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    Epigenomics ag rna-seq data
    Rna Seq Data, supplied by Epigenomics ag, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/rna+seq+data+processing/rna+seq+data/pmc04557131-176-0-5
    Average 90 stars, based on 1 article reviews
    rna-seq data - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Gene Expression:

    Article Title: Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles
    Article Snippet: The independent test dataset was also extracted in , including RNA-seq data and DNase-seq data in 70 paired samples from Roadmap Epigenomics Project .

    Article Title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia
    Article Snippet: The RNA-seq data for CD4 naive, CD8 naive, CD4 memory and fetal thymus were obtained from Roadmap Epigenomics Project and processed uniformly using our pipeline.

    Article Title: 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes.
    Article Snippet: In this study, we generated CUT&RUN data in primary human chondrocytes and Hi-C data in a human chondrocyte cell line and intersected them with publicly available RNA-seq data from our ex vivo OA model, ChIP-seq data from the Roadmap Epigenomics project, and OA GWAS variants from Boer et al.

    Article Title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer.
    Article Snippet: Background: DNA hydroxymethylation (5hmC) is known to be altered in human prostate cancer.. An animal model is required to study the functional roles of the ten eleven translocation (TET) DNA dioxygenases and the 5hmC modification in prostate cancer development and progression.. Methods:We characterized Tet expression, global genomic 5hmC, and genome‐wide 5hmC patterns, and the transcriptome, in the TRansgenic Adenocarcinoma of Mouse Prostate (TRAMP) autochthonous model of prostate cancer.

    Article Title: Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
    Article Snippet: To calculate the gene expression, we collected raw read count files or TPM files of RNA-seq data from Roadmap Epigenomics Project [ ], Encode project [ ], Cancer Cell Line Encyclopedia (CCLE) [ ] and published data or studies [ – ], respectively.

    Article Title: Differential exon usage of developmental genes is associated with deregulated epigenetic marks.
    Article Snippet: RNA-seq and ChIP-seq data used in this study are parts of the Roadmap Epigenomics Project21 and are available on ENCODE database34 at https:// www. encod eproj ect. org/.

    Article Title: A regulatory circuit controlled by extranuclear and nuclear retinoic acid receptor α determines T cell activation and function.
    Article Snippet: In brief Nuclear retinoic acid receptor alpha (RARa) regulates gene transcription upon the binding of retinoic acid (RA).. Larange, Takazawa, Kakugawa, Thiault et al. identify anRARa isoform in the cytoplasm of T cells (cRARa) and reveal that cRARa binds the TCR-ZAP-70 complex, thereby regulating T cell proliferation and effector differentiation.. RA counteracts TCRengaged RARa, resulting in suboptimal TCR activation but enhanced Treg cell differentiation.

    Article Title: Transcription factor binding site orientation and order are major drivers of gene regulatory activity
    Article Snippet: RNA-seq data from HepG2 were derived from the Roadmap Epigenomics Consortium using the processed FPKM expression matrix.

    RNA Sequencing:

    Article Title: Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles
    Article Snippet: The independent test dataset was also extracted in , including RNA-seq data and DNase-seq data in 70 paired samples from Roadmap Epigenomics Project .

    Article Title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia
    Article Snippet: The RNA-seq data for CD4 naive, CD8 naive, CD4 memory and fetal thymus were obtained from Roadmap Epigenomics Project and processed uniformly using our pipeline.

    Article Title: 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes.
    Article Snippet: In this study, we generated CUT&RUN data in primary human chondrocytes and Hi-C data in a human chondrocyte cell line and intersected them with publicly available RNA-seq data from our ex vivo OA model, ChIP-seq data from the Roadmap Epigenomics project, and OA GWAS variants from Boer et al.

    Article Title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer.
    Article Snippet: Background: DNA hydroxymethylation (5hmC) is known to be altered in human prostate cancer.. An animal model is required to study the functional roles of the ten eleven translocation (TET) DNA dioxygenases and the 5hmC modification in prostate cancer development and progression.. Methods:We characterized Tet expression, global genomic 5hmC, and genome‐wide 5hmC patterns, and the transcriptome, in the TRansgenic Adenocarcinoma of Mouse Prostate (TRAMP) autochthonous model of prostate cancer.

    Article Title: Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
    Article Snippet: To calculate the gene expression, we collected raw read count files or TPM files of RNA-seq data from Roadmap Epigenomics Project [ ], Encode project [ ], Cancer Cell Line Encyclopedia (CCLE) [ ] and published data or studies [ – ], respectively.

    Article Title: Differential exon usage of developmental genes is associated with deregulated epigenetic marks.
    Article Snippet: RNA-seq and ChIP-seq data used in this study are parts of the Roadmap Epigenomics Project21 and are available on ENCODE database34 at https:// www. encod eproj ect. org/.

