About
Immune
Non-immune
A repository of standardized single cell RNA-Seq datasets for analysis and visualization at the single cell level
Immune Datasets (120 Entries)
Dataset ID  | Dataset Description | Paper Title | Citation | Organism | Conditions (#) | Cell (#) | File Size (Gb) | BAM | BAI |
| Fresh 68k PBMCs (Donor A) | Fresh 68k PBMCs (Donor A) | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 68579 | 0 | |||||||
| GSE107727 | Single cell RNA sequencing of murine basophil/mast cell progenitors and granulocyte/monocyte progenitors | A single-cell hematopoietic landscape resolves 8 lineagetrajectories and defects in Kit mutant mice. | Dahlin ... Wilson Blood 2018 | Mus musculus | In Process | 44802 | 0 | |||||||
| GSE98969 | Transcriptional profiling of single cells from immune populations of mouse models of neurodegenerative diseases with matched controls | A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease. | Keren-Shaul ... Amit Cell 2017 | Mus musculus (mm10) | 28 | 35242 | 94.8 |  | ||||||
| 1. Cerebellum_5XFAD_CD45+_Alzheimer_disease_6_months | 2280 | 6.3 | | | ||||||||||
| 2. Cerebellum_C57BL_CD45+_Alzheimer_disease_6_months | 1520 | 4 | | | ||||||||||
| 3. Cortex_5XFAD_CD45+_Alzheimer_disease_6_months | 2280 | 6.4 | | | ||||||||||
| 4. Cortex_C57BL_CD45+_Alzheimer_disease_6_months | 1520 | 4 | | | ||||||||||
| 5. Spinal_cord_C57BL_CD45+_ALS_135_days | 760 | 1.9 | | | ||||||||||
| 6. Spinal_cord_C57BL_CD45+_ALS_80_days | 1712 | 3.7 | | | ||||||||||
| 7. Spinal_cord_SOD1_CD45+_ALS_135_days | 760 | 1.6 | | | ||||||||||
| 8. Spinal_cord_SOD1_CD45+_ALS_80_days | 2280 | 4.6 | | | ||||||||||
| 9. Whole_brain_5XFAD_CD45+_Alzheimer_disease_6_months | 6080 | 14.1 | | | ||||||||||
| 10. Whole_brain_5XFAD_CD45-intCD11bintCD11c+Gr1-_Alzheimer_disease_1_month | 584 | 2.1 | | | ||||||||||
| 11. Whole_brain_5XFAD_CD45-intCD11bintCD11c+Gr1-_Alzheimer_disease_3_months | 122 | 0.6 | | | ||||||||||
| 12. Whole_brain_5XFAD_CD45-intCD11b-intCD11c+Gr1-_Alzheimer_disease_6_months | 380 | 3.6 | | | ||||||||||
| 13. Whole_brain_5XFAD_CD45-intCD11bintCD11c+Gr1-_Alzheimer_disease_9 | 187 | 0.8 | | | ||||||||||
| 14. Whole_brain_5XFAD_CD45-intCD11b-intCD11c+Gr1-_and_CD45-intCD11b-intGr1- | 324 | 1.1 | | | ||||||||||
| 15. Whole_brain_5XFAD_CD45-intCD11b-intGr1-_Alzheimer_disease_6_months_ | 1004 | 1 | | | ||||||||||
| 16. Whole_brain_C57BL_CD45+_Alzheimer_disease_6_months | 6080 | 16 | | | ||||||||||
| 17. Whole_brain_C57BL_CD45+CD11b+Gr1-_Aging_20_months | 760 | 1.7 | | | ||||||||||
| 18. Whole_brain_C57BL_CD45+CD11b+Gr1-_Aging_7_weeks | 1140 | 3.4 | | | ||||||||||
| 19. Whole_brain_C57BL_CD45-intCD11b-intCD11c+Gr1-_Aging_20_months | 155 | 0.7 | | | ||||||||||
| 20. Whole_brain_C57BL_CD45-intCD11b-intCD11c+Gr1-_Alzheimer_disease_6 | 760 | 0.6 | | | ||||||||||
| 21. Whole_brain_C57BL_CD45-intCD11bintGr1-_Alzheimer_disease_1_month | 380 | 2.1 | | | ||||||||||
| 22. Whole_brain_C57BL_CD45-intCD11bintGr1-_Alzheimer_disease_3_months | 380 | 1.5 | | | ||||||||||
| 23. Whole_brain_C57BL_CD45-intCD11b-intGr1-_Alzheimer_disease_6_months | 327 | 2.1 | | | ||||||||||
| 24. Whole_brain_C57BL_CD45-intCD11b-intGr1-_Alzheimer_disease_8_months | 380 | 1.2 | | | ||||||||||
| 25. Whole_brain_Trem2KO_5XFAD_CD45-intCD11b-intCD11c+Gr1-_Alzheimer_disease_6_months | 1140 | 2.9 | | | ||||||||||
| 26. Whole_brain_Trem2KO_5XFAD_CD45-intCD11b-intGr1-_Alzheimer_disease_6_months | 1140 | 3.6 | | | ||||||||||
| 27. Whole_brain_Trem2KO_CD45-intCD11b-intCD11c+Gr1-_Alzheimer_disease_6_months | 272 | 0.7 | | | ||||||||||
| 28. Whole_brain_Trem2KO_CD45-intCD11b-intGr1-_Alzheimer_disease_6_months | 535 | 2.6 | | | ||||||||||
