| HCA CB |
Umbilical cord blood PBMCs from the Human Cell Atlas; in total ~254,000 cells from 8 patients. |
Single cell, 10x genomics, UMI counts. |
Li et al [38], Rozenblatt-Rosen et al [39]. The data can be downloaded from https://data.humancellatlas.org/, Census of immune cells. |
| LC |
~39,000 cells from the tumor microenvironment of lung cancers and ~13,000 cells from adjacent healthy tissue. The cells originate from 5 patients. |
Single cell, 10x genomics, UMI counts. |
Lambrechts et al [40]. The data is available in in ArrayExpress under accessions E-MTAB-6149 and E-MTAB-6653. |
| PBMC68k |
~68,000 PBMCs from blood, one patient. |
Single cell, 10x genomics, UMI counts. |
Zheng G.X.Y. et al [4]. The data is available at 10x Genomics’ home page. |
| B10k |
~10,000 FACS-sorted CD19+ B cells from blood, one patient. |
Single cell, 10x genomics, UMI counts. |
Zheng G.X.Y. et al [4]. The data is available at 10x Genomics’ home page. |
| CD4TMEM |
~10,000 FACS-sorted CD4+/CD45RO+ Memory T Cells, one patient. |
Single cell, 10x genomics, UMI counts. |
Zheng G.X.Y. et al [4]. The data is available at 10x Genomics’ home page. |
| TCD8 |
~10,000 FACS-sorted CD8+ T cells from the blood of a single patient. |
Single cell, 10x genomics, UMI counts. |
Chen et al [41]. The data is available for download on GEO data repository, accession number GSE 112845. |
| MEL |
~4,600 cells from the tumor microenvironment of Melanoma, 19 patients. |
Single cell, SMART-Seq2, TPM |
Tirosh et al [42]. The data is available for download on GEO data repository, accession number GSE 72056. |
| EVAL |
Dataset produced for evaluating the performance of existing single-cell technologies. Data from mouse brain, PBMC and cell lines. Data includes 7 single-cell technologies and bulk, all performed on the same samples. |
Single cell data from 7 different technologies and corresponding bulk samples, counts/ UMI counts/ TPM |
Ding et al [26]. The data is available for download at the Single Cell Portal, id SCP425. |
| BULK 1 |
In total 6 bulk samples from B cells of varying origin. |
Bulk RNA-Seq, FASTQ files |
The ENCODE Consortium [43, 44], Gingeras. The samples can be downloaded individually from ENCODE. |
| BULK 2 |
In total 7 bulk samples from B cells (1) and T cells (6) of varying origin. |
Bulk RNA-Seq, FASTQ files |
The ENCODE Consortium [43, 44], Stamatoyannopoulos and Weng. The samples can be downloaded individually from ENCODE. |
| BULK 3 |
In total 12 bulk samples from B cells (6) and T cells (6) of varying origin. |
Bulk RNA-Seq, FASTQ files |
The functional annotation of the mammalian genome 5 (FANTOM5) [45, 46]. The data can be downloaded from FANTOM5. |
| BULK 4 |
In total 39 bulk samples from B cells (16) and T cells (23) of varying origin. |
Bulk RNA-Seq, FASTQ files |
The BLUEPRINT Epigenome Project [47]. The samples can be downloaded individually from BLUEPRINT. |
| BULK 5 |
In total 10 PBMC bulk samples from B cells (5) and T cells (5). |
Bulk RNA-Seq, RPKM/counts |
Pabst et al [48], GSE 51984. |