    Article Title: A regulatory circuit controlled by extranuclear and nuclear retinoic acid receptor α determines T cell activation and function.
    Article Snippet: In brief Nuclear retinoic acid receptor alpha (RARa) regulates gene transcription upon the binding of retinoic acid (RA).. Larange, Takazawa, Kakugawa, Thiault et al. identify anRARa isoform in the cytoplasm of T cells (cRARa) and reveal that cRARa binds the TCR-ZAP-70 complex, thereby regulating T cell proliferation and effector differentiation.. RA counteracts TCRengaged RARa, resulting in suboptimal TCR activation but enhanced Treg cell differentiation.

    Article Title: Transcription factor binding site orientation and order are major drivers of gene regulatory activity
    Article Snippet: RNA-seq data from HepG2 were derived from the Roadmap Epigenomics Consortium using the processed FPKM expression matrix.

    Expressing:

    Article Title: Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles
    Article Snippet: The independent test dataset was also extracted in , including RNA-seq data and DNase-seq data in 70 paired samples from Roadmap Epigenomics Project .

    Article Title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia
    Article Snippet: The RNA-seq data for CD4 naive, CD8 naive, CD4 memory and fetal thymus were obtained from Roadmap Epigenomics Project and processed uniformly using our pipeline.

    Article Title: 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes.
    Article Snippet: In this study, we generated CUT&RUN data in primary human chondrocytes and Hi-C data in a human chondrocyte cell line and intersected them with publicly available RNA-seq data from our ex vivo OA model, ChIP-seq data from the Roadmap Epigenomics project, and OA GWAS variants from Boer et al.

    Article Title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer.
    Article Snippet: Background: DNA hydroxymethylation (5hmC) is known to be altered in human prostate cancer.. An animal model is required to study the functional roles of the ten eleven translocation (TET) DNA dioxygenases and the 5hmC modification in prostate cancer development and progression.. Methods:We characterized Tet expression, global genomic 5hmC, and genome‐wide 5hmC patterns, and the transcriptome, in the TRansgenic Adenocarcinoma of Mouse Prostate (TRAMP) autochthonous model of prostate cancer.

    Article Title: Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
    Article Snippet: To calculate the gene expression, we collected raw read count files or TPM files of RNA-seq data from Roadmap Epigenomics Project [ ], Encode project [ ], Cancer Cell Line Encyclopedia (CCLE) [ ] and published data or studies [ – ], respectively.

    Article Title: Differential exon usage of developmental genes is associated with deregulated epigenetic marks.
    Article Snippet: RNA-seq and ChIP-seq data used in this study are parts of the Roadmap Epigenomics Project21 and are available on ENCODE database34 at https:// www. encod eproj ect. org/.

    Article Title: A regulatory circuit controlled by extranuclear and nuclear retinoic acid receptor α determines T cell activation and function.
    Article Snippet: In brief Nuclear retinoic acid receptor alpha (RARa) regulates gene transcription upon the binding of retinoic acid (RA).. Larange, Takazawa, Kakugawa, Thiault et al. identify anRARa isoform in the cytoplasm of T cells (cRARa) and reveal that cRARa binds the TCR-ZAP-70 complex, thereby regulating T cell proliferation and effector differentiation.. RA counteracts TCRengaged RARa, resulting in suboptimal TCR activation but enhanced Treg cell differentiation.

    Article Title: Transcription factor binding site orientation and order are major drivers of gene regulatory activity
    Article Snippet: RNA-seq data from HepG2 were derived from the Roadmap Epigenomics Consortium using the processed FPKM expression matrix.

    Derivative Assay:

    Article Title: Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles
    Article Snippet: The independent test dataset was also extracted in , including RNA-seq data and DNase-seq data in 70 paired samples from Roadmap Epigenomics Project .

    Article Title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia
    Article Snippet: The RNA-seq data for CD4 naive, CD8 naive, CD4 memory and fetal thymus were obtained from Roadmap Epigenomics Project and processed uniformly using our pipeline.

    Article Title: 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes.
    Article Snippet: In this study, we generated CUT&RUN data in primary human chondrocytes and Hi-C data in a human chondrocyte cell line and intersected them with publicly available RNA-seq data from our ex vivo OA model, ChIP-seq data from the Roadmap Epigenomics project, and OA GWAS variants from Boer et al.

    Article Title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer.
    Article Snippet: Background: DNA hydroxymethylation (5hmC) is known to be altered in human prostate cancer.. An animal model is required to study the functional roles of the ten eleven translocation (TET) DNA dioxygenases and the 5hmC modification in prostate cancer development and progression.. Methods:We characterized Tet expression, global genomic 5hmC, and genome‐wide 5hmC patterns, and the transcriptome, in the TRansgenic Adenocarcinoma of Mouse Prostate (TRAMP) autochthonous model of prostate cancer.

