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A repository of standardized single cell RNA-Seq datasets for analysis and visualization at the single cell level


Immune Datasets (88 Entries)

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BAMBAI
E-MTAB-2512T helper 2 (Th2) cellsSingle-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.Mahata ... Teichmann
Cell Reports 2014
Mus musculus (mm10)191190.2Download BAM
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Th291190.2Download BAMDownload BAI
E-MTAB-3346Mouse medullary thyme ephitelial cells (mTECs) - mature (MHCIIhi) mTECs and 3 subsets selected for their particular tissue-restricted self antigensSingle-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cellsBrennecke ... Steinmetz
Nature Immunology 2015
Mus musculus (mm10)4341261.4Download BAM
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1. MHCIIhi_Ceacam13330.4Download BAMDownload BAI
2. MHCIIhi_Tspan84938.8Download BAMDownload BAI
3. MHCIIhi211162.7Download BAMDownload BAI
4. MHCIIlow4829.5Download BAMDownload BAI
E-MTAB-3857CD4+ 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 transcriptomesStubbington ... Teichmann
Nature Methods 2016
Mus musculus (mm10)3272157.9Download BAM
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1. day_05035.7Download BAMDownload BAI
2. day_1411062.2Download BAMDownload BAI
3. day_4911260Download BAMDownload BAI
E-MTAB-4619CD4 T-helper cells from 3 sites, 5 days after Nippostrongylus brasiliensis infectionSingle-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferationProserpio ... Teichmann
Genome Biology 2016
Mus musculus (mm10)321021.5Download BAM
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1. mediastinal_lymph_nodes687.2Download BAMDownload BAI
2. mesenteric_lymph_nodes686.3Download BAMDownload BAI
3. lung748Download BAMDownload BAI
ERP010829Wildtype 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)3288185.3Download BAM
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1. 8wk_WT9685Download BAMDownload BAI
2. BL6_HSC9624.4Download BAMDownload BAI
3. Mut_HSC9675.8Download BAMDownload BAI
GSE48968Primary 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)2424121296Download BAM
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1. Ifnar1_KO_LPS_2h6118.2Download BAMDownload BAI
2. Ifnar1_KO_LPS_4h9625.8Download BAMDownload BAI
3. IFNB_2h9459.1Download BAMDownload BAI
4. LPS_1h9684.7Download BAMDownload BAI
5. LPS_2h220130.3Download BAMDownload BAI
6. LPS_4h_GolgiPlug_0h5618.3Download BAMDownload BAI
7. LPS_4h_GolgiPlug_1h4611Download BAMDownload BAI
8. LPS_4h_GolgiPlug_2h539.3Download BAMDownload BAI
9. LPS_4h328248.4Download BAMDownload BAI
10. LPS_4h_Tenth4923.9Download BAMDownload BAI
11. LPS_6h9670.1Download BAMDownload BAI
12. On_Chip_Stimulation_LPS_4h9017.6Download BAMDownload BAI
13. On_Chip_Unstim389.5Download BAMDownload BAI
14. PAM_1h9664.4Download BAMDownload BAI
15. PAM_2h9661.4Download BAMDownload BAI
16. PAM_4h8542.7Download BAMDownload BAI
17. PAM_6h6434.8Download BAMDownload BAI
18. PIC_1h9670.3Download BAMDownload BAI
19. PIC_2h8461.9Download BAMDownload BAI
20. PIC_4h9067.5Download BAMDownload BAI
21. PIC_6h9616.3Download BAMDownload BAI
22. Stat1_KO_LPS_4h9412.7Download BAMDownload BAI
23. Tnfr_KO_LPS_4h9617.6Download BAMDownload BAI
24. Unstimulated192120.2Download BAMDownload BAI
GSE54006Dendritic 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)13446830.1Download BAM
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1. B_cell480.6Download BAMDownload BAI
2. CD8+CD86-951.4Download BAMDownload BAI
3. CD8+CD86+950.9Download BAMDownload BAI
4. CD8+pDC950.1Download BAMDownload BAI
5. CD8-CD4+ESAM+951.9Download BAMDownload BAI
6. CD8-pDC951.9Download BAMDownload BAI
7. GC_B_cell471Download BAMDownload BAI
8. CD11c+70113.4Download BAMDownload BAI
9. CD11c+_LPS15284Download BAMDownload BAI
10. CD11c+_PBS15283.6Download BAMDownload BAI
11. monocyte_or_neutrophil470.6Download BAMDownload BAI
12. NK_cell470.4Download BAMDownload BAI
13. splenocyte470.5Download BAMDownload BAI
GSE59114Long-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 miceSingle-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)122089252.1Download BAM
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1. old_C57BL6_LTHSC38457.8Download BAMDownload BAI
2. old_C57BL6_MPP19230Download BAMDownload BAI
