Selection of scRNA-seq data sets and resources relevant to hematopoiesis
| Reference . | Cell n . | Cell populations . | Platform . | Summary . | Online resource . |
|---|---|---|---|---|---|
| HSCs | |||||
| 71 | >130 | BM: LT-HSCs (LSK, CD150+, CD48−)* | C1 + SMARTer | Profiling of young and old mice reveals expansion of platelet-biased HSCs | No |
| 37 | >1 100 | BM: LT-HSCs (LSK, CD150+, CD48−), ST-HSCs (LSK, CD150−, CD48−), MPPs (LSK, CD150−, CD48+)* | SMART-Seq | Analysis of most immature stem and progenitor populations from old and young mice | Yes122 |
| 38 | >90 | BM: LT-HSCs (LSK, CD34−, Flt3−, CD48−, CD150−)* | SMART-Seq2 | Analysis of the LT-HSCs reveals subpopulations with highest repopulation potential; surface marker data allow immunophenotyping | No |
| 69 | >310 | BM: LT-HSCs (LSK, CD34−, CD48−, CD150+, CD135−), LRC/non-LRC* | C1 + SMARTer | Comparison of active and dormant HSC populations | No |
| Narrow gate data sets (HSPCs) | |||||
| 36 | >2 700 | BM: Lin−, Kit+, Sca1− cells* | MARS-Seq | Dissection of heterogeneity and lineage bias within CMPs, MEPs, GMPs; surface marker data allow immunophenotyping | No |
| 63 | >1 600 | BM: HSPCs including: LT-HSCs, LMPPs, MPPs, MEPs, CMPs, GMPs* | SMART-Seq2 | Reconstruction of 3 differentiation trajectories (erythroid, granulocytic-monocytic, lymphoid); surface marker data allow immunophenotyping | Yes123 |
| 92 | >2 800 | BM: LSK, LMPPs, CLPs + unipotent progenitors (ie, B cells, DCs, NK cells, Neu, and erythrocytes)* | CEL-Seq2 | Highlights trajectories toward B cells, neutrophils/monocytes, DCs, and erythrocytes | Yes124 |
| 39 | >380 | BM: LSK, CMPs, GMPs, (Lin− Kit+, CD34+)* | C1 + SMARTer | Dissection of heterogeneity and lineage bias in the intermediate progenitors | Yes125 |
| 19 | >4 900 | BM: LT-HSCs, ST-HSCs, MPP2s, MPP3s, MPP4s* | inDrops | Highlights lineage priming in the multipotent progenitor compartment and direct HSC-megakaryocyte differentiation trajectory | Yes126 |
| 70 | >1 400 | BM: HSPCs (CD34+, Lin−)† | Quartz-Seq | Transcriptomics/functional data suggest cloud HSC state in human followed by unipotent progenitors; surface marker data allow immunophenotyping | Yes127 |
| Broad gate data sets (HSPCs + differentiated cells) | |||||
| 47 | >2 300 | PB: range of DC and monocyte populations* | SMART-Seq2 | Analysis proposes a new taxonomy for human DCs and monocytes | Yes128 |
| 43 | >400 000 | 51 mouse tissues, including total BM and c-Kit+ fraction* | Microwell-Seq | Large-scale overview of the bone marrow and its progenitor compartment; also includes polymorphonuclear cells | Yes129 |
| BM: >38 000 | |||||
| 41 | >7 300 | BM: c-Kit+* | inDrops | Highlights basophil, megakaryocyte, and erythrocyte differentiation branches and effects of EPO stimulation | Yes130 |
| 40 | >58 000 | BM: LSK, LK* | 10X | Multiple differentiation trajectories and identification of basophil/mast cell progenitors; comparison with c-Kit–defective hematopoietic system | Yes131 |
| 26 | >180 000 | PBMCs (WT) + BMMC (AML patients + controls)† | 10X | Overview of the PBMCs (WT patients) and BMMCs before and after transplantation | No |
| 97 | >15 400 | PBMCs: CD3+ T cells, CD11b+ myeloid cells, CD19+ B cells† | 10X + REAP-Seq | Simultaneous analysis of the whole transcriptome and protein levels for 45 surface markers | No |
| 42, 44 | >270 000 | BMMCs† | 10X | Largest data set of human bone marrow yet | Yes132 |