    Article Title: Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
    Article Snippet: To calculate the gene expression, we collected raw read count files or TPM files of RNA-seq data from Roadmap Epigenomics Project [ ], Encode project [ ], Cancer Cell Line Encyclopedia (CCLE) [ ] and published data or studies [ – ], respectively.

    Article Title: Differential exon usage of developmental genes is associated with deregulated epigenetic marks.
    Article Snippet: RNA-seq and ChIP-seq data used in this study are parts of the Roadmap Epigenomics Project21 and are available on ENCODE database34 at https:// www. encod eproj ect. org/.

    Article Title: A regulatory circuit controlled by extranuclear and nuclear retinoic acid receptor α determines T cell activation and function.
    Article Snippet: In brief Nuclear retinoic acid receptor alpha (RARa) regulates gene transcription upon the binding of retinoic acid (RA).. Larange, Takazawa, Kakugawa, Thiault et al. identify anRARa isoform in the cytoplasm of T cells (cRARa) and reveal that cRARa binds the TCR-ZAP-70 complex, thereby regulating T cell proliferation and effector differentiation.. RA counteracts TCRengaged RARa, resulting in suboptimal TCR activation but enhanced Treg cell differentiation.

    Article Title: Transcription factor binding site orientation and order are major drivers of gene regulatory activity
    Article Snippet: RNA-seq data from HepG2 were derived from the Roadmap Epigenomics Consortium using the processed FPKM expression matrix.

    Generated:

    Article Title: Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles
    Article Snippet: The independent test dataset was also extracted in , including RNA-seq data and DNase-seq data in 70 paired samples from Roadmap Epigenomics Project .

    Article Title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia
    Article Snippet: The RNA-seq data for CD4 naive, CD8 naive, CD4 memory and fetal thymus were obtained from Roadmap Epigenomics Project and processed uniformly using our pipeline.

    Article Title: 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes.
    Article Snippet: In this study, we generated CUT&RUN data in primary human chondrocytes and Hi-C data in a human chondrocyte cell line and intersected them with publicly available RNA-seq data from our ex vivo OA model, ChIP-seq data from the Roadmap Epigenomics project, and OA GWAS variants from Boer et al.

    Article Title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer.
    Article Snippet: Background: DNA hydroxymethylation (5hmC) is known to be altered in human prostate cancer.. An animal model is required to study the functional roles of the ten eleven translocation (TET) DNA dioxygenases and the 5hmC modification in prostate cancer development and progression.. Methods:We characterized Tet expression, global genomic 5hmC, and genome‐wide 5hmC patterns, and the transcriptome, in the TRansgenic Adenocarcinoma of Mouse Prostate (TRAMP) autochthonous model of prostate cancer.

    Article Title: Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
    Article Snippet: To calculate the gene expression, we collected raw read count files or TPM files of RNA-seq data from Roadmap Epigenomics Project [ ], Encode project [ ], Cancer Cell Line Encyclopedia (CCLE) [ ] and published data or studies [ – ], respectively.

    Article Title: Differential exon usage of developmental genes is associated with deregulated epigenetic marks.
    Article Snippet: RNA-seq and ChIP-seq data used in this study are parts of the Roadmap Epigenomics Project21 and are available on ENCODE database34 at https:// www. encod eproj ect. org/.

    Article Title: A regulatory circuit controlled by extranuclear and nuclear retinoic acid receptor α determines T cell activation and function.
    Article Snippet: In brief Nuclear retinoic acid receptor alpha (RARa) regulates gene transcription upon the binding of retinoic acid (RA).. Larange, Takazawa, Kakugawa, Thiault et al. identify anRARa isoform in the cytoplasm of T cells (cRARa) and reveal that cRARa binds the TCR-ZAP-70 complex, thereby regulating T cell proliferation and effector differentiation.. RA counteracts TCRengaged RARa, resulting in suboptimal TCR activation but enhanced Treg cell differentiation.

    Article Title: Transcription factor binding site orientation and order are major drivers of gene regulatory activity
    Article Snippet: RNA-seq data from HepG2 were derived from the Roadmap Epigenomics Consortium using the processed FPKM expression matrix.

    Hi-C:

    Article Title: Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles
    Article Snippet: The independent test dataset was also extracted in , including RNA-seq data and DNase-seq data in 70 paired samples from Roadmap Epigenomics Project .

    Article Title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia
    Article Snippet: The RNA-seq data for CD4 naive, CD8 naive, CD4 memory and fetal thymus were obtained from Roadmap Epigenomics Project and processed uniformly using our pipeline.

    Article Title: 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes.
    Article Snippet: In this study, we generated CUT&RUN data in primary human chondrocytes and Hi-C data in a human chondrocyte cell line and intersected them with publicly available RNA-seq data from our ex vivo OA model, ChIP-seq data from the Roadmap Epigenomics project, and OA GWAS variants from Boer et al.