| 33k PBMCs from a Healthy Donor | Peripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc3k and pbmc6k). | ... 2016 | Homo sapiens | In Process | 33148 | 0 | ||||||||
| EGAS00001002560 | single-cell RNA sequencing in ~25,000 peripheral blood mononuclear cells (PBMCs) of 45 donors | Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs. | van der Wijst ... Franke Nat Genet 2018 | Homo sapiens | In Process | 28855 | 0 | |||||||
| GSE107910 | A single-cell atlas of the developing mouse thymus | A Single-Cell Transcriptomic Atlas of Thymus Organogenesis Resolves Cell Types and Developmental Maturation | Kernfeld ... Maehr Immunity 2018 | Mus musculus (mm10) | 11 | 24279 | 55.1 | | ||||||
| 1. E12_5_wholeThy_venus | 1747 | 7.8 | | | ||||||||||
| 2. E13_5_wholeThy | 3769 | 8.8 | | | ||||||||||
| 3. E14_5_wholeThy | 1654 | 5.2 | | | ||||||||||
| 4. E15_5_wholeThy | 1506 | 4.5 | | | ||||||||||
| 5. E16_5_wholeThy | 2831 | 3.9 | | | ||||||||||
| 6. E17_5_wholeThy | 2036 | 5.4 | | | ||||||||||
| 7. E18_5_wholeThy | 913 | 2.6 | | | ||||||||||
| 8. FTOC_PBSDMSO | 3660 | 4.2 | | | ||||||||||
| 9. FTOC_RA | 3178 | 7.2 | | | ||||||||||
| 10. P0_wholeThy | 973 | 2.6 | | | ||||||||||
| 11. Rag1KO_wholeThy | 2012 | 2.9 | | | ||||||||||
| GSE90486 | Myeloid cells infected with lentiviral vectors carrying different gRNAs | Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq | Jaitin ... Amit Cell 2016 | Mus musculus (mm10) | 14 | 23808 | 91 | | ||||||
| 1. dendritic_spleen_GFP+BFP+CD3-TCRb-CD19-NK-1.1-Ly6g-CD11c++LPS_in_vivo_mix_BFP | 768 | 2.8 | | | ||||||||||
| 2. myeloid_bone_marrow_GFP+BFP+_mCherry+CD11c++unstimulated_Cebpb_BFP_x_Rela_mCherry | 384 | 1.9 | | | ||||||||||
| 3. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_Cebpb_BFP_x_Rela_mCherry | 768 | 2.2 | | | ||||||||||
| 4. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_developmental_genes_mix_BFP | 1152 | 4.7 | | | ||||||||||
| 5. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_INF_AV_gRNA_pool_BFP | 6144 | 21.5 | | | ||||||||||
| 6. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_INF_AV_mix1_BFP | 4224 | 16 | | | ||||||||||
| 7. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_INF_AV_mix2_BFP | 4224 | 18.2 | | | ||||||||||
| 8. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_Irf9_x_Rela_BFP | 1152 | 4.9 | | | ||||||||||
| 9. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_Itgam-BFP_x_Cebpb-mCherry | 384 | 1.2 | | | ||||||||||
| 10. myeloid_bone_marrow_GFP+BFP+CD11c++unstimulated_Cebpb_BFP | 384 | 2.2 | | | ||||||||||
| 11. myeloid_bone_marrow_GFP+BFP+CD11c++unstimulated_Cebpb_BFP_x_Rela_mCherry | 1152 | 4.6 | | | ||||||||||
| 12. myeloid_bone_marrow_GFP+BFP+CD11c++unstimulated_control_gRNA | 384 | 1.9 | | | ||||||||||
| 13. myeloid_bone_marrow_GFP+BFP+CD11c++unstimulated_Itgam-BFP_x_Cebpb-mCherry | 384 | 1 | | | ||||||||||
| 14. myeloid_spleen_GFP+BFP+CD3-TCRb-CD19-NK-1.1-Ly6g-+LPS_in_vivo_mix_BFP | 2304 | 7.9 | | | ||||||||||
| GSE117498 | Single-cell mRNA sequencing of freshly isolated hematopoietic progenitors from human bone marrow | A comprehensive single cell transcriptional landscape of human hematopoietic progenitors | Pellin ... Biasco Nat Commun 2019 | Homo sapiens (hg38) | 11 | 21312 | 22.1 | | ||||||
| 1. CMP | 1282 | 1.5 | | | ||||||||||
| 2. GMP | 215 | 1.7 | | | ||||||||||
| 3. HSC | 123 | 1.7 | | | ||||||||||
| 4. Lin-CD34-CD164high | 592 | 2 | | | ||||||||||
| 5. Lin-CD34-CD164low | 1211 | 1.3 | | | ||||||||||
| 6. Lin-CD34+CD164+ | 1576 | 3.5 | | | ||||||||||
| 7. Lin-CD34lowCD164high | 1012 | 3.7 | | | ||||||||||
| 8. MEP | 6343 | 1.8 | | | ||||||||||
| 9. MLP | 4434 | 1.7 | | | ||||||||||
| 10. MPP | 4266 | 1.5 | | | ||||||||||
| 11. Pre_NK | 358 | 1.6 | | | ||||||||||
