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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/rna+seq+data/pmc04557131-176-0-5
    Average 90 stars, based on 1 article reviews
    rna-seq data - by Bioz Stars, 2026-10
    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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    Increased IFITM and decreased DHODH expression characterize the placenta in the context of HDPs (A) Volcano plot of transcriptomic changes identified by <t>RNA-seq.</t> Transcripts highlighted in red or blue were significantly altered ( q value < 0.05). (B) Differentially expressed genes were classified by functional enrichment analysis using the Reactome pathway database and Gene Ontology (GO) biological processes or cellular components. (C) Heatmap of mitochondria-related genes downregulated in the placenta in the context of HDPs. Genes with higher expression are shown in green, and those with lower expression are shown in red. Ctrl: premature delivery, n = 5; HDP, n = 5. (D) Expression of DHODH, OPA1, DNM1L, MFN1, TFAM, and IFITM1-3 in trophoblast BeWo cells treated with forskolin (FSK, 2.5 μM) and rotenone (Rote, 50 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗ p < 0.05, ∗∗ p < 0.01 vs. FSK alone (Tukey’s test). (E) Expression of IFITMs in BeWo cells treated with FSK (2.5 μM), orludodstat (Orlu, 1 nM), or brequinar (Bre, 25 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗∗ p < 0.01 vs. Ctrl; † p < 0.05, †† p < 0.01, ††† p < 0.001 vs. FSK alone (Tukey’s test).
    Rna Seq Data, supplied by Novogene, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Increased IFITM and decreased DHODH expression characterize the placenta in the context of HDPs (A) Volcano plot of transcriptomic changes identified by <t>RNA-seq.</t> Transcripts highlighted in red or blue were significantly altered ( q value < 0.05). (B) Differentially expressed genes were classified by functional enrichment analysis using the Reactome pathway database and Gene Ontology (GO) biological processes or cellular components. (C) Heatmap of mitochondria-related genes downregulated in the placenta in the context of HDPs. Genes with higher expression are shown in green, and those with lower expression are shown in red. Ctrl: premature delivery, n = 5; HDP, n = 5. (D) Expression of DHODH, OPA1, DNM1L, MFN1, TFAM, and IFITM1-3 in trophoblast BeWo cells treated with forskolin (FSK, 2.5 μM) and rotenone (Rote, 50 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗ p < 0.05, ∗∗ p < 0.01 vs. FSK alone (Tukey’s test). (E) Expression of IFITMs in BeWo cells treated with FSK (2.5 μM), orludodstat (Orlu, 1 nM), or brequinar (Bre, 25 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗∗ p < 0.01 vs. Ctrl; † p < 0.05, †† p < 0.01, ††† p < 0.001 vs. FSK alone (Tukey’s test).
    Bulk Rna Seq Data Analysis, supplied by Azenta, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Increased IFITM and decreased DHODH expression characterize the placenta in the context of HDPs (A) Volcano plot of transcriptomic changes identified by <t>RNA-seq.</t> Transcripts highlighted in red or blue were significantly altered ( q value < 0.05). (B) Differentially expressed genes were classified by functional enrichment analysis using the Reactome pathway database and Gene Ontology (GO) biological processes or cellular components. (C) Heatmap of mitochondria-related genes downregulated in the placenta in the context of HDPs. Genes with higher expression are shown in green, and those with lower expression are shown in red. Ctrl: premature delivery, n = 5; HDP, n = 5. (D) Expression of DHODH, OPA1, DNM1L, MFN1, TFAM, and IFITM1-3 in trophoblast BeWo cells treated with forskolin (FSK, 2.5 μM) and rotenone (Rote, 50 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗ p < 0.05, ∗∗ p < 0.01 vs. FSK alone (Tukey’s test). (E) Expression of IFITMs in BeWo cells treated with FSK (2.5 μM), orludodstat (Orlu, 1 nM), or brequinar (Bre, 25 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗∗ p < 0.01 vs. Ctrl; † p < 0.05, †† p < 0.01, ††† p < 0.001 vs. FSK alone (Tukey’s test).
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    Increased IFITM and decreased DHODH expression characterize the placenta in the context of HDPs (A) Volcano plot of transcriptomic changes identified by <t>RNA-seq.</t> Transcripts highlighted in red or blue were significantly altered ( q value < 0.05). (B) Differentially expressed genes were classified by functional enrichment analysis using the Reactome pathway database and Gene Ontology (GO) biological processes or cellular components. (C) Heatmap of mitochondria-related genes downregulated in the placenta in the context of HDPs. Genes with higher expression are shown in green, and those with lower expression are shown in red. Ctrl: premature delivery, n = 5; HDP, n = 5. (D) Expression of DHODH, OPA1, DNM1L, MFN1, TFAM, and IFITM1-3 in trophoblast BeWo cells treated with forskolin (FSK, 2.5 μM) and rotenone (Rote, 50 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗ p < 0.05, ∗∗ p < 0.01 vs. FSK alone (Tukey’s test). (E) Expression of IFITMs in BeWo cells treated with FSK (2.5 μM), orludodstat (Orlu, 1 nM), or brequinar (Bre, 25 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗∗ p < 0.01 vs. Ctrl; † p < 0.05, †† p < 0.01, ††† p < 0.001 vs. FSK alone (Tukey’s test).
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    Image Search Results