3. old_C57BL6_STHSC38449.4Download BAMDownload BAI
4. old_DBA_LTHSC1407.9Download BAMDownload BAI
5. old_DBA_MPP704.1Download BAMDownload BAI
6. old_DBA_STHSC683.7Download BAMDownload BAI
7. young_C57BL6_LTHSC19229.7Download BAMDownload BAI
8. young_C57BL6_MPP19233.5Download BAMDownload BAI
9. young_C57BL6_STHSC19222.7Download BAMDownload BAI
10. young_DBA_LTHSC1155.3Download BAMDownload BAI
11. young_DBA_MPP894.5Download BAMDownload BAI
12. young_DBA_STHSC713.6Download BAMDownload BAI
GSE60297Mature (MHCII high) medullary thymic epithelial cells (mTEC)Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia.Sansom SN ... Hollander GA
Genome Research 2014
Mus musculus (mm10)117449Download BAM
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mhcIIhi4wk-wildtype17449Download BAMDownload BAI
GSE60781Macrophage DC progenitor (MDP), common DC progenitor (CDP), and pre-DCIdentification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrowSchlitzer ... Ginhoux
Nature Immunology 2015
Mus musculus (mm10)325122.1Download BAM
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1. MDP597.7Download BAMDownload BAI
2. CDP967.2Download BAMDownload BAI
3. Pre-DC967.2Download BAMDownload BAI
GSE61533Haematopoietic stem cells (HSC)Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations.Wilson ... Gottgens
Cell Stem Cell 2015
Mus musculus (mm10)19632.1Download BAM
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HSC9632.1Download BAMDownload BAI
GSE64002Hematopoietic stem and progenitor cells from bone marrow cellsInflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors.Haas ... Essers
Cell Stem Cell 2015
Mus musculus (mm10)22018.7Download BAM
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1. cd150minus1110.4Download BAMDownload BAI
2. cd150plus98.3Download BAMDownload BAI
GSE65528Macrophages at 4 time points after Salmonella exposurePathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.Avraham ... Hung
Cell 2015
Mus musculus (mm10)1019227.8Download BAM
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1. time_0243.7Download BAMDownload BAI
2. time_2.5162Download BAMDownload BAI
3. time_2.5_pHrodo162.2Download BAMDownload BAI
4. time_2.5_pHrodo_GFP162Download BAMDownload BAI
5. time_4243.6Download BAMDownload BAI
6. time_4_pHrodo244.1Download BAMDownload BAI
7. time_4_pHrodo_GFP243.6Download BAMDownload BAI
8. time_8162Download BAMDownload BAI
9. time_8_pHrodo162.4Download BAMDownload BAI
10. time_8_pHrodo_GFP162.3Download BAMDownload BAI
GSE65529Macrophages at 4 time points after LPS exposurePathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.Avraham ... Hung
Cell 2015
Mus musculus (mm10)59612.7Download BAM
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1. time_0242.4Download BAMDownload BAI
2. time_4_No_No182.2Download BAMDownload BAI
3. time_4_No_Yes181.8Download BAMDownload BAI
4. time_4_Yes_No183.9Download BAMDownload BAI
5. time_4_Yes_Yes182.4Download BAMDownload BAI
GSE67120Several mouse cell populations closely related to HSC formationTracing haematopoietic stem cell formation at single-cell resolution.Zhou ... Liu
Nature 2016
Mus musculus (mm10)8181115.3Download BAM
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1. Adult_HSC3018.6Download BAMDownload BAI
2. E12_FL2111.1Download BAMDownload BAI
3. E14_FL1611.2Download BAMDownload BAI
4. EC1712.5Download BAMDownload BAI
5. T1CD201neg2115.3Download BAMDownload BAI
6. T12814.6Download BAMDownload BAI
7. T2_CD41low2616.5Download BAMDownload BAI
8. T22215.4Download BAMDownload BAI
GSE70657Young (2-3 months) and old (20-25 months) mouse HSCsSingle-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cellGrover ... Nerlov
Nature Communications 2016
Mus musculus (mm10)213531.9Download BAM
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1. young6116.5Download BAMDownload BAI
2. old7415.4Download BAMDownload BAI
GSE70798Wildtype and AireKO thymic epithelial cellsAire controls gene expression in the thymic epithelium with ordered stochasticity.Meredith ... Benoist
Nature Immunology 2015
Mus musculus (mm10)22004.4Download BAM
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1. Aire_KO_AireGFP1002.2Download BAMDownload BAI
2. WT_AireGFP1002.2Download BAMDownload BAI
GSE72857Bone marrow myeloid progenitorsTranscriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors.Paul ... Amit
Cell 2015
Mus musculus (mm10)81026048.7Download BAM
