Table 1.
List of the real datasets used to perform the clustering evaluation.
| Single cell dataset | Organism | Cells under study | Protocol | Accession |
|---|---|---|---|---|
| Baron2016_m | Mouse | Pancreas | inDrop | GSE84133 |
| Klein2015 | Mouse | Embryonic stem cells | inDrop | GSE65525 |
| Zeisel2015 | Mouse | Cerebral cortex | STRT/C1 UMI | GSE60361 |
| Darmanis2015 | Human | Brain | SMARTer | GSE67835 |
| Deng2014_raw | Mouse | Preimplantation embryos | Smart-Seq | GSE45719 |
| Goolam2016 | Mouse | Early embryos | Smart-Seq2 | E-MTAB-3321 |
| Kolodziejczyk2015 | Mouse | Stem cells | SMARTer | E-MTAB-2600 |
| Li2017 | Human | Colorectal tumors | SMARTer | GSE81861 |
| Romanov2016 | Mouse | Hypothalamus | Fluidigm C1 | GSE74672 |
| Tasic2016_raw | Mouse | Brain | SMARTer | GSE71585 |
| Deng2014_rpkm | Mouse | Preimplantation embryos | Smart-Seq | GSE45719 |
| Segerstolpe2016 | Human | Pancreas | Smart-Seq2 | E-MTAB-5061 |
| Tasic2016_rpkm | Mouse | Brain | SMARTer | GSE71585 |
| Xin2016 | Human | Pancreas | SMARTer | GSE81608 |
| Yan2013 | Human | Preimplantation embryos | Tang | GSE36552 |
| Biase2014 | Mouse | Embryos | SMARTer | GSE57249 |
| Treutlein2014 | Mouse | Lung epithelial cells | SMARTer | GSE52583 |
Datasets (named by the author and date of publication) contain gene expression of cells from various organisms and tissues that have been processed by different experimental protocols. Protocols include 3’ or 5’ tag and droplet-based approaches (inDrop and STRT/C1 UMI), or full-length plate-based approaches, such as Smart-Seq, Smart-Seq2, SMARTer or Fluidigm C1. Tang protocol corresponds to mRNA-Seq assay described in (Tang et al., 2009). For more information about protocols see (Svensson et al., 2018).