    Article Title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer.
    Article Snippet: Background: DNA hydroxymethylation (5hmC) is known to be altered in human prostate cancer.. An animal model is required to study the functional roles of the ten eleven translocation (TET) DNA dioxygenases and the 5hmC modification in prostate cancer development and progression.. Methods:We characterized Tet expression, global genomic 5hmC, and genome‐wide 5hmC patterns, and the transcriptome, in the TRansgenic Adenocarcinoma of Mouse Prostate (TRAMP) autochthonous model of prostate cancer.

    Article Title: Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
    Article Snippet: To calculate the gene expression, we collected raw read count files or TPM files of RNA-seq data from Roadmap Epigenomics Project [ ], Encode project [ ], Cancer Cell Line Encyclopedia (CCLE) [ ] and published data or studies [ – ], respectively.

    Article Title: Differential exon usage of developmental genes is associated with deregulated epigenetic marks.
    Article Snippet: RNA-seq and ChIP-seq data used in this study are parts of the Roadmap Epigenomics Project21 and are available on ENCODE database34 at https:// www. encod eproj ect. org/.

    Article Title: A regulatory circuit controlled by extranuclear and nuclear retinoic acid receptor α determines T cell activation and function.
    Article Snippet: In brief Nuclear retinoic acid receptor alpha (RARa) regulates gene transcription upon the binding of retinoic acid (RA).. Larange, Takazawa, Kakugawa, Thiault et al. identify anRARa isoform in the cytoplasm of T cells (cRARa) and reveal that cRARa binds the TCR-ZAP-70 complex, thereby regulating T cell proliferation and effector differentiation.. RA counteracts TCRengaged RARa, resulting in suboptimal TCR activation but enhanced Treg cell differentiation.

    Article Title: Transcription factor binding site orientation and order are major drivers of gene regulatory activity
    Article Snippet: RNA-seq data from HepG2 were derived from the Roadmap Epigenomics Consortium using the processed FPKM expression matrix.

    Ex Vivo:

    Article Title: Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles
    Article Snippet: The independent test dataset was also extracted in , including RNA-seq data and DNase-seq data in 70 paired samples from Roadmap Epigenomics Project .

    Article Title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia
    Article Snippet: The RNA-seq data for CD4 naive, CD8 naive, CD4 memory and fetal thymus were obtained from Roadmap Epigenomics Project and processed uniformly using our pipeline.

    Article Title: 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes.
    Article Snippet: In this study, we generated CUT&RUN data in primary human chondrocytes and Hi-C data in a human chondrocyte cell line and intersected them with publicly available RNA-seq data from our ex vivo OA model, ChIP-seq data from the Roadmap Epigenomics project, and OA GWAS variants from Boer et al.

    Article Title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer.
    Article Snippet: Background: DNA hydroxymethylation (5hmC) is known to be altered in human prostate cancer.. An animal model is required to study the functional roles of the ten eleven translocation (TET) DNA dioxygenases and the 5hmC modification in prostate cancer development and progression.. Methods:We characterized Tet expression, global genomic 5hmC, and genome‐wide 5hmC patterns, and the transcriptome, in the TRansgenic Adenocarcinoma of Mouse Prostate (TRAMP) autochthonous model of prostate cancer.

    Article Title: Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
    Article Snippet: To calculate the gene expression, we collected raw read count files or TPM files of RNA-seq data from Roadmap Epigenomics Project [ ], Encode project [ ], Cancer Cell Line Encyclopedia (CCLE) [ ] and published data or studies [ – ], respectively.

    Article Title: Differential exon usage of developmental genes is associated with deregulated epigenetic marks.
    Article Snippet: RNA-seq and ChIP-seq data used in this study are parts of the Roadmap Epigenomics Project21 and are available on ENCODE database34 at https:// www. encod eproj ect. org/.

    Article Title: A regulatory circuit controlled by extranuclear and nuclear retinoic acid receptor α determines T cell activation and function.
    Article Snippet: In brief Nuclear retinoic acid receptor alpha (RARa) regulates gene transcription upon the binding of retinoic acid (RA).. Larange, Takazawa, Kakugawa, Thiault et al. identify anRARa isoform in the cytoplasm of T cells (cRARa) and reveal that cRARa binds the TCR-ZAP-70 complex, thereby regulating T cell proliferation and effector differentiation.. RA counteracts TCRengaged RARa, resulting in suboptimal TCR activation but enhanced Treg cell differentiation.

    Article Title: Transcription factor binding site orientation and order are major drivers of gene regulatory activity
    Article Snippet: RNA-seq data from HepG2 were derived from the Roadmap Epigenomics Consortium using the processed FPKM expression matrix.

    Chromatin Immunoprecipitation:

    Article Title: Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles
    Article Snippet: The independent test dataset was also extracted in , including RNA-seq data and DNase-seq data in 70 paired samples from Roadmap Epigenomics Project .