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1. Cebpa_control11406.4Download BAMDownload BAI
2. Cebpa_KO228011.4Download BAMDownload BAI
3. Cebpe_control3802Download BAMDownload BAI
4. Cebpe_KO7603.5Download BAMDownload BAI
5. CMP_CD413801.1Download BAMDownload BAI
6. CMP_Flt3+_Csf1r+11405.3Download BAMDownload BAI
7. CMP_Irf8-GFP+_MHCII+11409.1Download BAMDownload BAI
8. Unsorted_myeloid30409.9Download BAMDownload BAI
GSE74833Th17 cell pathogenicity. SubSeries: GSE75107, GSE75108, GSE75109, GSE75110, GSE75111Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.Gaublomme ... Regev
Cell 2015
Mus musculus (mm10)5722324.6Download BAM
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1. EAE-CNS-IL-17A_GFP+ (GSE75107)16695.1Download BAMDownload BAI
2. EAE-LN-IL-17A_GFP+ (GSE75108)13655.2Download BAMDownload BAI
3. IL1B_IL6_IL23-48h-IL-17A_GFP+ (GSE75109)13947.2Download BAMDownload BAI
4. TGFB1_IL6-48h (GSE75110)13062.5Download BAMDownload BAI
5. TGFB1_IL6-48h-IL-17A_GFP+ (GSE75111)15164.6Download BAMDownload BAI
GSE74923Lymphocytic leukemia cell line (L1210) and CD8 T cellsA microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.Kimmerling ... Manalis
Nature Communications 2016
Mus musculus (mm10)219414.6Download BAM
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1. Lymphocytic leukemia cell line (L1210)884.7Download BAMDownload BAI
2. CD8 T cells10610Download BAMDownload BAI
GSE81682Haematopoeitic stem and progenitor cellsA single cell resolution map of mouse haematopoietic stem and progenitor cell differentiation.Nestorowa ... Gottgens
Blood 2016
Mus musculus (mm10)31920662.6Download BAM
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1. Haematopoietic progenitor cell Prog (HPCP)852361.8Download BAMDownload BAI
2. Haematopoietic stem cell/multipotent progenitor HSPC (HSC)852228.7Download BAMDownload BAI
3. Long term haematopoeitic stem cells (LT-HSC)21672.1Download BAMDownload BAI
GSE68981HSC and MPPs from normal and bled miceSingle cell transcriptomics reveals unanticipated features of early hematopoietic precursorsYang ... Weissman
Nucleic Acids Research 2016
Mus musculus (mm10)446085Download BAM
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1. bled_HSC5313.8Download BAMDownload BAI
2. HSC22143.1Download BAMDownload BAI
3. bled_MPP16318Download BAMDownload BAI
4. MPP112310.2Download BAMDownload BAI
GSE71794Murine hematopoietic stem cells, ESC, and HSC-like cells derived from differentiation of embryonic stem cellsEngineered Murine HSCs Reconstitute Multi-lineage Hematopoiesis and Adaptive ImmunityLu ... Daley
Cell Reports 2016
Mus musculus (mm10)431623.8Download BAM
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1. Eng_BM-HSC952.9Download BAMDownload BAI
2. Eng_ES-HSC491.5Download BAMDownload BAI
3. ESC783.8Download BAMDownload BAI
4. FL_HSC9415.5Download BAMDownload BAI
E-MTAB-4825Mouse B cells early class switching of IgEIntrinsic transcriptional heterogeneity in B cells controls early class switching to IgEWu ... Rada
JEM 2016
Mus musculus (mm10)521350.2Download BAM
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1. GFP_female6510.9Download BAMDownload BAI
2. GFP_male2510Download BAMDownload BAI
3. neg_female417Download BAMDownload BAI
4. Tom_female517.8Download BAMDownload BAI
5. Tom_male3114.5Download BAMDownload BAI
GSE74596Mouse Va14 iNKT thymocyte subsetsInnate-like functions of natural killer T cell subsets result from highly divergent gene programsEngel ... Kronenberg
Nature Immunology 2016
Mus musculus (mm10)420351.7Download BAM
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1. NKT04510.5Download BAMDownload BAI
2. NKT14610.3Download BAMDownload BAI
3. NKT17448.1Download BAMDownload BAI
4. NKT26822.9Download BAMDownload BAI
ERP011804Transcriptional regulatory network during ILC2 commitmentSingle-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathwayYu ... Liu
Nature 2016
Mus musculus (mm10)1768129.4Download BAM
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1. ILC2768129.4Download BAMDownload BAI
GSE77740LMPP isolated from the bone marrow of 4mo and 14mo wild-type C57BL/6J female miceProgressive alterations in multipotent hematopoietic progenitors underlie lymphoid cell loss in agingYoung ... Trowbridge
JEM 2016
Mus musculus (mm10)216763.5Download BAM
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1. LMPP_4_month8419.2Download BAMDownload BAI