| CD8+/CD45RA+ Naive Cytotoxic T Cells | CD8+/CD45RA+ Naive Cytotoxic T Cells enriched from fresh PBMCs. 99% pure by FACS | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 11953 | 0 | |||||||
| CD4+ Helper T Cells | CD4+ Helper T Cells enriched from fresh PBMCs. 99% pure by FACS | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 11213 | 0 | |||||||
| CD4+/CD45RA+/CD25- Naive T cells | CD4+/CD45RA+/CD25- Naive T cells enriched from fresh PBMCs. 98% pure by FACS | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 10479 | 0 | |||||||
| CD4+/CD25+ Regulatory T Cells | CD4+/CD25+ Regulatory T Cells enriched from fresh PBMCs. 95% pure by FACS | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 10263 | 0 | |||||||
| GSE72857 | Bone marrow myeloid progenitors | Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. | Paul ... Amit Cell 2015 | Mus musculus (mm10) | 8 | 10260 | 48.7 | | ||||||
| 1. Cebpa_control | 1140 | 6.4 | | | ||||||||||
| 2. Cebpa_KO | 2280 | 11.4 | | | ||||||||||
| 3. Cebpe_control | 380 | 2 | | | ||||||||||
| 4. Cebpe_KO | 760 | 3.5 | | | ||||||||||
| 5. CMP_CD41 | 380 | 1.1 | | | ||||||||||
| 6. CMP_Flt3+_Csf1r+ | 1140 | 5.3 | | | ||||||||||
| 7. CMP_Irf8-GFP+_MHCII+ | 1140 | 9.1 | | | ||||||||||
| 8. Unsorted_myeloid | 3040 | 9.9 | | | ||||||||||
| CD4+/CD45RO+ Memory T Cells | CD4+/CD45RO+ Memory T Cells enriched from fresh PBMCs. 98% pure by FACS | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 10224 | 0 | |||||||
| CD8+ Cytotoxic T cells | CD8+ Cytotoxic T cells enriched from fresh PBMCs. 98% pure by FACS | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 10209 | 0 | |||||||
| CD19+ B Cells | CD19+ B Cells enriched from fresh PBMCs. | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 10085 | 0 | |||||||
| Frozen PBMCs (Donor C) | Frozen PBMCs (Donor C) | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 9519 | 0 | |||||||
| CD34+ Cells | CD34+ Cells enriched from fresh PBMCs, 45% pure by FACS | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 9232 | 0 | |||||||
| 8k PBMCs from a Healthy Donor | Peripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc4k). | ... 2017 | Homo sapiens | In Process | 8391 | 0 | ||||||||
| CD56+ Natural Killer Cells | CD56+ NK cells enriched from fresh PBMCs. 92% pure by FACS | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens (hg38) | 1 | 8385 | 12.7 | | ||||||
| 1. NK | 8385 | 12.7 | | | ||||||||||
| Frozen PBMCs (Donor B) | Frozen PBMCs (Donor B) | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 7783 | 0 | |||||||
| 6k PBMCs from a Healthy Donor | Peripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc3k). | ... 2016 | Homo sapiens | In Process | 5419 | 0 | ||||||||
| GSE98638 | T cells isolated from peripheral blood, tumor and adjacent normal tissues from hepatocellular carcinoma patients. | Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing | Zheng ... Zhang Cell 2017 | Homo sapiens | In Process | 5063 | 0 | |||||||
| 4k Pan T Cells from a Healthy Donor | Pan T cells isolated from mononuclear cells of a healthy donor (same donor as t_3k). | ... 2017 | Homo sapiens | In Process | 4532 | 0 | ||||||||
| GSE54006 | Dendritic cells and additional hematopoietic cell types in steady state and after pathogen activation (LPS) | Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. | Jaitin ... Amit Science 2014 | Mus musculus (mm10) | 13 | 4468 | 30.1 | | ||||||
| 1. B_cell | 48 | 0.6 | | | ||||||||||
| 2. CD8+CD86- | 95 | 1.4 | | | ||||||||||
| 3. CD8+CD86+ | 95 | 0.9 | | | ||||||||||
| 4. CD8+pDC | 95 | 0.1 | | | ||||||||||
| 5. CD8-CD4+ESAM+ | 95 | 1.9 | | | ||||||||||
| 6. CD8-pDC | 95 | 1.9 | | | ||||||||||