    Increased IFITM and decreased DHODH expression characterize the placenta in the context of HDPs (A) Volcano plot of transcriptomic changes identified by RNA-seq. Transcripts highlighted in red or blue were significantly altered ( q value < 0.05). (B) Differentially expressed genes were classified by functional enrichment analysis using the Reactome pathway database and Gene Ontology (GO) biological processes or cellular components. (C) Heatmap of mitochondria-related genes downregulated in the placenta in the context of HDPs. Genes with higher expression are shown in green, and those with lower expression are shown in red. Ctrl: premature delivery, n = 5; HDP, n = 5. (D) Expression of DHODH, OPA1, DNM1L, MFN1, TFAM, and IFITM1-3 in trophoblast BeWo cells treated with forskolin (FSK, 2.5 μM) and rotenone (Rote, 50 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗ p < 0.05, ∗∗ p < 0.01 vs. FSK alone (Tukey’s test). (E) Expression of IFITMs in BeWo cells treated with FSK (2.5 μM), orludodstat (Orlu, 1 nM), or brequinar (Bre, 25 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗∗ p < 0.01 vs. Ctrl; † p < 0.05, †† p < 0.01, ††† p < 0.001 vs. FSK alone (Tukey’s test).

    Journal: iScience

    Article Title: DHODH regulates trophoblast fusion via IFITM-reduced plasma membrane fluidity: Implications for hypertensive disorders of pregnancy

    doi: 10.1016/j.isci.2026.116163

    Figure Lengend Snippet: Increased IFITM and decreased DHODH expression characterize the placenta in the context of HDPs (A) Volcano plot of transcriptomic changes identified by RNA-seq. Transcripts highlighted in red or blue were significantly altered ( q value < 0.05). (B) Differentially expressed genes were classified by functional enrichment analysis using the Reactome pathway database and Gene Ontology (GO) biological processes or cellular components. (C) Heatmap of mitochondria-related genes downregulated in the placenta in the context of HDPs. Genes with higher expression are shown in green, and those with lower expression are shown in red. Ctrl: premature delivery, n = 5; HDP, n = 5. (D) Expression of DHODH, OPA1, DNM1L, MFN1, TFAM, and IFITM1-3 in trophoblast BeWo cells treated with forskolin (FSK, 2.5 μM) and rotenone (Rote, 50 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗ p < 0.05, ∗∗ p < 0.01 vs. FSK alone (Tukey’s test). (E) Expression of IFITMs in BeWo cells treated with FSK (2.5 μM), orludodstat (Orlu, 1 nM), or brequinar (Bre, 25 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗∗ p < 0.01 vs. Ctrl; † p < 0.05, †† p < 0.01, ††† p < 0.001 vs. FSK alone (Tukey’s test).

    Article Snippet: • Raw RNA-seq data derived from human placental samples and trophoblast cell lines have been deposited at the DNA DataBank of Japan (DDBJ) Sequence Read Archive as DDBJ: DRA021720 and DRA021721 and are publicly available as of the date of publication.