2. LPMM_14_month8344.3Download BAMDownload BAI
GSE90486Myeloid cells infected with lentiviral vectors carrying different gRNAsDissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-SeqJaitin ... Amit
Cell 2016
Mus musculus (mm10)142380891Download BAM
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1. dendritic_spleen_GFP+BFP+CD3-TCRb-CD19-NK-1.1-Ly6g-CD11c++LPS_in_vivo_mix_BFP7682.8Download BAMDownload BAI
2. myeloid_bone_marrow_GFP+BFP+_mCherry+CD11c++unstimulated_Cebpb_BFP_x_Rela_mCherry3841.9Download BAMDownload BAI
3. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_Cebpb_BFP_x_Rela_mCherry7682.2Download BAMDownload BAI
4. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_developmental_genes_mix_BFP11524.7Download BAMDownload BAI
5. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_INF_AV_gRNA_pool_BFP614421.5Download BAMDownload BAI
6. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_INF_AV_mix1_BFP422416Download BAMDownload BAI
7. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_INF_AV_mix2_BFP422418.2Download BAMDownload BAI
8. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_Irf9_x_Rela_BFP11524.9Download BAMDownload BAI
9. myeloid_bone_marrow_GFP+BFP+CD11c++LPS_Itgam-BFP_x_Cebpb-mCherry3841.2Download BAMDownload BAI
10. myeloid_bone_marrow_GFP+BFP+CD11c++unstimulated_Cebpb_BFP3842.2Download BAMDownload BAI
11. myeloid_bone_marrow_GFP+BFP+CD11c++unstimulated_Cebpb_BFP_x_Rela_mCherry11524.6Download BAMDownload BAI
12. myeloid_bone_marrow_GFP+BFP+CD11c++unstimulated_control_gRNA3841.9Download BAMDownload BAI
13. myeloid_bone_marrow_GFP+BFP+CD11c++unstimulated_Itgam-BFP_x_Cebpb-mCherry3841Download BAMDownload BAI
14. myeloid_spleen_GFP+BFP+CD3-TCRb-CD19-NK-1.1-Ly6g-+LPS_in_vivo_mix_BFP23047.9Download BAMDownload BAI
GSE70245CMP. SubSeries: GSE70236, GSE70238, GSE70239, GSE70240, GSE70241, GSE70242, GSE70243, GSE70244, GSE78907Single-cell analysis of mixed-lineage states leading to a binary cell fate choiceOlsson ... Grimes
Nature 2016
Mus musculus (mm10)9660240.9Download BAM
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1. CMP9639.9Download BAMDownload BAI
2. Gfi1-GFP_GMP3918.7Download BAMDownload BAI
3. Gfi1-_GMP8019.4Download BAMDownload BAI
4. GMP13651.3Download BAMDownload BAI
5. Irf8-GFP_GMP3715.1Download BAMDownload BAI
6. Irf8_KO_GMP6314.7Download BAMDownload BAI
7. LK_CD346620.4Download BAMDownload BAI
8. LSK9641.6Download BAMDownload BAI
9. Gfi1-_Irf8-_GMP4719.9Download BAMDownload BAI
GSE85152Small intestinal ILCs (Innate lymphoid cells)The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the MicrobiomeGury-BenAri ... Amit
Cell 2016
Mus musculus (mm10)3270126.4Download BAM
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1. gut_ILC12829.4Download BAMDownload BAI
2. gut_ILC_GF110813.7Download BAMDownload BAI
3. gut_ILC_NoGFP3113.3Download BAMDownload BAI
E-MTAB-4888CD4+ T cells from young and old mice of CAST/EiJ and C57BL/6Aging increases cell-to-cell transcriptional variability upon immune stimulationEling ... Odom
Science 2017
Mus musculus (mm10)111506544.9Download BAM
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1. B6_o_memory_anti_CD3e_CD285517.3Download BAMDownload BAI
2. B6_o_memory_none13343.8Download BAMDownload BAI
3. B6_o_naive_anti_CD3e_CD28236106.7Download BAMDownload BAI
4. B6_o_naive_none422152.6Download BAMDownload BAI
5. B6_y_memory_anti_CD3e_CD2817419.6Download BAMDownload BAI
6. B6_y_naive_anti_CD3e_CD289246.5Download BAMDownload BAI
7. B6_y_naive_none19675.1Download BAMDownload BAI
8. CAST_o_naive_anti_CD3e_CD285927.7Download BAMDownload BAI
9. CAST_o_naive_none6926.3Download BAMDownload BAI
10. CAST_y_naive_anti_CD3e_CD283516.4Download BAMDownload BAI
11. CAST_y_naive_none3512.9Download BAMDownload BAI
GSE86042CD8 TILs from WT and MTKO mice. SubSeries: GSE86028, GSE86030, GSE86031, GSE86039A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T CellsSinger ... Anderson
Cell 2016
Mus musculus (mm10)21061109Download BAM
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1. WT51650Download BAMDownload BAI
2. MTKO54559.1Download BAMDownload BAI
ERP015644CD4 T cells 7 days after infection or immunisationOpposing Development of Cytotoxic and Follicular Helper CD4? T Cells Controlled by the TCF-1-Bcl6 NexusDonnarumma ... Kassiotis
Cell Reports 2016
Mus musculus (mm10)456767Download BAM