| 7. GC_B_cell | 47 | 1 | | | ||||||||||
| 8. CD11c+ | 701 | 13.4 | | | ||||||||||
| 9. CD11c+_LPS | 1528 | 4 | | | ||||||||||
| 10. CD11c+_PBS | 1528 | 3.6 | | | ||||||||||
| 11. monocyte_or_neutrophil | 47 | 0.6 | | | ||||||||||
| 12. NK_cell | 47 | 0.4 | | | ||||||||||
| 13. splenocyte | 47 | 0.5 | | | ||||||||||
| 4k PBMCs from a Healthy Donor | Peripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc8k). | ... 2017 | Homo sapiens | In Process | 4352 | 0 | ||||||||
| AML027 Post-transplant BMMCs | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 3965 | 0 | ||||||||
| AML027 Pre-transplant BMMCs | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 3933 | 0 | ||||||||
| AML035 Pre-transplant BMMCs | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 3592 | 0 | ||||||||
| 3k Pan T Cells from a Healthy Donor | Pan T cells isolated from mononuclear cells of a healthy donor (same donor as t_4k). | ... 2017 | Homo sapiens | In Process | 3551 | 0 | ||||||||
| Jurkat Cells | Jurkat Cells | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 3258 | 0 | |||||||
| Frozen PBMCs (Donor A) | Frozen PBMCs (Donor A) | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 2900 | 0 | |||||||
| GSE85152 | Small intestinal ILCs (Innate lymphoid cells) | The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome | Gury-BenAri ... Amit Cell 2016 | Mus musculus (mm10) | 3 | 2701 | 26.4 | | ||||||
| 1. gut_ILC | 1282 | 9.4 | | | ||||||||||
| 2. gut_ILC_GF | 1108 | 13.7 | | | ||||||||||
| 3. gut_ILC_NoGFP | 311 | 3.3 | | | ||||||||||
| 3k PBMCs from a Healthy Donor | Peripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc6k). | ... 2016 | Homo sapiens | In Process | 2700 | 0 | ||||||||
| CD14+ Monocytes | CD14+ Monocytes enriched from fresh PBMCs. | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens (hg38) | 1 | 2612 | 8.2 | | ||||||
| 1. cd14 | 2612 | 8.2 | | | ||||||||||
| Frozen BMMCs (Healthy Control 2) | Frozen BMMCs (Healthy Control 2) | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 2472 | 0 | |||||||
| GSE75478 | Single-cell indexed RNA-Seq of human hematopoietic stem and progenitors | Human haematopoietic stem cell lineage commitment is a continuous process. | Velten ... Steinmetz Nat Cell Biol. 2017 | Homo sapiens (hg38) | 5 | 2414 | 377.9 | | ||||||
| 1. Lin-CD34+CD38+CD45RA-CD90+_QUARTZ-Seq | 96 | 18.8 | | | ||||||||||
| 2. Lin-CD34+CD38+_QUARTZ-Seq | 384 | 74.5 | | | ||||||||||
| 3. Lin-CD34+CD38-_smart-seq2 | 526 | 65.2 | | | ||||||||||
| 4. Lin-CD34+CD38+_smart-seq2 | 736 | 89.4 | | | ||||||||||
| 5. Lin-CD34+CD38-_QUARTZ-Seq | 672 | 130 | | | ||||||||||
| GSE48968 | Primary mouse dendritic cells (DCs) stimulated with three pathogenic components (LPS, PAM, PIC) at different time points after stimulation (0h,1h, 2h, 4h, 6h) | Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. | Shalek ... Regev Nature 2014 | Mus musculus (mm10) | 24 | 2412 | 1296 | | ||||||
| 1. Ifnar1_KO_LPS_2h | 61 | 18.2 | | | ||||||||||
| 2. Ifnar1_KO_LPS_4h | 96 | 25.8 | | | ||||||||||
| 3. IFNB_2h | 94 | 59.1 | | | ||||||||||
| 4. LPS_1h | 96 | 84.7 | | | ||||||||||
| 5. LPS_2h | 220 | 130.3 | | | ||||||||||
| 6. LPS_4h_GolgiPlug_0h | 56 | 18.3 | | | ||||||||||
| 7. LPS_4h_GolgiPlug_1h | 46 | 11 | | | ||||||||||
| 8. LPS_4h_GolgiPlug_2h | 53 | 9.3 | | | ||||||||||
| 9. LPS_4h | 328 | 248.4 | | | ||||||||||
| 10. LPS_4h_Tenth | 49 | 23.9 | | | ||||||||||
| 11. LPS_6h | 96 | 70.1 | | | ||||||||||
| 12. On_Chip_Stimulation_LPS_4h | 90 | 17.6 | | | ||||||||||
| 13. On_Chip_Unstim | 38 | 9.5 | | | ||||||||||
| 14. PAM_1h | 96 | 64.4 | | | ||||||||||
| 15. PAM_2h | 96 | 61.4 | | | ||||||||||
| 16. PAM_4h | 85 | 42.7 | | | ||||||||||