| 10X Genomics | >8 300 | PBMCs† | 10X | PBMCs from a from a healthy human donor | No |
| 116 | >3 600 | PBMCs† | Seq-Well | Resolves major cell types and highlights heterogeneity in the monocyte population | No |
| 96 | >8 000 | CBMCs† | 10X + CITE-Seq | Simultaneous analysis of the whole transcriptome and protein levels for 13 surface markers | No |
| 117 | >21 300 | CB: CD34+† | Drop-Seq | Analysis reconstructs trajectories toward 4 distinct cell fates in the most immature compartment | Yes133 |
| 42 | >270 000 | CBMCs† | 10X | The largest data set of human cord blood yet | No |
| 118 | >8 000 | BM: unfractionated + LSK, B cells, T cells/NK cells, granulocyte and monocyte fractions* | SMART-Seq2 + 10X | >100 000 cells profiled from 20 mouse organs | Yes134 |
| Gene perturbations and diseases | |||||
| 109 | ∼70 000 | BM: DCs* | 10X | CRISPR perturbations provide insight into regulators of DCs | Yes135 |
| 112 | >10 000 | BM: myeloid cells (CD11c+) cells and HSPCs (LSK)* | MARS-Seq | CRISPR perturbations provide insight into regulators of myeloid cells in vitro and in vivo | No |
| 115 | >2 000 | BM: Lin−, CD34+, CD38− HSPCs† | SMART-Seq2 | Simultaneous analysis of leukemic and normal cells from patients with chronic myeloid leukemia; modification to SMART-Seq2 protocol allows mutation detection | No |
| 119 | >970 | BM: CD34+† | C1 + SMARTer | Use of scRNA-seq to detect aneuploidy in patients | No |
| Reference . | Cell n . | Cell populations . | Platform . | Summary . | Online resource . |
|---|---|---|---|---|---|
| HSCs | |||||
| 71 | >130 | BM: LT-HSCs (LSK, CD150+, CD48−)* | C1 + SMARTer | Profiling of young and old mice reveals expansion of platelet-biased HSCs | No |
| 37 | >1 100 | BM: LT-HSCs (LSK, CD150+, CD48−), ST-HSCs (LSK, CD150−, CD48−), MPPs (LSK, CD150−, CD48+)* | SMART-Seq | Analysis of most immature stem and progenitor populations from old and young mice | Yes122 |
| 38 | >90 | BM: LT-HSCs (LSK, CD34−, Flt3−, CD48−, CD150−)* | SMART-Seq2 | Analysis of the LT-HSCs reveals subpopulations with highest repopulation potential; surface marker data allow immunophenotyping | No |
| 69 | >310 | BM: LT-HSCs (LSK, CD34−, CD48−, CD150+, CD135−), LRC/non-LRC* | C1 + SMARTer | Comparison of active and dormant HSC populations | No |
| Narrow gate data sets (HSPCs) | |||||
| 36 | >2 700 | BM: Lin−, Kit+, Sca1− cells* | MARS-Seq | Dissection of heterogeneity and lineage bias within CMPs, MEPs, GMPs; surface marker data allow immunophenotyping | No |
| 63 | >1 600 | BM: HSPCs including: LT-HSCs, LMPPs, MPPs, MEPs, CMPs, GMPs* | SMART-Seq2 | Reconstruction of 3 differentiation trajectories (erythroid, granulocytic-monocytic, lymphoid); surface marker data allow immunophenotyping | Yes123 |
| 92 | >2 800 | BM: LSK, LMPPs, CLPs + unipotent progenitors (ie, B cells, DCs, NK cells, Neu, and erythrocytes)* | CEL-Seq2 | Highlights trajectories toward B cells, neutrophils/monocytes, DCs, and erythrocytes | Yes124 |
| 39 | >380 | BM: LSK, CMPs, GMPs, (Lin− Kit+, CD34+)* | C1 + SMARTer | Dissection of heterogeneity and lineage bias in the intermediate progenitors | Yes125 |
| 19 | >4 900 | BM: LT-HSCs, ST-HSCs, MPP2s, MPP3s, MPP4s* | inDrops | Highlights lineage priming in the multipotent progenitor compartment and direct HSC-megakaryocyte differentiation trajectory | Yes126 |
