FANTOM5 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 Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities. Design Type(s) organism part comparison design • species comparison design • cell type comparison design • organism development design Measurement Type(s) DNA-templated transcription, initiation Technology Type(s) cap analysis of gene expression Factor Type(s) Species • Organism Part • life cycle stage • cell type Sample Characteristic(s) Mus musculus • Homo sapiens • cerebellum • visual cortex • ileum • Peyer's patch • stomach • axillary lymph node • aorta • substantia nigra • hippocampal formation • brain • heart • liver • meningeal cluster • bone marrow • spinal cord • raphe nuclei • corpus striatum • cortex • peripheral nervous system • kidney • neural system • hemolymphoid system • blood • spleen • mesoderm • hematopoietic system • ventral wall of dorsal aorta • placenta • ganglion • spiral organ of cochlea • small intestine • intestine • adrenal gland • eyeball of camera-type eye • pituitary gland • thymus • lung • female gonad • testis • bone tissue • diencephalon • muscle organ • medulla oblongata • forelimb • pancreas • gonad • corpora quadrigemina • skin of body • tongue • colon • caecum • vesicular gland • epididymis • amnion • mammary gland • uterus • submandibular gland • prostate gland • intestinal mucosa • urinary bladder • vagina • oviduct Machine-accessible metadata file describing the reported data (ISA-Tab format)