NAR Molecular Biology Database Collection entry number 116
Kasukawa, Takeya; Abugessaisa, Imad; Noguchi, Shuhei; Böttcher, Michael; Hasegawa, Akira; Kouno, Tsukasa; Kato, Sachi; Tada, Yuhki; Ura, Hiroki; Abe, Kuniya; Shin, Jay; Plessy, Charles; Carninci, Piero
1 Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
2 RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
Contact single-cell-

Database Description

Published single-cell datasets are rich resources for investigators who want to address questions not originally asked by the creators of the datasets. The single-cell datasets might be obtained by different protocols and diverse analysis strategies. The main challenge in utilizing such single-cell data is how we can make the various large-scale datasets to be comparable and reusable in a different context. To challenge this issue, we developed the single-cell centric database ‘SCPortalen’. The current version of the database covers human and mouse single-cell transcriptomics datasets that are publicly available from the INSDC sites. The original metadata was manually curated and single-cell samples were annotated with standard ontology terms. Following that, common quality assessment procedures were conducted to check the quality of the raw sequence. Furthermore, primary data processing of the raw data followed by advanced analyses and interpretation have been performed from scratch using our pipeline. In addition to the transcriptomics data, SCPortalen provides access to single-cell image files whenever available.


This work was supported by research grants for the RIKEN Single Cell Project and for the RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (RIKEN CLST (DGT)) from the MEXT, Japan.


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