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Transcriptional dynamics during human adipogenesis and its link to adipose morphology and distributionOur results suggest a complex but highly coordinated regulation of adipogenesis
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On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBaseSlideBase, a web tool which offers a new way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed/used in a specified set of cells/tissues
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Association of gestational age and growth measures at birth with infection-related admissions to hospital throughout childhoodChildren who were born with reduced gestational age, birthweight, and birth length have persistently increased rates of infection-related admissions to hospital until age 18 years
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Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter UsageThis study helps us understand how cancer cells are regulated by key genes and their corresponding networks to alter their fate in response to specific...
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Mapping mammalian cell-type-specific transcriptional regulatory networks using KD-CAGE and ChIP-seq data in the TC-YIK cell line.Examining the overlap between genes perturbed in the KD-CAGE experiments and genes with a ChIP-seq peak within 50 kb of their promoter, we identified direct...
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Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cellsOur data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during...
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Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early responseThe immediate-early response mediates cell fate in response to a variety of extracellular stimuli and is dysregulated in many cancers.
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Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cellsThe generation of myeloid cells from their progenitors is regulated at the level of transcription by combinatorial control of key transcription factors...
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Gateways to the FANTOM5 promoter level mammalian expression atlasThe FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE.
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TagDust2: A generic method to extract reads from sequencing data.Arguably the most basic step in the analysis of next generation sequencing data (NGS) involves the extraction of mappable reads from the raw reads...