| 17. PAM_6h | 64 | 34.8 | | | ||||||||||
| 18. PIC_1h | 96 | 70.3 | | | ||||||||||
| 19. PIC_2h | 84 | 61.9 | | | ||||||||||
| 20. PIC_4h | 90 | 67.5 | | | ||||||||||
| 21. PIC_6h | 96 | 16.3 | | | ||||||||||
| 22. Stat1_KO_LPS_4h | 94 | 12.7 | | | ||||||||||
| 23. Tnfr_KO_LPS_4h | 96 | 17.6 | | | ||||||||||
| 24. Unstimulated | 192 | 120.2 | | | ||||||||||
| GSE94820 | Enriched immune cell fractions isolated from healthy blood PBMCs | Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors | Villani ... Hacohen Science 2017 | Homo sapiens | In Process | 2384 | 0 | |||||||
| GSE59114 | Long-term hematopoietic stem cells (LT-HSC), short-term hematopoietic stem cells (ST-HSCs), and multipotent progenitors (MPPs) from two mouse strains (C57BL/6 and DBA/2) from young and old mice | Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. | Kowalczyk ... Regev Genome Research 2015 | Mus musculus (mm10) | 12 | 2089 | 252.1 | | ||||||
| 1. old_C57BL6_LTHSC | 384 | 57.8 | | | ||||||||||
| 2. old_C57BL6_MPP | 192 | 30 | | | ||||||||||
| 3. old_C57BL6_STHSC | 384 | 49.4 | | | ||||||||||
| 4. old_DBA_LTHSC | 140 | 7.9 | | | ||||||||||
| 5. old_DBA_MPP | 70 | 4.1 | | | ||||||||||
| 6. old_DBA_STHSC | 68 | 3.7 | | | ||||||||||
| 7. young_C57BL6_LTHSC | 192 | 29.7 | | | ||||||||||
| 8. young_C57BL6_MPP | 192 | 33.5 | | | ||||||||||
| 9. young_C57BL6_STHSC | 192 | 22.7 | | | ||||||||||
| 10. young_DBA_LTHSC | 115 | 5.3 | | | ||||||||||
| 11. young_DBA_MPP | 89 | 4.5 | | | ||||||||||
| 12. young_DBA_STHSC | 71 | 3.6 | | | ||||||||||
| Frozen BMMCs (Healthy Control 1) | Frozen BMMCs (Healthy Control 1) | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 1985 | 0 | |||||||
| GSE81682 | Haematopoeitic stem and progenitor cells | A single cell resolution map of mouse haematopoietic stem and progenitor cell differentiation. | Nestorowa ... Gottgens Blood 2016 | Mus musculus (mm10) | 3 | 1920 | 662.6 | | ||||||
| 1. Haematopoietic progenitor cell Prog (HPCP) | 852 | 361.8 | | | ||||||||||
| 2. Haematopoietic stem cell/multipotent progenitor HSPC (HSC) | 852 | 228.7 | | | ||||||||||
| 3. Long term haematopoeitic stem cells (LT-HSC) | 216 | 72.1 | | | ||||||||||
| GSE97168 | Human stage IA lung adenocarcinoma lesion and adjacent non-involved lung | Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses | Lavin ... Merad Cell 2017 | Homo sapiens (hg38) | 2 | 1920 | 7.5 | | ||||||
| 1. lung | 768 | 2.8 | | | ||||||||||
| 2. tumor | 1152 | 4.6 | | | ||||||||||
| E-MTAB-4388 | transcriptional states of individual CD4+ T cells during blood-stage Plasmodium chabaudi infection in mice. | Single-cell? RNA-seq? and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria | Lonnberg ... Teichmann Sci Immunol. 2017 | Mus musculus (mm10) | 12 | 1598 | 566 | | ||||||
| 1. Dendritic_3d_Plasmodium | 39 | 6 | | | ||||||||||
| 2. Dendritic_CD8a-_0d_none | 50 | 21.8 | | | ||||||||||
| 3. Dendritic_CD8a+_0d_none | 46 | 26.4 | | | ||||||||||
| 4. Monocyte_0d_none | 96 | 52.7 | | | ||||||||||
| 5. Monocyte_3d_Plasmodium | 79 | 36.5 | | | ||||||||||
| 6. Tcell_0d_none | 362 | 91.5 | | | ||||||||||
| 7. Tcell_2d_Plasmodium | 135 | 61.4 | | | ||||||||||
| 8. Tcell_3d_Plasmodium | 21 | 10.7 | | | ||||||||||
| 9. Tcell_4d_Plasmodium | 281 | 125 | | | ||||||||||
| 10. Tcell_7d_naive | 89 | 19.2 | | | ||||||||||
| 11. Tcell_7d_none | 143 | 40.4 | | | ||||||||||
| 12. cell_7d_Plasmodium | 257 | 75 | | | ||||||||||
| E-MTAB-4888 | CD4+ T cells from young and old mice of CAST/EiJ and C57BL/6 | Aging increases cell-to-cell transcriptional variability upon immune stimulation | Eling ... Odom Science 2017 | Mus musculus (mm10) | 11 | 1506 | 544.9 | | ||||||
