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Open AccessOVCH1 Antisense RNA 1 is differentially expressed between non-frail and frail old adults
While some old adults stay healthy and non-frail up to late in life, others experience multimorbidity and frailty often accompanied by a pro-inflammatory state. The underlying molecular mechanisms for those di...
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Article
Open AccessROR2 expression predicts human induced pluripotent stem cell differentiation into neural stem/progenitor cells and GABAergic neurons
Despite the development of various in vitro differentiation protocols for the efficient derivation of specific cell types, human induced pluripotent stem cell (hiPSC) lines have varing ability to differentiate...
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Open AccessAuthor Correction: IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells
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Open AccessAuthor Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
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Open AccessPrediction of transcription factors associated with DNA demethylation during human cellular development
DNA methylation of CpG dinucleotides is an important epigenetic modification involved in the regulation of mammalian gene expression, with each type of cell develo** a specific methylation profile during its...
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Article
Open AccessIκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells
Inflammatory stimuli triggers the degradation of three inhibitory κB (IκB) proteins, allowing for nuclear translocation of nuclear factor-κB (NFκB) for transcriptional induction of its target genes. Of these t...
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Article
Open AccessThe choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background
The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism’s physiological function. Despite their common developmental origin, they present distinct functional...
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Article
Open AccessDiscovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them ...
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Open AccessAuthor Correction: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions
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Open AccessRADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions
Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromat...
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Open AccessC1 CAGE detects transcription start sites and enhancer activity at single-cell resolution
Single-cell transcriptomic profiling is a powerful tool to explore cellular heterogeneity. However, most of these methods focus on the 3′-end of polyadenylated transcripts and provide only a partial view of th...
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Open AccessAuthor Correction: Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
The authors regret that Luba M. Pardo was omitted in error from the author list of the original version of this Data Descriptor. This omission has now been corrected in the HTML and PDF versions. The authors a...
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Open AccessMonitoring transcription initiation activities in rat and dog
The promoter landscape of several non-human model organisms is far from complete. As a part of FANTOM5 data collection, we generated 13 profiles of transcription initiation activities in dog and rat aortic smo...
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Open AccessSelf-patterning of rostral-caudal neuroectoderm requires dual role of Fgf signaling for localized Wnt antagonism
The neuroectoderm is patterned along a rostral-caudal axis in response to localized factors in the embryo, but exactly how these factors act as positional information for this patterning is not yet fully under...
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Open AccessTranscription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
Rhesus macaque was the second non-human primate whose genome has been fully sequenced and is one of the most used model organisms to study human biology and disease, thanks to the close evolutionary relationsh...
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Open AccessLinking FANTOM5 CAGE peaks to annotations with CAGEscan
The FANTOM5 expression atlas is a quantitative measurement of the activity of nearly 200,000 promoter regions across nearly 2,000 different human primary cells, tissue types and cell lines. Generation of this ...
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Open AccessFANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies
The FANTOM5 consortium described the promoter-level expression atlas of human and mouse by using CAGE (Cap Analysis of Gene Expression) with single molecule sequencing. In the original publications, GRCh37/hg1...
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Open AccessThe FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types
The latest project from the FANTOM consortium, an international collaborative effort initiated by RIKEN, generated atlases of transcriptomes, in particular promoters, transcribed enhancers, and long-noncoding ...
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Open AccessFANTOM5 CAGE profiles of human and mouse samples
In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expres...
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Article
Open AccessCell-cycle-independent transitions in temporal identity of mammalian neural progenitor cells
During cerebral development, many types of neurons are sequentially generated by self-renewing progenitor cells called apical progenitors (APs). Temporal changes in AP identity are thought to be responsible fo...
