An increasing number of non-coding RNAs (ncRNAs) are implicated in various human diseases including cancer; however ncRNA transcriptome of hepatocellular carcinoma (HCC) remains largely unexplored. We use CAGE (Cap Analysis of Gene Expression) to comprehensively map transcription start sites (TSSs) across different etiologies of human HCC as well as mouse HCC, with particular emphasis on ncRNAs distant from protein-coding genes. We find thousands of significantly up-regulated distal ncRNAs in HCC tumors compared to their matched non-tumors, which are as many as protein-coding genes. Moreover, we identify many LTR retroviral promoters activated in HCC tissues and expressed in a subfamily-specific manner, which account for approximately 20% of the up-regulated distal ncRNAs. The transcripts derived from LTRs, determined by 3'' RACE, are multi-exon nuclear ncRNAs typically 0.5-2kb in length. This study sheds light on ncRNA transcriptome of human and mouse HCC. Overall design: Expression profiles using CAGE for 37 mouse HCC. The human data are archived at dbGaP (phs000885.v1.p1). An umbrella BioProject has been created to associate the GEO and dbGaP BioProjects: PRJNA278792
Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress.
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View SamplesThe aim of this study was to identify differential gene expression resulting from the inhibition of RORgt in human CD4+ T cells.
Pharmacologic inhibition of RORγt regulates Th17 signature gene expression and suppresses cutaneous inflammation in vivo.
Specimen part, Treatment
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Differential innate immune signalling via Ca(2+) sensor protein kinases.
Age, Specimen part, Time
View SamplesThe goal of this experiment was to identify the early responsive genes activated by the 22 amino acid peptide of bacterial flagellin (flg22) in Arabidopsis mesophyll cells that are involved in the initial responses important for plant innate immunity.
Differential innate immune signalling via Ca(2+) sensor protein kinases.
Age, Specimen part, Time
View SamplesThe goal of this experiment was to identify the early target genes of constitutively activated CPK5ac and CPK11ac in Arabidopsis mesophyll cells that are involved in early flagellin responses important for plant innate immunity.
Differential innate immune signalling via Ca(2+) sensor protein kinases.
Age, Specimen part
View SamplesThe goal of this experiment was to identify the early responsive genes activated by the 22 amino acid peptide of bacterial flagellin (flg22) in Arabidopsis seedlings that are involved in the initial responses important for plant innate immunity.
Differential innate immune signalling via Ca(2+) sensor protein kinases.
Age, Specimen part, Time
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Tailoring high-density oligonucleotide arrays for transcript profiling of different Arabidopsis thaliana accessions using a sequence-based approach.
Specimen part
View SamplesIn order to identify differentially expressed genes in developing seeds of Arabidopsis thaliana three different stages of seed development were analysed (9-10, 10-11 and 12-13 days after flower opening) for two Arabidopsis thaliana accessions, Col-0 and C24. For each stage and accession three biological replicates were analysed.
Tailoring high-density oligonucleotide arrays for transcript profiling of different Arabidopsis thaliana accessions using a sequence-based approach.
Specimen part
View SamplesIn order to identify differentially expressed genes in developing seeds of Arabidopsis thaliana three different stages of seed development were analysed (9-10, 10-11 and 12-13 days after flower opening) for two Arabidopsis thaliana accessions, Col-0 and C24. For each stage and accession three biological replicates were analysed.
Tailoring high-density oligonucleotide arrays for transcript profiling of different Arabidopsis thaliana accessions using a sequence-based approach.
Specimen part
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Genome Wide Mapping of NR4A Binding Reveals Cooperativity with ETS Factors to Promote Epigenetic Activation of Distal Enhancers in Acute Myeloid Leukemia Cells.
Cell line, Treatment
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