| 1. B6_o_memory_anti_CD3e_CD28 | 55 | 17.3 | | | ||||||||||
| 2. B6_o_memory_none | 133 | 43.8 | | | ||||||||||
| 3. B6_o_naive_anti_CD3e_CD28 | 236 | 106.7 | | | ||||||||||
| 4. B6_o_naive_none | 422 | 152.6 | | | ||||||||||
| 5. B6_y_memory_anti_CD3e_CD28 | 174 | 19.6 | | | ||||||||||
| 6. B6_y_naive_anti_CD3e_CD28 | 92 | 46.5 | | | ||||||||||
| 7. B6_y_naive_none | 196 | 75.1 | | | ||||||||||
| 8. CAST_o_naive_anti_CD3e_CD28 | 59 | 27.7 | | | ||||||||||
| 9. CAST_o_naive_none | 69 | 26.3 | | | ||||||||||
| 10. CAST_y_naive_anti_CD3e_CD28 | 35 | 16.4 | | | ||||||||||
| 11. CAST_y_naive_none | 35 | 12.9 | | | ||||||||||
| GSE86042 | CD8 TILs from WT and MTKO mice. SubSeries: GSE86028, GSE86030, GSE86031, GSE86039 | A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells | Singer ... Anderson Cell 2016 | Mus musculus (mm10) | 2 | 1061 | 109 | | ||||||
| 1. WT | 516 | 50 | | | ||||||||||
| 2. MTKO | 545 | 59.1 | | | ||||||||||
| GSE90799 | Molecular reprogramming of granulocyte/macrophage progenitor (GMP) clusters. SubSeries: GSE90797, GSE90140 | Myeloid progenitor cluster formation drives emergency and leukaemic myelopoiesis. | Herault ... Passegue Nature 2017 | Mus musculus (mm10) | 7 | 958 | 63.9 | | ||||||
| 1. Day0 | 96 | 5.9 | | | ||||||||||
| 2. Day8 | 190 | 12.9 | | | ||||||||||
| 3. Day10 | 96 | 6.3 | | | ||||||||||
| 4. Day12 | 96 | 5.9 | | | ||||||||||
| 5. Day14 | 96 | 2.9 | | | ||||||||||
| 6. control | 96 | 7.7 | | | ||||||||||
| 7. BCR_ABL | 288 | 22.2 | | | ||||||||||
| GSE89232 | Primary human conventional dendritic cells (cDCs), cord blood and blood pre-cDCs | Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+?? or CD141+ DCs | Breton ... Nussenzweig JEM 2016 | Homo sapiens (hg19) | 3 | 957 | 17.7 | | ||||||
| 1. blood_DC | 164 | 3.4 | | | ||||||||||
| 2. blood_pre-cDC | 341 | 3.8 | | | ||||||||||
| 3. CB_pre-cDC | 452 | 10.4 | | | ||||||||||
| AML035 Post-transplant BMMCs | Massively parallel digital transcriptional profiling of single cells. | Zheng ... Bielas Nat Commun 2017 | Homo sapiens | In Process | 909 | 0 | ||||||||
| GSE75659 | Human T-cells. Mouse fibroblasts from this experiment can be found in the non-immune part. | Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq | Reinius ... Sandberg Nature Genetics 2016 | Homo sapiens (hg38) | 3 | 892 | 105 | | ||||||
| 1. Tcell.ex.vivo | 347 | 58.5 | | | ||||||||||
| 2. Tcell.in.vivo.D136 | 73 | 7.9 | | | ||||||||||
| 2. Tcell.in.vivo.D15 | 472 | 38.5 | | | ||||||||||
| GSE94383 | RAW 264.7 Cell Line (murine Macrophage) stimulated with LPS on a fluidigm C1 chip | Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-kB Activation. | Lane ... Covert Cell Syst. 2017 | Mus musculus | In Process | 839 | 0 | |||||||
| ERP011804 | Transcriptional regulatory network during ILC2 commitment | Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway | Yu ... Liu Nature 2016 | Mus musculus (mm10) | 1 | 768 | 129.4 | | ||||||
| 1. ILC2 | 768 | 129.4 | | | ||||||||||
| GSE74833 | Th17 cell pathogenicity. SubSeries: GSE75107, GSE75108, GSE75109, GSE75110, GSE75111 | Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity. | Gaublomme ... Regev Cell 2015 | Mus musculus (mm10) | 5 | 722 | 324.6 | | ||||||
| 1. EAE-CNS-IL-17A_GFP+ (GSE75107) | 166 | 95.1 | | | ||||||||||
| 2. EAE-LN-IL-17A_GFP+ (GSE75108) | 136 | 55.2 | | | ||||||||||
| 3. IL1B_IL6_IL23-48h-IL-17A_GFP+ (GSE75109) | 139 | 47.2 | | | ||||||||||
| 4. TGFB1_IL6-48h (GSE75110) | 130 | 62.5 | | | ||||||||||
| 5. TGFB1_IL6-48h-IL-17A_GFP+ (GSE75111) | 151 | 64.6 | | | ||||||||||
| GSE70245 | CMP. SubSeries: GSE70236, GSE70238, GSE70239, GSE70240, GSE70241, GSE70242, GSE70243, GSE70244, GSE78907 | Single-cell analysis of mixed-lineage states leading to a binary cell fate choice | Olsson ... Grimes Nature 2016 | Mus musculus (mm10) | 9 | 660 | 240.9 | | ||||||