| 70 | >1 400 | BM: HSPCs (CD34+, Lin−)† | Quartz-Seq | Transcriptomics/functional data suggest cloud HSC state in human followed by unipotent progenitors; surface marker data allow immunophenotyping | Yes127 |
| Broad gate data sets (HSPCs + differentiated cells) | |||||
| 47 | >2 300 | PB: range of DC and monocyte populations* | SMART-Seq2 | Analysis proposes a new taxonomy for human DCs and monocytes | Yes128 |
| 43 | >400 000 | 51 mouse tissues, including total BM and c-Kit+ fraction* | Microwell-Seq | Large-scale overview of the bone marrow and its progenitor compartment; also includes polymorphonuclear cells | Yes129 |
| BM: >38 000 | |||||
| 41 | >7 300 | BM: c-Kit+* | inDrops | Highlights basophil, megakaryocyte, and erythrocyte differentiation branches and effects of EPO stimulation | Yes130 |
| 40 | >58 000 | BM: LSK, LK* | 10X | Multiple differentiation trajectories and identification of basophil/mast cell progenitors; comparison with c-Kit–defective hematopoietic system | Yes131 |
| 26 | >180 000 | PBMCs (WT) + BMMC (AML patients + controls)† | 10X | Overview of the PBMCs (WT patients) and BMMCs before and after transplantation | No |
| 97 | >15 400 | PBMCs: CD3+ T cells, CD11b+ myeloid cells, CD19+ B cells† | 10X + REAP-Seq | Simultaneous analysis of the whole transcriptome and protein levels for 45 surface markers | No |
| 42, 44 | >270 000 | BMMCs† | 10X | Largest data set of human bone marrow yet | Yes132 |
| 10X Genomics | >8 300 | PBMCs† | 10X | PBMCs from a from a healthy human donor | No |
| 116 | >3 600 | PBMCs† | Seq-Well | Resolves major cell types and highlights heterogeneity in the monocyte population | No |
| 96 | >8 000 | CBMCs† | 10X + CITE-Seq | Simultaneous analysis of the whole transcriptome and protein levels for 13 surface markers | No |
| 117 | >21 300 | CB: CD34+† | Drop-Seq | Analysis reconstructs trajectories toward 4 distinct cell fates in the most immature compartment | Yes133 |
| 42 | >270 000 | CBMCs† | 10X | The largest data set of human cord blood yet | No |
| 118 | >8 000 | BM: unfractionated + LSK, B cells, T cells/NK cells, granulocyte and monocyte fractions* | SMART-Seq2 + 10X | >100 000 cells profiled from 20 mouse organs | Yes134 |
| Gene perturbations and diseases | |||||
| 109 | ∼70 000 | BM: DCs* | 10X | CRISPR perturbations provide insight into regulators of DCs | Yes135 |
| 112 | >10 000 | BM: myeloid cells (CD11c+) cells and HSPCs (LSK)* | MARS-Seq | CRISPR perturbations provide insight into regulators of myeloid cells in vitro and in vivo | No |
| 115 | >2 000 | BM: Lin−, CD34+, CD38− HSPCs† | SMART-Seq2 | Simultaneous analysis of leukemic and normal cells from patients with chronic myeloid leukemia; modification to SMART-Seq2 protocol allows mutation detection | No |
| 119 | >970 | BM: CD34+† | C1 + SMARTer | Use of scRNA-seq to detect aneuploidy in patients | No |
Raw and processed data can be obtained from the European Bioinformatics Institute Single Cell Expression Atlas120 or Gene Expression Omnibus121 databases.
AML, acute myeloid leukemia; BM, bone marrow; BMMC, bone marrow mononuclear cell; CB, cord blood; CBMC, cord blood mononuclear cell; DC, dendritic cell; EPO, erythropoietin; LK, Lin−, Kit+; LMPP, lymphoid-primed MPP; LRC, label-retaining cell; LSK, Lin−, Kit+, Sca1+; NK, natural killer; PB, peripheral blood; PBMC, peripheral blood mononuclear cell; WT, wild type.
Mouse.
Human.