    Techniques: Expressing, RNA Sequencing, Functional Assay

    DHODH regulates IFITM expression via IRF1 (A–H) BeWo cells or DHODH-KD BeWo cells were treated with FSK (2.5 μM), Orlu (1 nM), or Bre (25 nM) for 48 h. (A) Volcano plot showing transcriptomic changes identified by RNA-seq. Transcripts highlighted in red or blue were considered differentially expressed, as indicated by an expression change ≥2-fold ( p < 0.05). (B) Correlation analysis of RNA-seq data from Orlu-, Bre-treated, and DHODH-KD cells. (C) Differentially expressed genes were classified by functional enrichment analysis using the Wiki pathway database and GO biological processes or cellular components. (D) RNA-seq was used to evaluate the expression levels of genes associated with syncytialization. (E) RNA-seq was used to evaluate the expression levels of IRF family genes. (F) Immunoblotting for IRF1, total IRF3, and p -IRF3. GAPDH was used as a loading control. Representative data from three independent experiments are shown. The graph shows the total IRF3 and p -IRF3 levels normalized to GAPDH levels from three independent experiments. ∗∗ p < 0.01, ∗∗∗ p < 0.001 vs. Ctrl (Tukey’s test). Values represent the mean ± SEM. (G) ChIP assay showing IRF1 binding to upstream regulatory regions (up to 3 kbp) of the IFITM1, IFITM2, and IFITM3 loci in BeWo cells treated with FSK alone (2.5 μM) for 48 h. ∗ p < 0.05 vs. Ctrl; † p < 0.05, †† p < 0.01, ††† p < 0.001 vs. FSK alone (Tukey’s test). (H) Immunofluorescence staining of IRF1 (red). Nuclei were counterstained with DAPI (blue). Scale bars, 5 μm. The graph shows the number of staining cells from three independent experiments. Values represent the mean ± SEM. ∗∗∗ p < 0.001 vs. FSK.

    Journal: iScience

    Article Title: DHODH regulates trophoblast fusion via IFITM-reduced plasma membrane fluidity: Implications for hypertensive disorders of pregnancy

    doi: 10.1016/j.isci.2026.116163

    Figure Lengend Snippet: DHODH regulates IFITM expression via IRF1 (A–H) BeWo cells or DHODH-KD BeWo cells were treated with FSK (2.5 μM), Orlu (1 nM), or Bre (25 nM) for 48 h. (A) Volcano plot showing transcriptomic changes identified by RNA-seq. Transcripts highlighted in red or blue were considered differentially expressed, as indicated by an expression change ≥2-fold ( p < 0.05). (B) Correlation analysis of RNA-seq data from Orlu-, Bre-treated, and DHODH-KD cells. (C) Differentially expressed genes were classified by functional enrichment analysis using the Wiki pathway database and GO biological processes or cellular components. (D) RNA-seq was used to evaluate the expression levels of genes associated with syncytialization. (E) RNA-seq was used to evaluate the expression levels of IRF family genes. (F) Immunoblotting for IRF1, total IRF3, and p -IRF3. GAPDH was used as a loading control. Representative data from three independent experiments are shown. The graph shows the total IRF3 and p -IRF3 levels normalized to GAPDH levels from three independent experiments. ∗∗ p < 0.01, ∗∗∗ p < 0.001 vs. Ctrl (Tukey’s test). Values represent the mean ± SEM. (G) ChIP assay showing IRF1 binding to upstream regulatory regions (up to 3 kbp) of the IFITM1, IFITM2, and IFITM3 loci in BeWo cells treated with FSK alone (2.5 μM) for 48 h. ∗ p < 0.05 vs. Ctrl; † p < 0.05, †† p < 0.01, ††† p < 0.001 vs. FSK alone (Tukey’s test). (H) Immunofluorescence staining of IRF1 (red). Nuclei were counterstained with DAPI (blue). Scale bars, 5 μm. The graph shows the number of staining cells from three independent experiments. Values represent the mean ± SEM. ∗∗∗ p < 0.001 vs. FSK.

    Article Snippet: • Raw RNA-seq data derived from human placental samples and trophoblast cell lines have been deposited at the DNA DataBank of Japan (DDBJ) Sequence Read Archive as DDBJ: DRA021720 and DRA021721 and are publicly available as of the date of publication.

    Techniques: Expressing, RNA Sequencing, Functional Assay, Western Blot, Control, Binding Assay, Immunofluorescence, Staining