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transcriptomics datasets  (Epigenomics ag)

 
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    Epigenomics ag transcriptomics datasets
    Transcriptomics Datasets, 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/transcriptomic+and+epigenomic+data/transcriptomics+data/pm36162821-5-2-3
    Average 90 stars, based on 1 article reviews
    transcriptomics datasets - by Bioz Stars, 2026-09
    90/100 stars

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    other:

    Article Title: Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition
    Article Snippet: To address those questions, we took advantage of publicly available transcriptomics and epigenomics data from the Roadmap Epigenomics and ENCODE projects to identify, by using machine learning approaches, the chromatin modifications that were informative to classify alternatively spliced exons in different splicing groups (Fig. and Supplementary Data ).

    Article Title: MIKB: A manually curated and comprehensive knowledge base for myocardial infarction
    Article Snippet: In recent years, with the rapid development of high-throughput sequencing technology, multi-omics data, that is, datasets containing various types of high-dimensional molecular variables (including genomics, epigenomics, transcriptomics, proteomics, metabolomics, etc.), are increasingly used in the research of various diseases , , , , and no exception for cardiovascular disease (CVD) .

    Expressing:

    Article Title: Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells
    Article Snippet: .. To survey inferred allele and genotype frequencies at SNPs within IGHV1 −2 among different population subgroups, we first leveraged naïve B cell-derived transcriptomic data from the DICE cohort (database of immune cell expression, expression quantitative trait loci and epigenomics) , representing an ethnically diverse collection of donors (n=75; African American, n=5; Asian, n=17; Caucasian, n=34; Hawaiian/Pacific Islander, n=3; Mixed ethnicity, n=15; Unknown, n=1). ..

    Article Title: Immune disease variants modulate gene expression in regulatory CD4 + T cells
    Article Snippet: .. Therefore, we used transcriptomics data from 91 individuals sampled by the Database of Immune Cell eQTLs Expression Epigenomics (DICE) consortium, where different immune cell types were assayed from the same donors ( ). ..

    Article Title: Immune disease variants modulate gene expression in regulatory CD4 + T cells.
    Article Snippet: .. Therefore, we used transcriptomics data from 91 individuals sampled by the Database of Immune Cell eQTLs Expression Epigenomics (DICE) consortium,18 where different immune cell types were assayed from the same donors (STAR Methods). ..

    Transcriptomics:

    Article Title: Immune disease variants modulate gene expression in regulatory CD4 + T cells
    Article Snippet: .. Therefore, we used transcriptomics data from 91 individuals sampled by the Database of Immune Cell eQTLs Expression Epigenomics (DICE) consortium, where different immune cell types were assayed from the same donors ( ). ..

    Article Title: Immune disease variants modulate gene expression in regulatory CD4 + T cells.
    Article Snippet: .. Therefore, we used transcriptomics data from 91 individuals sampled by the Database of Immune Cell eQTLs Expression Epigenomics (DICE) consortium,18 where different immune cell types were assayed from the same donors (STAR Methods). ..



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    Functional impact of RB1 mutation on mRNA expression in Bladder Cancer. ( A ) In the <t>TCGA</t> BLCA (Bladder urothelial carcinoma) cohort, 1518 genes showed significant up-regulation (dark red dots, FDR < 0.01) in RB1 mutated samples whereas 1294 genes showed significant down-regulation (dark green dots, FDR < 0.01). ( B ) Among the most significant genes, up-regulation was found for CDKN2A and E2F1 (positive rank #1 and #22) whereas down-regulation was found for RB1 and CCND1 (negative rank #1 and #29). ( C ) The 1518 up-regulated genes were significantly enriched with transcriptional targets of E2F1 (Fisher's exact test, top 10 most enriched target sets).
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    Image Search Results


    Genelab datasets analyzed in the manuscript.

    Journal: Scientific Reports

    Article Title: Aging and putative frailty biomarkers are altered by spaceflight

    doi: 10.1038/s41598-024-57948-5

    Figure Lengend Snippet: Genelab datasets analyzed in the manuscript.

    Article Snippet: OSD-99 , Rodent Research-1 (RR1) NASA Validation Flight: Mouse extensor digitorum longus muscle transcriptomic and epigenomic data , Galazka J, Globus R "Rodent Research 1", GeneLab, Version 4, http://doi.org/10.26030/1h3m-3q49 , Extensor digitorum longus muscle.

    Techniques: Gene Expression, Expressing, Biomarker Discovery, Irradiation

    Genelab datasets analyzed in the manuscript.

    Journal: Scientific Reports

    Article Title: Aging and putative frailty biomarkers are altered by spaceflight

    doi: 10.1038/s41598-024-57948-5

    Figure Lengend Snippet: Genelab datasets analyzed in the manuscript.

    Article Snippet: OSD-105 , Rodent Research-1 (RR1) NASA Validation Flight: Mouse tibialis anterior muscle transcriptomic, proteomic, and epigenomic data , Galazka J, Globus R "Rodent Research 1", GeneLab, Version 4, http://doi.org/10.26030/xgw6-6t64 , Tibialis anterior muscle.

    Techniques: Gene Expression, Expressing, Biomarker Discovery, Irradiation

    Genelab datasets analyzed in the manuscript.

    Journal: Scientific Reports

    Article Title: Aging and putative frailty biomarkers are altered by spaceflight

    doi: 10.1038/s41598-024-57948-5

    Figure Lengend Snippet: Genelab datasets analyzed in the manuscript.