    Article Title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia
    Article Snippet: The RNA-seq data for CD4 naive, CD8 naive, CD4 memory and fetal thymus were obtained from Roadmap Epigenomics Project and processed uniformly using our pipeline.

    Article Title: 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes.
    Article Snippet: In this study, we generated CUT&RUN data in primary human chondrocytes and Hi-C data in a human chondrocyte cell line and intersected them with publicly available RNA-seq data from our ex vivo OA model, ChIP-seq data from the Roadmap Epigenomics project, and OA GWAS variants from Boer et al.

    Article Title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer.
    Article Snippet: Background: DNA hydroxymethylation (5hmC) is known to be altered in human prostate cancer.. An animal model is required to study the functional roles of the ten eleven translocation (TET) DNA dioxygenases and the 5hmC modification in prostate cancer development and progression.. Methods:We characterized Tet expression, global genomic 5hmC, and genome‐wide 5hmC patterns, and the transcriptome, in the TRansgenic Adenocarcinoma of Mouse Prostate (TRAMP) autochthonous model of prostate cancer.

    Article Title: Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
    Article Snippet: To calculate the gene expression, we collected raw read count files or TPM files of RNA-seq data from Roadmap Epigenomics Project [ ], Encode project [ ], Cancer Cell Line Encyclopedia (CCLE) [ ] and published data or studies [ – ], respectively.

    Article Title: Differential exon usage of developmental genes is associated with deregulated epigenetic marks.
    Article Snippet: RNA-seq and ChIP-seq data used in this study are parts of the Roadmap Epigenomics Project21 and are available on ENCODE database34 at https:// www. encod eproj ect. org/.

    Article Title: A regulatory circuit controlled by extranuclear and nuclear retinoic acid receptor α determines T cell activation and function.
    Article Snippet: In brief Nuclear retinoic acid receptor alpha (RARa) regulates gene transcription upon the binding of retinoic acid (RA).. Larange, Takazawa, Kakugawa, Thiault et al. identify anRARa isoform in the cytoplasm of T cells (cRARa) and reveal that cRARa binds the TCR-ZAP-70 complex, thereby regulating T cell proliferation and effector differentiation.. RA counteracts TCRengaged RARa, resulting in suboptimal TCR activation but enhanced Treg cell differentiation.

    Article Title: Transcription factor binding site orientation and order are major drivers of gene regulatory activity
    Article Snippet: RNA-seq data from HepG2 were derived from the Roadmap Epigenomics Consortium using the processed FPKM expression matrix.

    GWAS:

    Article Title: Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles
    Article Snippet: The independent test dataset was also extracted in , including RNA-seq data and DNase-seq data in 70 paired samples from Roadmap Epigenomics Project .

    Article Title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia
    Article Snippet: The RNA-seq data for CD4 naive, CD8 naive, CD4 memory and fetal thymus were obtained from Roadmap Epigenomics Project and processed uniformly using our pipeline.

    Article Title: 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes.
    Article Snippet: In this study, we generated CUT&RUN data in primary human chondrocytes and Hi-C data in a human chondrocyte cell line and intersected them with publicly available RNA-seq data from our ex vivo OA model, ChIP-seq data from the Roadmap Epigenomics project, and OA GWAS variants from Boer et al.

    Article Title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer.
    Article Snippet: Background: DNA hydroxymethylation (5hmC) is known to be altered in human prostate cancer.. An animal model is required to study the functional roles of the ten eleven translocation (TET) DNA dioxygenases and the 5hmC modification in prostate cancer development and progression.. Methods:We characterized Tet expression, global genomic 5hmC, and genome‐wide 5hmC patterns, and the transcriptome, in the TRansgenic Adenocarcinoma of Mouse Prostate (TRAMP) autochthonous model of prostate cancer.

    Article Title: Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
    Article Snippet: To calculate the gene expression, we collected raw read count files or TPM files of RNA-seq data from Roadmap Epigenomics Project [ ], Encode project [ ], Cancer Cell Line Encyclopedia (CCLE) [ ] and published data or studies [ – ], respectively.

    Article Title: Differential exon usage of developmental genes is associated with deregulated epigenetic marks.
    Article Snippet: RNA-seq and ChIP-seq data used in this study are parts of the Roadmap Epigenomics Project21 and are available on ENCODE database34 at https:// www. encod eproj ect. org/.

    Article Title: A regulatory circuit controlled by extranuclear and nuclear retinoic acid receptor α determines T cell activation and function.
    Article Snippet: In brief Nuclear retinoic acid receptor alpha (RARa) regulates gene transcription upon the binding of retinoic acid (RA).. Larange, Takazawa, Kakugawa, Thiault et al. identify anRARa isoform in the cytoplasm of T cells (cRARa) and reveal that cRARa binds the TCR-ZAP-70 complex, thereby regulating T cell proliferation and effector differentiation.. RA counteracts TCRengaged RARa, resulting in suboptimal TCR activation but enhanced Treg cell differentiation.

