Table 1.
Data Elements in Stem Cell Databases
| Database Tittle | Author | Data Elements | Link |
|---|---|---|---|
| SyStemCell | Yu et al22 | Stem cell type and species; Gene annotations; DNA CpG 5 hmC/5 mC; | https://omictools.com/systemcell-tool |
| Histone modification; Karyotype; Treatments performed on cell; | |||
| miRNA-based regulation; Protein abundance; Protein phosphorylation; | |||
| Transcription factor regulation | |||
| CODEX | Sanchez-Castillo et al23 | Next Generation Sequencing data; Cell type, subtype, and species; | http://codex.stemcells.cam.ac.uk/ |
| Tissue ontology; Cell culture conditions; Cell drug treatments; | |||
| Human chromosomal abnormalities | |||
| ESTOOLS Data@Hand | Kong et al24 | Microarray data; Sequencing platform; Species, sex, and disease status of donor; Tissue of origin; Cell type of parent and | https://research.utu.fi/converis/portal/Publication/1716702 |
| current cell line; Differentiation status | |||
| Stem Cell Discovery Engine | Sui et al25 | Microarray data; Species, strain, developmental stage, disease state of donor; Cell type and drug treatment; Tissue type and histology; Transcription profiling; Histone modification profiling;Transcription factor binding site identification; Immunoprecipitation antibody; Phenotype quality; Cell surface marker | http://discovery.hsci.harvard.edu/ |
| StemFormatics | Wells et al26 | Gene expression data; Sequencing platform; Cell type and subtype; | https://www.stemformatics.org/ |
| Species, sex, age, and disease state of door; Tissue of origin | |||
| LINCS | Koleti et al27 | Species, disease state, mutation status, and genetic modification status of donor; Tissue of origin; Cell culture conditions; Protein treatment information; Antibody treatment; Small molecule treatment information; siRNA/shRNA treatment information | http://lincsportal.ccs.miami.edu/dcic-portal/ |
| LifeMap Discovery | Edgar et al28 | Gene expression data; Anatomic compartment and tissue of origin; Cell type and subtype; Cell culture conditions and treatments; Related clinical trials for cell therapies | https://discovery.lifemapsc.com/ |
| StemMapper | Pinto et al29 | Microarray data; Species, age, and mutation status of donor; Cell type and subtype | http://stemmapper.sysbiolab.eu/ |
| ESCAPE | Xu et al30 | Cell surface markers; mRNA expression; Protein-protein interactions; | http://www.maayanlab.net/ESCAPE/index.php |
| Chip-Seq interactions; miRNA target interactions; Histone modification; Gene annotations; Cell type | |||
| SKiP Stemcell Knowledge and Information Portal | Species, age, sex, disease state, and ethnicity of donor; Tissue of origin; | https://skip.stemcellinformatics.org/en/ | |
| Cell type; Cell morphology; Culture medium, feeders; Karyotype | |||
| hPSCreg | Sex and disease state of donor; Cell type; Cell derivation process; | https://hpscreg.eu/ | |
| Cell culture conditions; Cell surface markers | |||
| CellNet | Cahan et al31 | Stem cell subtype; Stem cell species; Sex of the donor; Transcription factors; | http://cahanlab.org/macellnet.html |
| Microarray data | |||
| StemCellNet | Pinto et al32 | Stem cell type; Stem cell lineage; Stem cell species; Cell surface markers; | http://stemcellnet.sysbiolab.eu/ |
| Transcription factors; Immunoprecipitation antibody; Microarray data; | |||
| Sequencing platform | |||
| HSC-explorer | Montrone et al33 | Stem cell lineage; Stem cell species; Differentiation status; Cell surface markers; Gene expression data; mRNA expression; Transcription profiling; | http://mips.helmholtz-muenchen.de/HSC/ |
| Sequencing platform | |||
| CORTECON | van de Leemput et al34 | Stem cell type; Stem cell lineage; Stem cell species; Disease state of the donor; Cell surface markers; Gene expression data | http://cortecon.neuralsci.org/ |
| ESCD | Jung et al35 | Stem cell type; Stem cell lineage; Stem cell species; Cell surface markers; | https://biit.cs.ut.ee/escd/ |
| Transcription factors; Immunoprecipitation antibody; Gene expression data; | |||
| Sequencing platform |