Shuhei Noguchi

Gestational weight gain mediates the effects of energy intake on birth weight among singleton pregnancies in the Japan Environment and Children’s Study

Marina Minami, Naw Awn J-P, Shuhei Noguchi, Masamitsu Eitoku et autres

BACKGROUND: Extra energy intake is commonly recommended for pregnant women to support fetal growth. However, relevant data regarding variations in energy intake and expenditure, body mass index and gestational weight gain (GWG) are frequently not considered. This study aimed to investigate how …

jp (code pays fourni par la source)

Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli et autres

The original version of this Article incorrectly included Kristina Hettne as a current member of the FANTOM consortium at the time of publication. This has now been corrected in both the PDF and HTML versions of the Article.

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Prediction of transcription factors associated with DNA demethylation during human cellular development

Yurina Miyajima, Shuhei Noguchi, Yuki Tanaka, Jingru Li et autres

DNA methylation of CpG dinucleotides is an important epigenetic modification involved in the regulation of mammalian gene expression, with each type of cell developing a specific methylation profile during its differentiation. Recently, it has been shown that a small subgroup of transcription …

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SkewC: Identifying cells with skewed gene body coverage in single-cell RNA sequencing data

Imad Abugessaisa, Akira Hasegawa, Shuhei Noguchi, Mélissa Cardon et autres

The analysis and interpretation of single-cell RNA sequencing (scRNA-seq) experiments are compromised by the presence of poor-quality cells. For meaningful analyses, such poor-quality cells should be excluded as they introduce noise in the data. We introduce SkewC, a quality-assessment tool, to identify …

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TF over-expressing 293T M-values with probe annotations

Yurina Miyajima, Shuhei Noguchi, Yuki Tanaka, Jingru Li et autres

This dateset is the DNA methylation profiles of transcription factor over-expressing HEK293T cells measured by Infinium MethylationEPIC arrays(Illumina). The M-value computation and normalized by the quartile normalization were performed using the lumi R package.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli et autres

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 could not be assigned to a specific gene and initiate at …

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Author Correction: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

Alessandro Bonetti, Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto et autres

Affiliation 13 incorrectly read ‘Department of Experimental Oncology, European Institute of Oncology, Milan, Italy’ instead of the correct ‘Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy’.

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FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

Imad Abugessaisa, Jordan A. Ramilowski, Marina Lizio, Jessica Severin et autres

The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the …

jp, se (code pays fourni par la source)

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli et autres

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 could not be assigned to a specific gene and initiate …

fr, jp, ca (code pays fourni par la source)

Functional annotation of human long noncoding RNAs via molecular phenotyping

Jordan A. Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang et autres

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular …

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Assessment of mapping strategies for determining the 5□-end of mRNAs and long-noncoding RNAs with short read sequences

Shuhei Noguchi, Hideya Kawaji, Takeya Kasukawa

Abstract Background Genome mapping is an essential step in data processing for transcriptome analysis, and many previous studies have evaluated various methods and strategies for mapping RNA-seq data. Cap Analysis of Gene Expression (CAGE) is a sequencing-based protocol particularly designed to capture …

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RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

Alessandro Bonetti, Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto et autres

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 chromatin remodeling. To investigate the function of such RNAs, methods to …

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