ..

    Article Title: Phosphorylation of Nur77 by the MEK-ERK-RSK cascade induces mitochondrial translocation and apoptosis in T cells.
    Article Snippet: The Gateway cassette was cloned from the MSCV2.2-IRES-GFP Gateway destination vector and inserted into BamHI and EcoRI sites of pRetroX-tight-Pur (Clontech), generating pRetroXtight-Pur-Gateway vector. .. Nur77-nuclear export sequence (NES) was generated in the MSCV 2.2-IRES-GFP vector by fusing the C terminus of Nur77 with NES (amino acids LALKLAGLDL) (25) using an in-fusion PCR cloning kit (Clontech). .. Nur77 and Nur77-NES were then PCR-cloned into EcoRI and NotI sites of pENTR1A (Invitrogen) followed by the insertion between SalI and EcoRI sites either of EGFP (from pEGFPC1, Clontech) or Flag tag at the N terminus of Nur77 coding sequence to generate pENTR1A-GFP-Nur77, pENTR1A-GFP-Nur77-NES, and pENTR 1A-Flag-Nur77-NES, respectively.

    Isolation:

    Article Title: Dynamic control of gene expression by ISGF3 and IRF1 during IFNβ and IFNγ signaling
    Article Snippet: .. The supernatant was removed and cells resuspended in 1 ml nuclear isolation buffer (NIB; 0.32 M sucrose, 3 mM CaCl 2 , 2 mM magnesium acetate, 0.1 mM EDTA, 10 mM Tris-HCl pH 8, 0.6% NP-40 and freshly added 1 mM DTT) supplemented with 0.2 U/μl recombinant RNase Inhibitor (Takara, Catalog # 2313B) and incubated for 5 min on ice. ..

    Article Title: Molecular characterization of SrSTP14, a sugar transporter from thermogenic skunk cabbage, and its possible role in developing pollen.
    Article Snippet: .. See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.2 | Isolation and sequencing of SrSTP1a, SrSTP1b, and SrSTP14 cDNAs To isolate SrSTP1 and SrSTP14 transcripts, total RNA was first extracted from the petals of female-stage spadices using the RNeasy Mini Kit (QIAGEN), and cDNAs were generated using a PrimeScript RT Reagent Kit (Takara). ..

    Incubation:

    Article Title: Dynamic control of gene expression by ISGF3 and IRF1 during IFNβ and IFNγ signaling
    Article Snippet: .. The supernatant was removed and cells resuspended in 1 ml nuclear isolation buffer (NIB; 0.32 M sucrose, 3 mM CaCl 2 , 2 mM magnesium acetate, 0.1 mM EDTA, 10 mM Tris-HCl pH 8, 0.6% NP-40 and freshly added 1 mM DTT) supplemented with 0.2 U/μl recombinant RNase Inhibitor (Takara, Catalog # 2313B) and incubated for 5 min on ice. ..

    Sequencing:

    Article Title: Molecular characterization of SrSTP14, a sugar transporter from thermogenic skunk cabbage, and its possible role in developing pollen.
    Article Snippet: .. See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.2 | Isolation and sequencing of SrSTP1a, SrSTP1b, and SrSTP14 cDNAs To isolate SrSTP1 and SrSTP14 transcripts, total RNA was first extracted from the petals of female-stage spadices using the RNeasy Mini Kit (QIAGEN), and cDNAs were generated using a PrimeScript RT Reagent Kit (Takara). ..

    Article Title: Phosphorylation of Nur77 by the MEK-ERK-RSK cascade induces mitochondrial translocation and apoptosis in T cells.
    Article Snippet: The Gateway cassette was cloned from the MSCV2.2-IRES-GFP Gateway destination vector and inserted into BamHI and EcoRI sites of pRetroX-tight-Pur (Clontech), generating pRetroXtight-Pur-Gateway vector. .. Nur77-nuclear export sequence (NES) was generated in the MSCV 2.2-IRES-GFP vector by fusing the C terminus of Nur77 with NES (amino acids LALKLAGLDL) (25) using an in-fusion PCR cloning kit (Clontech). .. Nur77 and Nur77-NES were then PCR-cloned into EcoRI and NotI sites of pENTR1A (Invitrogen) followed by the insertion between SalI and EcoRI sites either of EGFP (from pEGFPC1, Clontech) or Flag tag at the N terminus of Nur77 coding sequence to generate pENTR1A-GFP-Nur77, pENTR1A-GFP-Nur77-NES, and pENTR 1A-Flag-Nur77-NES, respectively.