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1. BCL6_Ad59612Download BAMDownload BAI
2. BCL6_FV9612.8Download BAMDownload BAI
3. WT_Ad519022.8Download BAMDownload BAI
4. WT_FV18519.5Download BAMDownload BAI
ERP005546Activated T helper cellsNo Publication ... The Wellcome Trust Sanger Institute
2016
Mus musculus (mm10)226282.7Download BAM
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1. mesLN10022.1Download BAMDownload BAI
2. spleen16260.6Download BAMDownload BAI
E-MTAB-4388transcriptional 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 malariaLonnberg ... Teichmann
Sci Immunol. 2017
Mus musculus (mm10)121598566Download BAM
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1. Dendritic_3d_Plasmodium396Download BAMDownload BAI
2. Dendritic_CD8a-_0d_none5021.8Download BAMDownload BAI
3. Dendritic_CD8a+_0d_none4626.4Download BAMDownload BAI
4. Monocyte_0d_none9652.7Download BAMDownload BAI
5. Monocyte_3d_Plasmodium7936.5Download BAMDownload BAI
6. Tcell_0d_none36291.5Download BAMDownload BAI
7. Tcell_2d_Plasmodium13561.4Download BAMDownload BAI
8. Tcell_3d_Plasmodium2110.7Download BAMDownload BAI
9. Tcell_4d_Plasmodium281125Download BAMDownload BAI
10. Tcell_7d_naive8919.2Download BAMDownload BAI
11. Tcell_7d_none14340.4Download BAMDownload BAI
12. cell_7d_Plasmodium25775Download BAMDownload BAI
GSE90799Molecular reprogramming of granulocyte/macrophage progenitor (GMP) clusters. SubSeries: GSE90797, GSE90140Myeloid progenitor cluster formation drives emergency and leukaemic myelopoiesis.Herault ... Passegue
Nature 2017
Mus musculus (mm10)795863.9Download BAM
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1. Day0965.9Download BAMDownload BAI
2. Day819012.9Download BAMDownload BAI
3. Day10966.3Download BAMDownload BAI
4. Day12965.9Download BAMDownload BAI
5. Day14962.9Download BAMDownload BAI
6. control967.7Download BAMDownload BAI
7. BCR_ABL28822.2Download BAMDownload BAI
GSE98048Single-cell comparison of vehicle (control) and HDAC inhibitor (ricolinostat)-treated tumor infiltrating T cells and macrophagesSynergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non-Small Cell Lung Cancer.Adeegbe ... Wong
Cancer Discov. 2017
Mus musculus (mm10)41921.3Download BAM
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1. Macrophage_ACY1215320.3Download BAMDownload BAI
2. Macrophage_Vehicle320.3Download BAMDownload BAI
3. Tcell_ACY1215640.3Download BAMDownload BAI
4. Tcell_Vehicle640.4Download BAMDownload BAI
E-MTAB-2512Th2 cellsSingle-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasisMahata ... Teichmann
Cell Reports 2014
Mus musculusIn Process960
GSE89405Gene expression profiles for key stages of T cell differentiationEarly transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA sequencing.Kakaradov ... Yeo
Nat Immunol. 2017
Mus musculusIn Process3040
GSE94383RAW 264.7 Cell Line (murine Macrophage) stimulated with LPS on a fluidigm C1 chipMeasuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-kB Activation.Lane ... Covert
Cell Syst. 2017
Mus musculusIn Process8390
GSE98969Transcriptional profiling of single cells from immune populations of mouse models of neurodegenerative diseases with matched controlsA Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease.Keren-Shaul ... Amit
Cell 2017
Mus musculusIn Process10000
GSE92495Profile thousands of primary human macrophages exposed to tuberculosis.Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.Gierahn ... Shalek
Nat Methods 2017
Homo sapiens; Mus musculusIn Process960
GSE99068RNA sequencing of two types of NK cells from mouse and human (IL6Ra negative NK cells vs. IL6Ra positive NK cells) and mouse organs (IL6Ra_NKdel vs. IL6Ra_NKflox)IL-6/Stat3-Dependent Induction of a Distinct, Obesity-Associated NK Cell Subpopulation Deteriorates Energy and Glucose HomeostasisTheurich ... Bruning
Cell Metab. 2017
Homo sapiens; Mus musculusIn Process630
GSE97168Human stage IA lung adenocarcinoma lesion and adjacent non-involved lungInnate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell AnalysesLavin ... Merad
Cell 2017
Homo sapiens (hg38)219207.5Download BAM
........................................................................................................................................................................................................................................................................................

