Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://single-cell.clst.riken.jp
Full name: Single-cell centric database
Description: SCPortalen 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.
Year founded: 2018
Last update:
Version:
Accessibility:
Manual:
Accessible
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Country/Region: Japan
Data type:
RNA
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Contact information

University/Institution: RIKEN
Address: Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
City: Yokohama
Province/State:
Country/Region: Japan
Contact name (PI/Team): Takeya Kasukawa
Contact email (PI/Helpdesk): takeya.kasukawa@riken.jp

Publications

29045713
SCPortalen: human and mouse single-cell centric database. [PMID: 29045713]
Abugessaisa I, Noguchi S, Böttcher M, Hasegawa A, Kouno T, Kato S, Tada Y, Ura H, Abe K, Shin JW, Plessy C, Carninci P, Kasukawa T.

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' (http://single-cell.clst.riken.jp/). 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. The target users of SCPortalen are all researchers interested in specific cell types or population heterogeneity. Through the web interface of SCPortalen users are easily able to search, explore and download the single-cell datasets of their interests.

Nucleic Acids Res. 2018:46(D1) | 11 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
1883/5061 (62.814%)
Raw bio-data:
153/487 (68.789%)
Expression:
363/924 (60.823%)
Metadata:
167/497 (66.6%)
1883
Total Rank
11
Citations
3.667
z-index

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Record metadata

Created on: 2018-01-29
Curated by:
Saba Arshad [2018-04-16]
Yang Zhang [2018-01-28]