    Modification:

    Article Title: Expression of bcl-X(L) restores cell survival, but not proliferation off effector differentiation, in CD28-deficient T lymphocytes.
    Article Snippet: .. The murine stem cell virus (MSCV) 2.2 vector (13) modified to contain an internal ribosomal binding site, IRES (Novagen), and the cDNA of green fluorescent protein (GFP) 1 (hGFP S65T; CLONTECH Laboratories, Inc.) were gifts of Dr. Bill Sha (University of California at Berkeley, Berkeley, CA; 14). ..

    Binding Assay:

    Article Title: Expression of bcl-X(L) restores cell survival, but not proliferation off effector differentiation, in CD28-deficient T lymphocytes.
    Article Snippet: .. The murine stem cell virus (MSCV) 2.2 vector (13) modified to contain an internal ribosomal binding site, IRES (Novagen), and the cDNA of green fluorescent protein (GFP) 1 (hGFP S65T; CLONTECH Laboratories, Inc.) were gifts of Dr. Bill Sha (University of California at Berkeley, Berkeley, CA; 14). ..

    Article Title: Role of high mobility group (HMG) chromatin proteins in DNA repair.
    Article Snippet: While the structure and composition of chromatin not only influences the type and extent of DNA damage incurred by eukaryotic cells, it also poses a major obstacle to the efficient repair of genomic lesions.. Understanding how DNA repair processes occur in the context of nuclear chromatin is a current experimental challenge, especially in mammalian cells where the powerful tools of genetic analysis that have been so successful in elucidating repair mechanisms in yeast have seen only limited application.. Even so, work over the last decade with both yeast and mammalian cells has provided a rather detailed description of how nucleosomes, the basic subunit of chromatin, influence both DNA damage and repair in all eukaryotic cells.

    Microarray:

    Article Title: Role of high mobility group (HMG) chromatin proteins in DNA repair.
    Article Snippet: While the structure and composition of chromatin not only influences the type and extent of DNA damage incurred by eukaryotic cells, it also poses a major obstacle to the efficient repair of genomic lesions.. Understanding how DNA repair processes occur in the context of nuclear chromatin is a current experimental challenge, especially in mammalian cells where the powerful tools of genetic analysis that have been so successful in elucidating repair mechanisms in yeast have seen only limited application.. Even so, work over the last decade with both yeast and mammalian cells has provided a rather detailed description of how nucleosomes, the basic subunit of chromatin, influence both DNA damage and repair in all eukaryotic cells.

    Expressing:

    Article Title: Role of high mobility group (HMG) chromatin proteins in DNA repair.
    Article Snippet: While the structure and composition of chromatin not only influences the type and extent of DNA damage incurred by eukaryotic cells, it also poses a major obstacle to the efficient repair of genomic lesions.. Understanding how DNA repair processes occur in the context of nuclear chromatin is a current experimental challenge, especially in mammalian cells where the powerful tools of genetic analysis that have been so successful in elucidating repair mechanisms in yeast have seen only limited application.. Even so, work over the last decade with both yeast and mammalian cells has provided a rather detailed description of how nucleosomes, the basic subunit of chromatin, influence both DNA damage and repair in all eukaryotic cells.

    Homologous Recombination:

    Article Title: Role of high mobility group (HMG) chromatin proteins in DNA repair.
    Article Snippet: While the structure and composition of chromatin not only influences the type and extent of DNA damage incurred by eukaryotic cells, it also poses a major obstacle to the efficient repair of genomic lesions.. Understanding how DNA repair processes occur in the context of nuclear chromatin is a current experimental challenge, especially in mammalian cells where the powerful tools of genetic analysis that have been so successful in elucidating repair mechanisms in yeast have seen only limited application.. Even so, work over the last decade with both yeast and mammalian cells has provided a rather detailed description of how nucleosomes, the basic subunit of chromatin, influence both DNA damage and repair in all eukaryotic cells.