1. lung7682.8Download BAMDownload BAI
2. tumor11524.6Download BAMDownload BAI
GSE75659Human 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-seqReinius ... Sandberg
Nature Genetics 2016
Homo sapiens (hg38)3892105Download BAM
........................................................................................................................................................................................................................................................................................

1. Tcell.ex.vivo34758.5Download BAMDownload BAI
2. Tcell.in.vivo.D136737.9Download BAMDownload BAI
2. Tcell.in.vivo.D1547238.5Download BAMDownload BAI
CD14+ MonocytesCD14+ Monocytes enriched from fresh PBMCs.Massively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiens (hg38)126128.2Download BAM
........................................................................................................................................................................................................................................................................................

1. cd1426128.2Download BAMDownload BAI
CD56+ Natural Killer CellsCD56+ NK cells enriched from fresh PBMCs. 92% pure by FACSMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiens (hg38)1838512.7Download BAM
........................................................................................................................................................................................................................................................................................

1. NK838512.7Download BAMDownload BAI
GSE75478Single-cell indexed RNA-Seq of human hematopoietic stem and progenitorsHuman haematopoietic stem cell lineage commitment is a continuous process.Velten ... Steinmetz
Nat Cell Biol. 2017
Homo sapiens (hg38)52414377.9Download BAM
........................................................................................................................................................................................................................................................................................

1. Lin-CD34+CD38+CD45RA-CD90+_QUARTZ-Seq9618.8Download BAMDownload BAI
2. Lin-CD34+CD38+_QUARTZ-Seq38474.5Download BAMDownload BAI
3. Lin-CD34+CD38-_smart-seq252665.2Download BAMDownload BAI
4. Lin-CD34+CD38+_smart-seq273689.4Download BAMDownload BAI
5. Lin-CD34+CD38-_QUARTZ-Seq672130Download BAMDownload BAI
GSE100618Single 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 cellsKaramitros ... Vyas
Nat Immunol. 2017
Homo sapiens (hg38)4420118Download BAM
........................................................................................................................................................................................................................................................................................

1. empty51.5Download BAMDownload BAI
2. GMP14036.6Download BAMDownload BAI
3. LMPP12835.4Download BAMDownload BAI
4. MLP14742.5Download BAMDownload BAI
GSE70580Human tonsil Innate lymphoid cells (ILCs)The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencingBjorklund ... Mjosberg
Nature Immunology 2016
Homo sapiens (hg19)464860.2Download BAM
........................................................................................................................................................................................................................................................................................

1. ILC112712.7Download BAMDownload BAI
2. ILC213913.9Download BAMDownload BAI
3. ILC330827.6Download BAMDownload BAI
4. NK746Download BAMDownload BAI
GSE87849Stem cell derived macrophages (wildtype and SAMHD1 knockout) were single-cell cultured for 1h or 8h under 4 different media conditionsThe 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)2450377.3Download BAM
........................................................................................................................................................................................................................................................................................