    Article Title: Transcription factor binding site orientation and order are major drivers of gene regulatory activity
    Article Snippet: RNA-seq data from HepG2 were derived from the Roadmap Epigenomics Consortium using the processed FPKM expression matrix.



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    Processed Single Cell Rna Seq Data, supplied by Mendeley Ltd, 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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    Association of BEND2 fusions with poor clinical outcomes (A) Diagram of sample composition for the pooled BEND2 cohort of <t>pNET.</t> (B) Kaplan-Meier curve of disease-specific survival rate regarding BEND2 rearrangement status. (C) Forest plot showing the hazard ratio (95% CI) in the univariate Cox regression and multivariate regression after adjusting for major clinicopathological features and the corresponding p values. The total number for the cohort, the number of cases per variable category, and the number of events (disease-specific deaths) for each level were also indicated.
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    rna-seq sample processing and data analysis  (Ribobio co)
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    Association of BEND2 fusions with poor clinical outcomes (A) Diagram of sample composition for the pooled BEND2 cohort of <t>pNET.</t> (B) Kaplan-Meier curve of disease-specific survival rate regarding BEND2 rearrangement status. (C) Forest plot showing the hazard ratio (95% CI) in the univariate Cox regression and multivariate regression after adjusting for major clinicopathological features and the corresponding p values. The total number for the cohort, the number of cases per variable category, and the number of events (disease-specific deaths) for each level were also indicated.
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    Association of BEND2 fusions with poor clinical outcomes (A) Diagram of sample composition for the pooled BEND2 cohort of <t>pNET.</t> (B) Kaplan-Meier curve of disease-specific survival rate regarding BEND2 rearrangement status. (C) Forest plot showing the hazard ratio (95% CI) in the univariate Cox regression and multivariate regression after adjusting for major clinicopathological features and the corresponding p values. The total number for the cohort, the number of cases per variable category, and the number of events (disease-specific deaths) for each level were also indicated.
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    Association of BEND2 fusions with poor clinical outcomes (A) Diagram of sample composition for the pooled BEND2 cohort of <t>pNET.</t> (B) Kaplan-Meier curve of disease-specific survival rate regarding BEND2 rearrangement status. (C) Forest plot showing the hazard ratio (95% CI) in the univariate Cox regression and multivariate regression after adjusting for major clinicopathological features and the corresponding p values. The total number for the cohort, the number of cases per variable category, and the number of events (disease-specific deaths) for each level were also indicated.
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    Association of BEND2 fusions with poor clinical outcomes (A) Diagram of sample composition for the pooled BEND2 cohort of <t>pNET.</t> (B) Kaplan-Meier curve of disease-specific survival rate regarding BEND2 rearrangement status. (C) Forest plot showing the hazard ratio (95% CI) in the univariate Cox regression and multivariate regression after adjusting for major clinicopathological features and the corresponding p values. The total number for the cohort, the number of cases per variable category, and the number of events (disease-specific deaths) for each level were also indicated.
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    Image Search Results


    Association of BEND2 fusions with poor clinical outcomes (A) Diagram of sample composition for the pooled BEND2 cohort of pNET. (B) Kaplan-Meier curve of disease-specific survival rate regarding BEND2 rearrangement status. (C) Forest plot showing the hazard ratio (95% CI) in the univariate Cox regression and multivariate regression after adjusting for major clinicopathological features and the corresponding p values. The total number for the cohort, the number of cases per variable category, and the number of events (disease-specific deaths) for each level were also indicated.

    Journal: Cell Reports Medicine

    Article Title: Molecular taxonomy of pancreatic neuroendocrine tumors reveals BEND2 -fusions-driven transcriptional plasticity and therapeutic vulnerabilities

    doi: 10.1016/j.xcrm.2026.102642

    Figure Lengend Snippet: Association of BEND2 fusions with poor clinical outcomes (A) Diagram of sample composition for the pooled BEND2 cohort of pNET. (B) Kaplan-Meier curve of disease-specific survival rate regarding BEND2 rearrangement status. (C) Forest plot showing the hazard ratio (95% CI) in the univariate Cox regression and multivariate regression after adjusting for major clinicopathological features and the corresponding p values. The total number for the cohort, the number of cases per variable category, and the number of events (disease-specific deaths) for each level were also indicated.

    Article Snippet: Pre-processed bulk RNA-seq data from pNET clinical samples and cell lines (this study) , Mendeley Data , https://data.mendeley.com/datasets/r9m66rjtxy/1.