| 1. CMP | 96 | 39.9 | | | ||||||||||
| 2. Gfi1-GFP_GMP | 39 | 18.7 | | | ||||||||||
| 3. Gfi1-_GMP | 80 | 19.4 | | | ||||||||||
| 4. GMP | 136 | 51.3 | | | ||||||||||
| 5. Irf8-GFP_GMP | 37 | 15.1 | | | ||||||||||
| 6. Irf8_KO_GMP | 63 | 14.7 | | | ||||||||||
| 7. LK_CD34 | 66 | 20.4 | | | ||||||||||
| 8. LSK | 96 | 41.6 | | | ||||||||||
| 9. Gfi1-_Irf8-_GMP | 47 | 19.9 | | | ||||||||||
| E-MTAB-3947 | CD41 expressing cells from kidney and heart of zebrafish | Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells | Macaulay ... Cvejic Cell Reports 2016 | Danio rerio (GRCz10) | 7 | 652 | 184.4 | | ||||||
| 1. F_Circulation_EGFP-high | 68 | 13.6 | | | ||||||||||
| 2. F_Circulation_EGFP-low | 24 | 4.6 | | | ||||||||||
| 3. F_Kidney_EarlyEnriched | 92 | 16.9 | | | ||||||||||
| 4. F_Kidney_EGFP-high | 46 | 7.8 | | | ||||||||||
| 5. F_Kidney_EGFP-low | 46 | 8.9 | | | ||||||||||
| 6. O_Kidney_EGFP-high | 188 | 65.7 | | | ||||||||||
| 7. O_Kidney_EGFP-low | 188 | 66.8 | | | ||||||||||
| GSE70580 | Human tonsil Innate lymphoid cells (ILCs) | The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing | Bjorklund ... Mjosberg Nature Immunology 2016 | Homo sapiens (hg19) | 4 | 648 | 60.2 | | ||||||
| 1. ILC1 | 127 | 12.7 | | | ||||||||||
| 2. ILC2 | 139 | 13.9 | | | ||||||||||
| 3. ILC3 | 308 | 27.6 | | | ||||||||||
| 4. NK | 74 | 6 | | | ||||||||||
| E-MTAB-6051 | Single-cell RNA sequencing of OT-I CD8+ T cells after stimulation with different affinity | T cell cytolytic capacity is independent of initial stimulation strength | Richard ... Griffiths Nat Immunol. 2018 | Mus musculus | In Process | 572 | 0 | |||||||
| ERP015644 | CD4 T cells 7 days after infection or immunisation | Opposing Development of Cytotoxic and Follicular Helper CD4?? T Cells Controlled by the TCF-1-Bcl6 Nexus | Donnarumma ... Kassiotis Cell Reports 2016 | Mus musculus (mm10) | 4 | 567 | 67 | | ||||||
| 1. BCL6_Ad5 | 96 | 12 | | | ||||||||||
| 2. BCL6_FV | 96 | 12.8 | | | ||||||||||
| 3. WT_Ad5 | 190 | 22.8 | | | ||||||||||
| 4. WT_FV | 185 | 19.5 | | | ||||||||||
| GSE87849 | Stem cell derived macrophages (wildtype and SAMHD1 knockout) were single-cell cultured for 1h or 8h under 4 different media conditions | The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq. | Wills ... Bowden BMC Genomics 2017 | Homo sapiens (hg19) | 24 | 503 | 77.3 | | ||||||
| 1. dNTPase_KO_1h_conditioned_LPS | 10 | 1.26 | | | ||||||||||
| 2. dNTPase_KO_1h_conditioned | 13 | 1.45 | | | ||||||||||
| 3. dNTPase_KO_1h_standard_LPS | 20 | 2.29 | | | ||||||||||
| 4. dNTPase_KO_1h_standard | 21 | 2.63 | | | ||||||||||
| 5. dNTPase_KO_8h_conditioned_LPS | 21 | 3.47 | | | ||||||||||
| 6. dNTPase_KO_8h_conditioned | 17 | 2.83 | | | ||||||||||
| 7. dNTPase_KO_8h_standard_LPS | 16 | 2.89 | | | ||||||||||
| 8. dNTPase_KO_8h_standard | 14 | 2.11 | | | ||||||||||
| 9. KO_1h_conditioned_LPS | 12 | 1.81 | | | ||||||||||
| 10. KO_1h_conditioned | 9 | 1.55 | | | ||||||||||
| 11. KO_1h_standard_LPS | 15 | 2.81 | | | ||||||||||
| 12. KO_1h_standard | 14 | 2.5 | | | ||||||||||
| 13. KO_8h_conditioned_LPS | 14 | 1.99 | | | ||||||||||
| 14. KO_8h_conditioned | 14 | 2.14 | | | ||||||||||
| 15. KO_8h_standard_LPS | 13 | 2.22 | | | ||||||||||
| 16. KO_8h_standard | 8 | 1.25 | | | ||||||||||
| 17. WT_1h_conditioned_LPS | 33 | 4.5 | | | ||||||||||
| 18. WT_1h_conditioned | 58 | 8.54 | | | ||||||||||
| 19. WT_1h_standard_LPS | 36 | 5.23 | | | ||||||||||
| 20. WT_1h_standard | 37 | 5.16 | | | ||||||||||
| 21. WT_8h_conditioned_LPS | 25 | 4.34 | | | ||||||||||