1. dNTPase_KO_1h_conditioned_LPS101.26Download BAMDownload BAI
2. dNTPase_KO_1h_conditioned131.45Download BAMDownload BAI
3. dNTPase_KO_1h_standard_LPS202.29Download BAMDownload BAI
4. dNTPase_KO_1h_standard212.63Download BAMDownload BAI
5. dNTPase_KO_8h_conditioned_LPS213.47Download BAMDownload BAI
6. dNTPase_KO_8h_conditioned172.83Download BAMDownload BAI
7. dNTPase_KO_8h_standard_LPS162.89Download BAMDownload BAI
8. dNTPase_KO_8h_standard142.11Download BAMDownload BAI
9. KO_1h_conditioned_LPS121.81Download BAMDownload BAI
10. KO_1h_conditioned91.55Download BAMDownload BAI
11. KO_1h_standard_LPS152.81Download BAMDownload BAI
12. KO_1h_standard142.5Download BAMDownload BAI
13. KO_8h_conditioned_LPS141.99Download BAMDownload BAI
14. KO_8h_conditioned142.14Download BAMDownload BAI
15. KO_8h_standard_LPS132.22Download BAMDownload BAI
16. KO_8h_standard81.25Download BAMDownload BAI
17. WT_1h_conditioned_LPS334.5Download BAMDownload BAI
18. WT_1h_conditioned588.54Download BAMDownload BAI
19. WT_1h_standard_LPS365.23Download BAMDownload BAI
20. WT_1h_standard375.16Download BAMDownload BAI
21. WT_8h_conditioned_LPS254.34Download BAMDownload BAI
22. WT_8h_conditioned325.71Download BAMDownload BAI
23. WT_8h_standard_LPS274.53Download BAMDownload BAI
24. WT_8h_standard244.05Download BAMDownload BAI
GSE85527CD8+ T-cells from 3 responders, with and without EOMES-associated inhibitory receptors (TIGIT, KLRG1).Partial exhaustion of CD8 T cells and clinical response to teplizumab in new-onset type 1 diabetesLong ... Linsley
Science Immunology 2016
Homo sapiens (hg19)621929.2Download BAM
........................................................................................................................................................................................................................................................................................

1. 927496_TIGIT-KLRG1-414.9Download BAMDownload BAI
2. 927496_TIGIT+KLRG1+464.8Download BAMDownload BAI
3. 928616_TIGIT-KLRG1-254.9Download BAMDownload BAI
4. 928616_TIGIT+KLRG1+504.9Download BAMDownload BAI
5. 930954_TIGIT-KLRG1-205.6Download BAMDownload BAI
6. 930954_TIGIT+KLRG1+374Download BAMDownload BAI
GSE83142Dormant (LRC) vs. dividing (non-LRC) cells or drug treated vs. non-treated cells from two PDX ALL SamplesCharacterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic LeukemiaEbinger ... Jeremias
Cancer Cell 2016
Homo sapiens (hg19)518514.3Download BAM
........................................................................................................................................................................................................................................................................................

1. ALL-265_non-LRC355.5Download BAMDownload BAI
2. ALL-265_LRC151.9Download BAMDownload BAI
3. ALL-199_non-treated322.7Download BAMDownload BAI
4. ALL-199_VCR_Cyclo904.1Download BAMDownload BAI
5. BCR-ABL130.06Download BAMDownload BAI
GSE84789Normal and tumor infiltrating B-cellsMultiparametric profiling of non-small-cell lung cancers reveals distinct immunophenotypesLizotte ... Wong
JCI Insight 2016
Homo sapiens (hg19)219216Download BAM
........................................................................................................................................................................................................................................................................................

1. Normal966.3Download BAMDownload BAI
2. Tumor969.7Download BAMDownload BAI
GSE89232Primary human conventional dendritic cells (cDCs), cord blood and blood pre-cDCsHuman dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+? or CD141+ DCsBreton ... Nussenzweig
JEM 2016
Homo sapiens (hg19)395717.7Download BAM
........................................................................................................................................................................................................................................................................................