    Techniques:

    Inter-tumor heterogeneity at single-nuclei level (A) UMAP representation of 43,619 nuclei isolated from nine pNET samples with tumor purity annotated at the top left corner. (B) UMAP showing a separation between tumor cells and non-tumor cells. Tumor cells were grouped according to the five-subtype bulk classification, referred as pseudo-bulk sn-clusters. (C) Dot plot of canonical marker genes across all identified cell populations. Dot size indicates the proportion of cells expressing a gene, and color intensity reflects mean expression levels. (D) Heatmap of the Hallmark signaling pathways specific for each of the five pseudo-bulk sn-clusters based on GSVA enrichment scores. (E) Regulon specificity plot showing the top six regulons identified for each of the five pseudo-bulk sn-clusters. The x axis of the plot represents the genes within the regulon, while the y axis represents the specificity score. (F) Validation of bulk subtype-specific regulon on the bulk pNET cohort using GSVA based on a set of target genes within a regulon.

    Journal: Cell Reports Medicine

    Article Title: Molecular taxonomy of pancreatic neuroendocrine tumors reveals BEND2 -fusions-driven transcriptional plasticity and therapeutic vulnerabilities

    doi: 10.1016/j.xcrm.2026.102642

    Figure Lengend Snippet: Inter-tumor heterogeneity at single-nuclei level (A) UMAP representation of 43,619 nuclei isolated from nine pNET samples with tumor purity annotated at the top left corner. (B) UMAP showing a separation between tumor cells and non-tumor cells. Tumor cells were grouped according to the five-subtype bulk classification, referred as pseudo-bulk sn-clusters. (C) Dot plot of canonical marker genes across all identified cell populations. Dot size indicates the proportion of cells expressing a gene, and color intensity reflects mean expression levels. (D) Heatmap of the Hallmark signaling pathways specific for each of the five pseudo-bulk sn-clusters based on GSVA enrichment scores. (E) Regulon specificity plot showing the top six regulons identified for each of the five pseudo-bulk sn-clusters. The x axis of the plot represents the genes within the regulon, while the y axis represents the specificity score. (F) Validation of bulk subtype-specific regulon on the bulk pNET cohort using GSVA based on a set of target genes within a regulon.

    Article Snippet: Pre-processed bulk RNA-seq data from pNET clinical samples and cell lines (this study) , Mendeley Data , https://data.mendeley.com/datasets/r9m66rjtxy/1.

    Techniques: Isolation, Marker, Expressing, Protein-Protein interactions, Biomarker Discovery

    Cell-cell communication network and in silico drug sensitivity prediction in pNET subtypes (A) Cell-cell communication network visualized in Cytoscape, depicting the number and strength of interactions between tumor and microenvironmental cell populations. Nodes represent cell types, and edges represent intercellular interactions, with edge width and color reflecting interaction strength and frequency. (B) Bubble plot of selected ligand-receptor pairs between tumor subtypes and non-tumor microenvironmental cell populations. (C) Correlation plots showing associations between gene expression and deconvoluted cell-type proportions in bulk pNET samples. (D) Kaplan-Meier survival curves showing different DSS rates between pNET patients with high and low expression of genes of interest, including NOTCH3 (left), CD74 (middle), and the geometric mean value of these two genes (right). Patients were categorized into different groups according to the optimal thresholding. (E) Mechanisms of action of the 10 compounds predicted by Connectivity Map (CMap) analysis to preferentially target the BEND2 fusion. (F) Predicted sensitivities to 12 HDAC inhibitors across pNET subtypes based on GDSC database analyses. Statistical comparisons were performed using the Kruskal-Wallis test. p < 0.1; ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001.

    Journal: Cell Reports Medicine

    Article Title: Molecular taxonomy of pancreatic neuroendocrine tumors reveals BEND2 -fusions-driven transcriptional plasticity and therapeutic vulnerabilities

    doi: 10.1016/j.xcrm.2026.102642

    Figure Lengend Snippet: Cell-cell communication network and in silico drug sensitivity prediction in pNET subtypes (A) Cell-cell communication network visualized in Cytoscape, depicting the number and strength of interactions between tumor and microenvironmental cell populations. Nodes represent cell types, and edges represent intercellular interactions, with edge width and color reflecting interaction strength and frequency. (B) Bubble plot of selected ligand-receptor pairs between tumor subtypes and non-tumor microenvironmental cell populations. (C) Correlation plots showing associations between gene expression and deconvoluted cell-type proportions in bulk pNET samples. (D) Kaplan-Meier survival curves showing different DSS rates between pNET patients with high and low expression of genes of interest, including NOTCH3 (left), CD74 (middle), and the geometric mean value of these two genes (right). Patients were categorized into different groups according to the optimal thresholding. (E) Mechanisms of action of the 10 compounds predicted by Connectivity Map (CMap) analysis to preferentially target the BEND2 fusion. (F) Predicted sensitivities to 12 HDAC inhibitors across pNET subtypes based on GDSC database analyses. Statistical comparisons were performed using the Kruskal-Wallis test. p < 0.1; ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001.

    Article Snippet: Pre-processed bulk RNA-seq data from pNET clinical samples and cell lines (this study) , Mendeley Data , https://data.mendeley.com/datasets/r9m66rjtxy/1.