    Ubiquitin Proteomics:

    Article Title: Role of high mobility group (HMG) chromatin proteins in DNA repair.
    Article Snippet: While the structure and composition of chromatin not only influences the type and extent of DNA damage incurred by eukaryotic cells, it also poses a major obstacle to the efficient repair of genomic lesions.. Understanding how DNA repair processes occur in the context of nuclear chromatin is a current experimental challenge, especially in mammalian cells where the powerful tools of genetic analysis that have been so successful in elucidating repair mechanisms in yeast have seen only limited application.. Even so, work over the last decade with both yeast and mammalian cells has provided a rather detailed description of how nucleosomes, the basic subunit of chromatin, influence both DNA damage and repair in all eukaryotic cells.

    RNA sequencing:

    Article Title: STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4-thiouridine (s4U) Alfa Aesar AAJ60679-MC Methane thiosulfonate biotin-XX (MTSEA-biotin-XX) Biotium 91022 Dynabeads MyOne Streptavidin C1 beads Thermo Fisher Scientific 65002 meta-chloroperoxybenzoic acid (mCPBA) Alfa Aesar AAAL00286-14 2,2,2-trifluoroethylamine (TFEA) Thermo Fisher Scientific AC303500010 Flavopiridol Sigma Aldrich F3055-1MG Triptolide Invivogen Ant-tpl Agencourt RNAClean XP beads Beckman Coulter A63987 SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Takara Bio USA 634413 Deposited data S2 Start-seq Krebs et al., 2017; Elrod et al., 2019 GEO: GSE77369 Kc167 ChIP-nexus pausing half-lives Shao and Zeitlinger, 2017 https://github.com/zeitlingerlab/Shao_NG_2017 S2 PRO-seq Elrod et al., 2019 GEO: GSE114467 S2 H3K4me3, H3K4me1, H3K27ac ChIP-seq Henriques et al., 2018 GEO: GSE85191 S2 H3K36me3 Chen et al., 2012 GEO: GSE27679 S2 ATAC-seq Elrod et al., 2019 GEO: GSE114467 S2 STARR-seq Arnold et al., 2013; Zabidi et al., 2015 GEO: GSE57876 HEK293T TT-TL-seq Rosa-Mercado et al., 2021 GEO: GSE152063 Raw and analyzed S2 STL-seq data This paper GEO: GSE166202 Raw and analyzed 293T STL-seq data This paper GEO: GSE166202 Raw and analyzed S2 TT-TL-seq data This paper GEO: GSE166202 Experimental models: Cell lines HEK293T cells Steitz Lab NA S2 cells Simon Lab NA Oligonucleotides STL-seq custom 30 DNA adaptor Table S1 NA STL-seq custom 50 RNA adaptor Table S1 NA STL-seq custom RT primer Table S1 NA STL-seq custom indexing primers Table S1 NA Software and algorithms SAMtools Li et al., 2009 NA BEDTools Quinlan and Hall, 2010 NA FastUniq Xu et al., 2012 NA Cutadapt Martin, 2011 NA Bismark Krueger and Andrews, 2011 NA Bowtie2 Langmead and Salzberg, 2012 NA HISAT2 Kim et al., 2019 NA HTSeq Anders et al., 2015 NA edgeR Robinson et al., 2010 NA deepTools Ramı́rez et al., 2016 NA Stan Carpenter et al., 2017 NA (Continued on next page) Molecular Cell 81, 4398–4412.e1–e7, November 4, 2021 e1 ..