1. blood_DC1643.4Download BAMDownload BAI
2. blood_pre-cDC3413.8Download BAMDownload BAI
3. CB_pre-cDC45210.4Download BAMDownload BAI
33k PBMCs from a Healthy DonorPeripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc3k and pbmc6k). ...
2016
Homo sapiensIn Process331480
3k Pan T Cells from a Healthy DonorPan T cells isolated from mononuclear cells of a healthy donor (same donor as t_4k). ...
2017
Homo sapiensIn Process35510
3k PBMCs from a Healthy DonorPeripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc6k). ...
2016
Homo sapiensIn Process27000
4k Pan T Cells from a Healthy DonorPan T cells isolated from mononuclear cells of a healthy donor (same donor as t_3k). ...
2017
Homo sapiensIn Process45320
4k PBMCs from a Healthy DonorPeripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc8k). ...
2017
Homo sapiensIn Process43520
6k PBMCs from a Healthy DonorPeripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc3k). ...
2016
Homo sapiensIn Process54190
8k PBMCs from a Healthy DonorPeripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc4k). ...
2017
Homo sapiensIn Process83910
AML027 Post-transplant BMMCsMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process39650
AML027 Pre-transplant BMMCsMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process39330
AML035 Post-transplant BMMCsMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process9090
AML035 Pre-transplant BMMCsMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process35920
CD19+ B CellsCD19+ B Cells enriched from fresh PBMCs.Massively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process100850
CD34+ CellsCD34+ Cells enriched from fresh PBMCs, 45% pure by FACSMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process92320
CD4+ Helper T CellsCD4+ Helper T Cells enriched from fresh PBMCs. 99% pure by FACSMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process112130
CD4+/CD25+ Regulatory T CellsCD4+/CD25+ Regulatory T Cells enriched from fresh PBMCs. 95% pure by FACSMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process102630
CD4+/CD45RA+/CD25- Naive T cellsCD4+/CD45RA+/CD25- Naive T cells enriched from fresh PBMCs. 98% pure by FACSMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process104790
CD4+/CD45RO+ Memory T CellsCD4+/CD45RO+ Memory T Cells enriched from fresh PBMCs. 98% pure by FACSMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process102240
CD8+ Cytotoxic T cellsCD8+ Cytotoxic T cells enriched from fresh PBMCs. 98% pure by FACSMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process102090
CD8+/CD45RA+ Naive Cytotoxic T CellsCD8+/CD45RA+ Naive Cytotoxic T Cells enriched from fresh PBMCs. 99% pure by FACSMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process119530
E-MTAB-4850Transcriptomic profiling of antigen-specific T cells at the single-cell level after clearance of hepatitis C virusImpact of sequencing depth and read length on single cell RNA sequencing data: lessons from T cellsRizzetto ... Luciani
bioRxiv 2017
Homo sapiensIn Process720
Fresh 68k PBMCs (Donor A)Fresh 68k PBMCs (Donor A)Massively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process685790
Frozen BMMCs (Healthy Control 1)Frozen BMMCs (Healthy Control 1)Massively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process19850
Frozen BMMCs (Healthy Control 2)Frozen BMMCs (Healthy Control 2)Massively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process24720
Frozen PBMCs (Donor A)Frozen PBMCs (Donor A)Massively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process29000
Frozen PBMCs (Donor B)Frozen PBMCs (Donor B)Massively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process77830
Frozen PBMCs (Donor C)Frozen PBMCs (Donor C)Massively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process95190
GSE80212Single-cell RNA-Seq Identifies A Highly Functional Dendritic Cell Subset In HIV-1 Elite Controllers Gayo-Martin ... Yu
2017
Homo sapiensIn Process1510
GSE94820Enriched immune cell fractions isolated from healthy blood PBMCsSingle-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitorsVillani ... Hacohen
Science 2017
Homo sapiensIn Process23840
GSE98638T 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 SequencingZheng ... Zhang
Cell 2017
Homo sapiensIn Process50630
Jurkat CellsJurkat CellsMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas
Nat Commun 2017
Homo sapiensIn Process32580
E-MTAB-4617Spleen-derived LCK-expressing cells from adult zebrafishSingel-cell transcriptome analysis of fish immune? cells? provides? insight? into the evolution? of? vertebrate immune? cell? typesCarmona ... Gfeller
Genome Research 2016
Danio rerio (GRCz10)227850Download BAM
........................................................................................................................................................................................................................................................................................

1. spleen_10_month9614.3Download BAMDownload BAI
2. spleen_3_month18235.7Download BAMDownload BAI
E-MTAB-3947CD41 expressing cells from kidney and heart of zebrafishSingle-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic CellsMacaulay ... Cvejic
Cell Reports 2016
Danio rerio (GRCz10)7652184.4Download BAM
........................................................................................................................................................................................................................................................................................

1. F_Circulation_EGFP-high6813.6Download BAMDownload BAI
2. F_Circulation_EGFP-low244.6Download BAMDownload BAI
3. F_Kidney_EarlyEnriched9216.9Download BAMDownload BAI
4. F_Kidney_EGFP-high467.8Download BAMDownload BAI
5. F_Kidney_EGFP-low468.9Download BAMDownload BAI
6. O_Kidney_EGFP-high18865.7Download BAMDownload BAI
7. O_Kidney_EGFP-low18866.8Download BAMDownload BAI
GSE100911Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish. SuperSeries: GSE100913Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolutionusing RNA sequencing.Tang ... Langenau
J Exp Med 2017
Danio rerio (GRCz10)624615Download BAM
........................................................................................................................................................................................................................................................................................

1. cd41_GFPlow433.2Download BAMDownload BAI
2. lck_GFP381.9Download BAMDownload BAI
3. lck_GFP_rag1313.2Download BAMDownload BAI
4. mpx_EGFP471.7Download BAMDownload BAI
5. rag2_GFP482.4Download BAMDownload BAI
6. Runx123_GFP392.6Download BAMDownload BAI








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