Human organoids as self-organizing three dimensional cultured systems recapitulate numerous core features of corresponding human organs, enable multiple measurements over a time course, and allow genetic and pharmacological manipulations. These engineered model systems hold tremendous potential as avatars for preclinical drug developments and interventional studies that are difficult or impossible to conduct in human subjects (Camp et al. Science 2019, PMID: 31604266). In recent few years, a growing number of single cell RNA-sequencing (scRNA-seq) studies have been reported to dissect the cellular and molecular heterogeneity in human organoids (Cowan et al. Cell 2020, PMID: 32946783). A large number of scRNA-seq datasets on human organoids have been generated and the relevant data will increase rapidly. However, due to the lack of efficient collection, standardized quality control, and analysis procedures, it is still a major challenge to efficiently integrate and reuse these data.
We thus introduce the scHOB (single-cell Human Organoid Bank) data portal, which is the first database consisting of all the scRNA-seq data on 10 kinds of widely-adopted human organoids spanning 1.2 million cells with 62 main cell types, as well as scRNA-seq datasets on the de facto human fetal organs, which serve as a reference for users to compare the similarity between engineered and real cells. scHOB provide easy-to-use web interfaces to facilitate the search, visualization, and download of the organoids scRNA-seq datasets. The scHOB could be a valuable resource for accelerating the identification of target genes for mechanistic researches and drug developments.
1) "Welcome to scHOB": This section shows the contents and functions of scHOB.
2) "Statistics": This section shows the statistics of all scRNA-seq data among human organoids.
3) "Brief information". This section shows five figures with detailed information on how data collection, processing and visualization in scHOB.
1) This home page contains all the collected scRNA-seq datasets of 10 kinds of human
organoids.
- A. An overview table of all collected human organoid single-cell transcriptomic profiles and samples.
- B. An extended page showing the knowledgebase for detailed experimental parameters for each organoid sample.
- C. A general analysis page including summary information, cellular composition, UMAP plot, and functional gene expression distribution.
2) Several search functions (such as keywords search) were provided in this browse, which help users to search specific datasets as their requirements.
3) User could click the triangular arrowheads to check knowledgebase for each item.
4) User could click the specific Experiment ID for open a new page that contains the four analysis module.
Here, we provided summary of four online analyzing functional modules equipped in scHOB. A. Single-cell analysis for scRNA-seq data from both human organoids and fetal organs. B. Comparison analysis module. C. Cell-to-cell interaction analysis module. D. Gene-drug interaction analysis module. We have provided the detailed usage in the note section of each corresponding analysis
scHOB provide three kinds of advanced search.
- A. ID search the data by experiment ID or Accession No.
- B. Type search the data by Organoid Types.
- C. Keywords search the data by using several keywords of information on cells, culture medium, and formation methods.
To download data in the database, select the menu Download. scHOB provides all kinds of downloadable files. The users can download all data including the processed human organoid scRNA-seq data, fetal scRNA-seq data and analyzed results.