    Article Snippet: OSD-104 , Rodent Research-1 (RR1) NASA Validation Flight: Mouse soleus muscle transcriptomic and epigenomic data , Galazka J, Globus R "Rodent Research 1", GeneLab, Version 4, http://doi.org/10.26030/em9r-w619 , Soleus muscle.

    Techniques: Gene Expression, Expressing, Biomarker Discovery, Irradiation

    Genelab datasets analyzed in the manuscript.

    Journal: Scientific Reports

    Article Title: Aging and putative frailty biomarkers are altered by spaceflight

    doi: 10.1038/s41598-024-57948-5

    Figure Lengend Snippet: Genelab datasets analyzed in the manuscript.

    Article Snippet: OSD-101 , Rodent Research-1 (RR1) NASA Validation Flight: Mouse left gastrocnemius muscle transcriptomic, proteomic, and epigenomic data , Galazka J, Globus R "Rodent Research 1", GeneLab, Version 5, http://doi.org/10.26030/sdmt-ae51 , Gastrocnemius muscle.

    Techniques: Gene Expression, Expressing, Biomarker Discovery, Irradiation

    Functional impact of RB1 mutation on mRNA expression in Bladder Cancer. ( A ) In the TCGA BLCA (Bladder urothelial carcinoma) cohort, 1518 genes showed significant up-regulation (dark red dots, FDR < 0.01) in RB1 mutated samples whereas 1294 genes showed significant down-regulation (dark green dots, FDR < 0.01). ( B ) Among the most significant genes, up-regulation was found for CDKN2A and E2F1 (positive rank #1 and #22) whereas down-regulation was found for RB1 and CCND1 (negative rank #1 and #29). ( C ) The 1518 up-regulated genes were significantly enriched with transcriptional targets of E2F1 (Fisher's exact test, top 10 most enriched target sets).

    Journal: Nucleic Acids Research

    Article Title: LinkedOmics: analyzing multi-omics data within and across 32 cancer types

    doi: 10.1093/nar/gkx1090

    Figure Lengend Snippet: Functional impact of RB1 mutation on mRNA expression in Bladder Cancer. ( A ) In the TCGA BLCA (Bladder urothelial carcinoma) cohort, 1518 genes showed significant up-regulation (dark red dots, FDR < 0.01) in RB1 mutated samples whereas 1294 genes showed significant down-regulation (dark green dots, FDR < 0.01). ( B ) Among the most significant genes, up-regulation was found for CDKN2A and E2F1 (positive rank #1 and #22) whereas down-regulation was found for RB1 and CCND1 (negative rank #1 and #29). ( C ) The 1518 up-regulated genes were significantly enriched with transcriptional targets of E2F1 (Fisher's exact test, top 10 most enriched target sets).

    Article Snippet: Genomic, epigenomic, and transcriptomic data for 32 TCGA cancer types were downloaded from the Firehose of the Broad Institute ( http://gdac.broadinstitute.org/ , January 2016 version).

    Techniques: Functional Assay, Mutagenesis, Expressing

    Pan-cancer analysis for survival-associated gene expression signatures. ( A ) Twelve cancer types in the TCGA project with >100 death events. ( B ) The heat map shows the top 30 poor survival-associated genes. Each cell represents the signed –log 10 ( P -value). The right panel bar plot depicts corresponding meta-analysis based FDR. A and B share the same order of cancer types, as indicated below the heat map. ( C ) Increased expression of genes in the cell cycle pathway is associated with increased death risk (FDR<0.001, gene set enrichment analysis). Leading-edge genes are highlighted in red boxes in C. ( D–G ) Patients with above- (red) and below- (green) median APCDD1L mRNA abundance had significantly different survival rates in multiple cancer types such as bladder urothelial carcinoma (BLCA, D), head and neck squamous cell carcinoma (HNSC, E), kidney renal clear cell carcinoma (KIRC, F), and brain lower grade glioma (LGG, G).

    Journal: Nucleic Acids Research

    Article Title: LinkedOmics: analyzing multi-omics data within and across 32 cancer types

    doi: 10.1093/nar/gkx1090

    Figure Lengend Snippet: Pan-cancer analysis for survival-associated gene expression signatures. ( A ) Twelve cancer types in the TCGA project with >100 death events. ( B ) The heat map shows the top 30 poor survival-associated genes. Each cell represents the signed –log 10 ( P -value). The right panel bar plot depicts corresponding meta-analysis based FDR. A and B share the same order of cancer types, as indicated below the heat map. ( C ) Increased expression of genes in the cell cycle pathway is associated with increased death risk (FDR<0.001, gene set enrichment analysis). Leading-edge genes are highlighted in red boxes in C. ( D–G ) Patients with above- (red) and below- (green) median APCDD1L mRNA abundance had significantly different survival rates in multiple cancer types such as bladder urothelial carcinoma (BLCA, D), head and neck squamous cell carcinoma (HNSC, E), kidney renal clear cell carcinoma (KIRC, F), and brain lower grade glioma (LGG, G).

    Article Snippet: Genomic, epigenomic, and transcriptomic data for 32 TCGA cancer types were downloaded from the Firehose of the Broad Institute ( http://gdac.broadinstitute.org/ , January 2016 version).

    Techniques: Gene Expression, Expressing