| 22. WT_8h_conditioned | 32 | 5.71 | | | ||||||||||
| 23. WT_8h_standard_LPS | 27 | 4.53 | | | ||||||||||
| 24. WT_8h_standard | 24 | 4.05 | | | ||||||||||
| GSE68981 | HSC and MPPs from normal and bled mice | Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors | Yang ... Weissman Nucleic Acids Research 2016 | Mus musculus (mm10) | 4 | 460 | 85 | | ||||||
| 1. bled_HSC | 53 | 13.8 | | | ||||||||||
| 2. HSC | 221 | 43.1 | | | ||||||||||
| 3. bled_MPP1 | 63 | 18 | | | ||||||||||
| 4. MPP1 | 123 | 10.2 | | | ||||||||||
| GSE100618 | Single Cell RNA sequencing analysis of human haemopoietic lympho-myeloid progenitor populations (LMPP, MLP and GMP) | Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells | Karamitros ... Vyas Nat Immunol. 2017 | Homo sapiens (hg38) | 4 | 420 | 118 | | ||||||
| 1. empty | 5 | 1.5 | | | ||||||||||
| 2. GMP | 140 | 36.6 | | | ||||||||||
| 3. LMPP | 128 | 35.4 | | | ||||||||||
| 4. MLP | 147 | 42.5 | | | ||||||||||
| GSE71794 | Murine hematopoietic stem cells, ESC, and HSC-like cells derived from differentiation of embryonic stem cells | Engineered Murine HSCs Reconstitute Multi-lineage Hematopoiesis and Adaptive Immunity | Lu ... Daley Cell Reports 2016 | Mus musculus (mm10) | 4 | 316 | 23.8 | | ||||||
| 1. Eng_BM-HSC | 95 | 2.9 | | | ||||||||||
| 2. Eng_ES-HSC | 49 | 1.5 | | | ||||||||||
| 3. ESC | 78 | 3.8 | | | ||||||||||
| 4. FL_HSC | 94 | 15.5 | | | ||||||||||
| GSE89405 | Gene expression profiles for key stages of T cell differentiation | Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA sequencing. | Kakaradov ... Yeo Nat Immunol. 2017 | Mus musculus | In Process | 304 | 0 | |||||||
| GSE89405 | Gene expression profiles for key stages of T cell differentiation | Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA sequencing. | Kakaradov ... Yeo Nat Immunol. 2017 | Mus musculus | In Process | 304 | 0 | |||||||
| GSE114895 | Thymic tuft cell single-cell mRNA analysis | Thymic tuft cells promote an IL-4-enriched medulla and shape thymocyte development | Miller ... Anderson Nature 2018 | Mus musculus | In Process | 300 | 0 | |||||||
| E-MTAB-3346 | Mouse medullary thyme ephitelial cells (mTECs) - mature (MHCIIhi) mTECs and 3 subsets selected for their particular tissue-restricted self antigens | Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells | Brennecke ... Steinmetz Nature Immunology 2015 | Mus musculus (mm10) | 4 | 293 | 210.6 | | ||||||
| 1. MHCII_high_Ceacam1 | 33 | 29.9 | | | ||||||||||
| 2. MHCII_high_Tspan8 | 49 | 36.2 | | | ||||||||||
| 3. MHCII_high | 163 | 115.6 | | | ||||||||||
| 4. MHCII_low | 48 | 28.9 | | | ||||||||||
| ERP010829 | Wildtype and Bcl11a deficient haematopoietic stem cells (HSC) | Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells. | Tsang ... Liu Genome Biology 2015 | Mus musculus (mm10) | 3 | 288 | 185.3 | | ||||||
| 1. 8wk_WT | 96 | 85 | | | ||||||||||
| 2. BL6_HSC | 96 | 24.4 | | | ||||||||||
| 3. Mut_HSC | 96 | 75.8 | | | ||||||||||
| E-MTAB-4617 | Spleen-derived LCK-expressing cells from adult zebrafish | Singel-cell transcriptome analysis of fish immune?? cells?? provides?? insight?? into the evolution?? of?? vertebrate immune?? cell?? types | Carmona ... Gfeller Genome Research 2016 | Danio rerio (GRCz10) | 2 | 278 | 50 | | ||||||
| 1. spleen_10_month | 96 | 14.3 | | | ||||||||||
| 2. spleen_3_month | 182 | 35.7 | | | ||||||||||
| E-MTAB-3857 | CD4+ T lymphocytes from uninfected mouse and 3 mice with Salmonella typhimurium infection (2 at day 14, 1 at day 49 post-infection) | T cell fate and clonality inference from single-cell transcriptomes | Stubbington ... Teichmann Nature Methods 2016 | Mus musculus (mm10) | 3 | 272 | 157.9 | | ||||||