    Chromatin Immunoprecipitation:

    Article Title: STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4-thiouridine (s4U) Alfa Aesar AAJ60679-MC Methane thiosulfonate biotin-XX (MTSEA-biotin-XX) Biotium 91022 Dynabeads MyOne Streptavidin C1 beads Thermo Fisher Scientific 65002 meta-chloroperoxybenzoic acid (mCPBA) Alfa Aesar AAAL00286-14 2,2,2-trifluoroethylamine (TFEA) Thermo Fisher Scientific AC303500010 Flavopiridol Sigma Aldrich F3055-1MG Triptolide Invivogen Ant-tpl Agencourt RNAClean XP beads Beckman Coulter A63987 SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Takara Bio USA 634413 Deposited data S2 Start-seq Krebs et al., 2017; Elrod et al., 2019 GEO: GSE77369 Kc167 ChIP-nexus pausing half-lives Shao and Zeitlinger, 2017 https://github.com/zeitlingerlab/Shao_NG_2017 S2 PRO-seq Elrod et al., 2019 GEO: GSE114467 S2 H3K4me3, H3K4me1, H3K27ac ChIP-seq Henriques et al., 2018 GEO: GSE85191 S2 H3K36me3 Chen et al., 2012 GEO: GSE27679 S2 ATAC-seq Elrod et al., 2019 GEO: GSE114467 S2 STARR-seq Arnold et al., 2013; Zabidi et al., 2015 GEO: GSE57876 HEK293T TT-TL-seq Rosa-Mercado et al., 2021 GEO: GSE152063 Raw and analyzed S2 STL-seq data This paper GEO: GSE166202 Raw and analyzed 293T STL-seq data This paper GEO: GSE166202 Raw and analyzed S2 TT-TL-seq data This paper GEO: GSE166202 Experimental models: Cell lines HEK293T cells Steitz Lab NA S2 cells Simon Lab NA Oligonucleotides STL-seq custom 30 DNA adaptor Table S1 NA STL-seq custom 50 RNA adaptor Table S1 NA STL-seq custom RT primer Table S1 NA STL-seq custom indexing primers Table S1 NA Software and algorithms SAMtools Li et al., 2009 NA BEDTools Quinlan and Hall, 2010 NA FastUniq Xu et al., 2012 NA Cutadapt Martin, 2011 NA Bismark Krueger and Andrews, 2011 NA Bowtie2 Langmead and Salzberg, 2012 NA HISAT2 Kim et al., 2019 NA HTSeq Anders et al., 2015 NA edgeR Robinson et al., 2010 NA deepTools Ramı́rez et al., 2016 NA Stan Carpenter et al., 2017 NA (Continued on next page) Molecular Cell 81, 4398–4412.e1–e7, November 4, 2021 e1 ..

    Software:

    Article Title: STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4-thiouridine (s4U) Alfa Aesar AAJ60679-MC Methane thiosulfonate biotin-XX (MTSEA-biotin-XX) Biotium 91022 Dynabeads MyOne Streptavidin C1 beads Thermo Fisher Scientific 65002 meta-chloroperoxybenzoic acid (mCPBA) Alfa Aesar AAAL00286-14 2,2,2-trifluoroethylamine (TFEA) Thermo Fisher Scientific AC303500010 Flavopiridol Sigma Aldrich F3055-1MG Triptolide Invivogen Ant-tpl Agencourt RNAClean XP beads Beckman Coulter A63987 SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Takara Bio USA 634413 Deposited data S2 Start-seq Krebs et al., 2017; Elrod et al., 2019 GEO: GSE77369 Kc167 ChIP-nexus pausing half-lives Shao and Zeitlinger, 2017 https://github.com/zeitlingerlab/Shao_NG_2017 S2 PRO-seq Elrod et al., 2019 GEO: GSE114467 S2 H3K4me3, H3K4me1, H3K27ac ChIP-seq Henriques et al., 2018 GEO: GSE85191 S2 H3K36me3 Chen et al., 2012 GEO: GSE27679 S2 ATAC-seq Elrod et al., 2019 GEO: GSE114467 S2 STARR-seq Arnold et al., 2013; Zabidi et al., 2015 GEO: GSE57876 HEK293T TT-TL-seq Rosa-Mercado et al., 2021 GEO: GSE152063 Raw and analyzed S2 STL-seq data This paper GEO: GSE166202 Raw and analyzed 293T STL-seq data This paper GEO: GSE166202 Raw and analyzed S2 TT-TL-seq data This paper GEO: GSE166202 Experimental models: Cell lines HEK293T cells Steitz Lab NA S2 cells Simon Lab NA Oligonucleotides STL-seq custom 30 DNA adaptor Table S1 NA STL-seq custom 50 RNA adaptor Table S1 NA STL-seq custom RT primer Table S1 NA STL-seq custom indexing primers Table S1 NA Software and algorithms SAMtools Li et al., 2009 NA BEDTools Quinlan and Hall, 2010 NA FastUniq Xu et al., 2012 NA Cutadapt Martin, 2011 NA Bismark Krueger and Andrews, 2011 NA Bowtie2 Langmead and Salzberg, 2012 NA HISAT2 Kim et al., 2019 NA HTSeq Anders et al., 2015 NA edgeR Robinson et al., 2010 NA deepTools Ramı́rez et al., 2016 NA Stan Carpenter et al., 2017 NA (Continued on next page) Molecular Cell 81, 4398–4412.e1–e7, November 4, 2021 e1 ..