    Techniques: In Silico, Gene Expression, Expressing

    BEND2 fusions induce transcriptional reprogramming and morphological plasticity in pNET tumor cells (A) Phase-contrast microscopy images of BON1 cells at 48 h post-induction showing morphological changes following overexpression of BEND2 -only, CHD7 - BEND2 , EWSR1 - BEND2 , or mCherry control. (B) Bar plot showing the number of differentially expressed genes at 12 and 48 h across all BON1 cell line models, including EWSR1 (E), BEND2 (B), CHD7 - BEND2 (CB), and EWSR1 - BEND2 (EB), compared to the mCherry (M) control. (C) Heatmap illustrating transcriptomic clustering of BON1 cell lines at 48 h (D) Venn diagram showing overlapping significantly upregulated transcription factors (TFs) in CHD7 - BEND2 and EWSR1 - BEND2 models compared to controls at 12 h (E) Bar plot of ASCL1 expression across BON1 cell line models at 12 and 48 h. Data are represented as mean ± SEM. (F) Heatmap showing transcriptional activation of neurodevelopmental, mesenchymal, and immune-related TFs in fusion-expressing BON1 cells at 48 h, accompanied by ASCL1 downregulation, activation of GAST-high subtype-specific regulons, and upregulation of immune checkpoint genes PDCD1 and CD274 . (G) Heatmap illustrating temporal transcriptomic shifts in BON1 fusion models using a 50-gene classifier (25 neuroendocrine and 25 non-neuroendocrine genes) derived from human SCLC lines. (H) GSEA results showing transcriptional reprogramming at 48 h in BEND2 fusion lines compared to 12 h (I) Bar plot showing GATA6 expression uniquely and robustly upregulated in BEND2 fusion lines at both 12 and 48 h. Data are represented as mean ± SEM. (J) Bar plot showing specific upregulation of POMC in BON1 cells expressing EWSR1 - BEND2 at 48 h. Data are represented as mean ± SEM. (K) Bar plot showing markedly higher POMC expression in the EWSR1 - BEND2 -positive tumor compared to the CHD7 - BEND2 -positive tumor in the clinical cohort.

    Journal: Cell Reports Medicine

    Article Title: Molecular taxonomy of pancreatic neuroendocrine tumors reveals BEND2 -fusions-driven transcriptional plasticity and therapeutic vulnerabilities

    doi: 10.1016/j.xcrm.2026.102642

    Figure Lengend Snippet: BEND2 fusions induce transcriptional reprogramming and morphological plasticity in pNET tumor cells (A) Phase-contrast microscopy images of BON1 cells at 48 h post-induction showing morphological changes following overexpression of BEND2 -only, CHD7 - BEND2 , EWSR1 - BEND2 , or mCherry control. (B) Bar plot showing the number of differentially expressed genes at 12 and 48 h across all BON1 cell line models, including EWSR1 (E), BEND2 (B), CHD7 - BEND2 (CB), and EWSR1 - BEND2 (EB), compared to the mCherry (M) control. (C) Heatmap illustrating transcriptomic clustering of BON1 cell lines at 48 h (D) Venn diagram showing overlapping significantly upregulated transcription factors (TFs) in CHD7 - BEND2 and EWSR1 - BEND2 models compared to controls at 12 h (E) Bar plot of ASCL1 expression across BON1 cell line models at 12 and 48 h. Data are represented as mean ± SEM. (F) Heatmap showing transcriptional activation of neurodevelopmental, mesenchymal, and immune-related TFs in fusion-expressing BON1 cells at 48 h, accompanied by ASCL1 downregulation, activation of GAST-high subtype-specific regulons, and upregulation of immune checkpoint genes PDCD1 and CD274 . (G) Heatmap illustrating temporal transcriptomic shifts in BON1 fusion models using a 50-gene classifier (25 neuroendocrine and 25 non-neuroendocrine genes) derived from human SCLC lines. (H) GSEA results showing transcriptional reprogramming at 48 h in BEND2 fusion lines compared to 12 h (I) Bar plot showing GATA6 expression uniquely and robustly upregulated in BEND2 fusion lines at both 12 and 48 h. Data are represented as mean ± SEM. (J) Bar plot showing specific upregulation of POMC in BON1 cells expressing EWSR1 - BEND2 at 48 h. Data are represented as mean ± SEM. (K) Bar plot showing markedly higher POMC expression in the EWSR1 - BEND2 -positive tumor compared to the CHD7 - BEND2 -positive tumor in the clinical cohort.

    Article Snippet: Pre-processed bulk RNA-seq data from pNET clinical samples and cell lines (this study) , Mendeley Data , https://data.mendeley.com/datasets/r9m66rjtxy/1.

    Techniques: Microscopy, Over Expression, Control, Expressing, Activation Assay, Derivative Assay