Euarchontoglires
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:We provide a comprehensive map of transcription start sites (TSSs) for HBV at single nucleotide resolution using CAGE.
2016-09-16 | GSE84186 | GEO
Project description:Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. Here, we report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. Here, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNA, then dual priming oligonucleotide system to specifically enrich 5’-end tags for genomic analysis.
2023-01-01 | GSE174479 | GEO
Project description:We used SLIC-CAGE to map transcriptional start sites in cortical neurons from Cornelia de Lange Syndrome (CdLS) patients and control individuals. SLIC-CAGE was performed using nuclear RNA isolated from pre-frontal cortical grey matter. Usage of nuclear RNA allows enrichment of unstable RNAs, such as RNA originating from enhancer transcription. We characterised promoter-level gene expression in cortical neurons from CdLS patients and found deregulation of hundreds of genes enriched for neuronal functions.
2021-02-27 | E-MTAB-9045 | biostudies-arrayexpress
Project description:MAPCap enables high-resolution detection and differential expression analysis of transcription start sites
| PRJNA517665 | ENA
Project description:Fission yeast, Schizosaccharomyces pombe, is an attractive model organism for transcriptional and chromatin biology research. Such research is contingent of accurate annotation of genes and in particular Transcription Start Sites (TSSs) and thereby core promoters. However, comprehensive genome-wide maps of TSS and their usage across commonly applied laboratorial conditions and treatments for S. pombe are lacking. To this end, we have applied Cap Analysis of Gene Expression (CAGE) to profile TSSs activity in S. pombe cultures exposed to heat shock, nitrogen starvation, peroxide and two commonly applied media, YES and EMM. CAGE allows for nucleotide resolution detection of TSS, which we show is substantially more accurate than existing PomBase annotation. On gene expression levels, we recapitulate known S. pombe stress response patterns, but our data also allowed us to detect many alternative TSSs within gene bodies that are changing their activity between conditions. Some of these have the potential to change the functions of encoded proteins due to coding sequence exclusion. We show that the immediate region around TSSs is almost as conserved as coding sequence across S. pombe strains, but the upstream promoter which houses transcription factor binding sites linked to stress response show high diversity. Our data constitute a central resource for S. pombe transcriptional regulation research.
2018-03-14 | GSE110976 | GEO
Project description:We develop a method Re-Cappable-seq for determining eukaryotic transcription start sites derived from all RNA polymerases at nucleotide resolution. In particular, this method identifies the Pol-I and Pol-III TSSs, which are missing by CAGE. Applied to human A549 cell line, our method results in the identification of 33,468 and 5,269 high confidence Pol-II and non-Pol-II TSS respectively. Re-Cappable-seq identifies Pol-II TSS with higher specificity than CAGE.
2019-06-14 | GSE132660 | GEO
Project description:<p>The ncRNA transcriptome of human hepatocellular carcinoma (HCC) is largely unexplored. We used CAGE to characterize transcription start sites across different etiologies of human HCCs with emphasis on ncRNAs. Here we report that retroviral LTR promoters, expressed in healthy tissues such as testis and placenta but not liver, are widely activated in HCC. Despite HCC heterogeneity, a subset of LTR-derived ncRNAs were more than 10-fold up-regulated in the vast majority of samples. HCCs with a high LTR activity mostly had a viral etiology, were less differentiated and showed higher risk of recurrence. CAGE enabled us to build a promoter map for HCC, which uncovers a new layer of complexity in HCC genomics.</p>
| phs000885 | dbGaP
Project description:H3K4me3 ChIP-seq was done to examine transcription start sites in a genome wide manner, and compare results to CAGE-seq
2012-11-30 | GSE38682 | GEO
Project description:<p>Hepatoblastoma (HB) is the most common pediatric liver tumor, affecting mostly children under 3 years of age. This rare tumor represents 1% of all pediatric cancers. Genetic studies have shown that HB is characterized by high frequency mutations of the CTNNB1 gene encoding beta-catenin (around 75%) and relative genomic stability. Here we have analyzed the transcriptional profile of 21 HBs compared to matched non-tumor livers by Cap Analysis of Gene Expression (CAGE), which provides accurate and quantitative profiling of all transcripts. CAGE analysis revealed strong upregulation of known Wnt target coding genes in most tumors analyzed, consistent with previous transcriptomic studies. To better define the Wnt-dependent transcriptional landscape of HB, we integrated CAGE data with TCF4 ChIP-seq data from a CTNNB1-mutated cancer cell line and with the FANTOM5 genomic coordinates of TCF/LEF binding motifs. Both TCF/LEF binding motifs and ChIP-seq peaks were strongly enriched in the immediate upstream region, not only for protein-coding genes, but also for non-coding transcripts. Among the selected 112 top Wnt target genes at FDR<1.0E-6 and fold change>8, we found clear over-representation (66%) of distant transcription start sites (TSSs) representing lncRNAs and enhancer RNAs, which raises the question of their role in HB pathogenesis. Analysis of the 112 promoters using CAGEd-oPOSSUM confirmed the predominant involvement of Tcf/Lef transcription factors, together with HNF4G, GATA2, Sox3 and Ets-related genes. Finally, the 112 Wnt target signature defined 3 tumor subclasses, T1, T2 and T3, characterized by progressive alteration of the non-coding part of the transcriptome and significant differences in clinical behavior.</p>
| phs001433 | dbGaP
Project description:To better understand the transcriptomic changes that occur in response to HDACi treatment, we perform CAGE on dermal fibroblasts, HepG2, and MCF7 cells after TSA or VPA treatment, at both bulk and single cell level. We make detailed annotation of the identified coding and noncoding RNA transcription start sites and enhancers, in addition to their expression levels.
2022-06-30 | GSE200186 | GEO