    Polymerase Chain Reaction:

    Article Title: Phosphorylation of Nur77 by the MEK-ERK-RSK cascade induces mitochondrial translocation and apoptosis in T cells.
    Article Snippet: The Gateway cassette was cloned from the MSCV2.2-IRES-GFP Gateway destination vector and inserted into BamHI and EcoRI sites of pRetroX-tight-Pur (Clontech), generating pRetroXtight-Pur-Gateway vector. .. Nur77-nuclear export sequence (NES) was generated in the MSCV 2.2-IRES-GFP vector by fusing the C terminus of Nur77 with NES (amino acids LALKLAGLDL) (25) using an in-fusion PCR cloning kit (Clontech). .. Nur77 and Nur77-NES were then PCR-cloned into EcoRI and NotI sites of pENTR1A (Invitrogen) followed by the insertion between SalI and EcoRI sites either of EGFP (from pEGFPC1, Clontech) or Flag tag at the N terminus of Nur77 coding sequence to generate pENTR1A-GFP-Nur77, pENTR1A-GFP-Nur77-NES, and pENTR 1A-Flag-Nur77-NES, respectively.

    Cloning:

    Article Title: Phosphorylation of Nur77 by the MEK-ERK-RSK cascade induces mitochondrial translocation and apoptosis in T cells.
    Article Snippet: The Gateway cassette was cloned from the MSCV2.2-IRES-GFP Gateway destination vector and inserted into BamHI and EcoRI sites of pRetroX-tight-Pur (Clontech), generating pRetroXtight-Pur-Gateway vector. .. Nur77-nuclear export sequence (NES) was generated in the MSCV 2.2-IRES-GFP vector by fusing the C terminus of Nur77 with NES (amino acids LALKLAGLDL) (25) using an in-fusion PCR cloning kit (Clontech). .. Nur77 and Nur77-NES were then PCR-cloned into EcoRI and NotI sites of pENTR1A (Invitrogen) followed by the insertion between SalI and EcoRI sites either of EGFP (from pEGFPC1, Clontech) or Flag tag at the N terminus of Nur77 coding sequence to generate pENTR1A-GFP-Nur77, pENTR1A-GFP-Nur77-NES, and pENTR 1A-Flag-Nur77-NES, respectively.



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    nuclear isolation buffer  (Thermo Fisher)
    99
    Thermo Fisher nuclear isolation buffer
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    nuclear isolation buffer - by Bioz Stars, 2026-11
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    nuclear isolation buffer nib 3  (Cell Signaling Technology Inc)
    96
    Cell Signaling Technology Inc nuclear isolation buffer nib 3
    Nuclear Isolation Buffer Nib 3, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    nuclear isolation buffer nib 3 - by Bioz Stars, 2026-11
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    nuclear isolation buffer  (Beijing Solarbio Science)
    90
    Beijing Solarbio Science nuclear isolation buffer
    Nuclear Isolation Buffer, supplied by Beijing Solarbio Science, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    nuclear isolation buffer  (TaKaRa)
    93
    TaKaRa nuclear isolation buffer
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