Dataset ID

Dataset Description

Paper Title

Citation

Organism

Conditions (#)

Cell (#)

File Size (Gb)

BAM

BAI

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)

2412

1296

.................................................................................................................................................................................................................................................................................... + .... -

1. Ifnar1_KO_LPS_2h

18.2

2. Ifnar1_KO_LPS_4h

25.8

3. IFNB_2h

59.1

4. LPS_1h

84.7

5. LPS_2h

220

130.3

6. LPS_4h_GolgiPlug_0h

18.3

7. LPS_4h_GolgiPlug_1h

8. LPS_4h_GolgiPlug_2h

9.3

9. LPS_4h

328

248.4

10. LPS_4h_Tenth

23.9

11. LPS_6h

70.1

12. On_Chip_Stimulation_LPS_4h

17.6

13. On_Chip_Unstim

9.5

14. PAM_1h

64.4

15. PAM_2h

61.4

16. PAM_4h

42.7

17. PAM_6h

34.8

18. PIC_1h

70.3

19. PIC_2h

61.9

20. PIC_4h

67.5

21. PIC_6h

16.3

22. Stat1_KO_LPS_4h

12.7

23. Tnfr_KO_LPS_4h

17.6

24. Unstimulated

192

120.2

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)

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

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)

1598

566

1. Dendritic_3d_Plasmodium

2. Dendritic_CD8a-_0d_none

21.8

3. Dendritic_CD8a+_0d_none

26.4

4. Monocyte_0d_none

52.7

5. Monocyte_3d_Plasmodium

36.5

6. Tcell_0d_none

362

91.5

7. Tcell_2d_Plasmodium

135

61.4

8. Tcell_3d_Plasmodium

10.7

9. Tcell_4d_Plasmodium

281

125

10. Tcell_7d_naive

19.2

11. Tcell_7d_none

143

40.4

12. cell_7d_Plasmodium

257

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)

1506

544.9

1. B6_o_memory_anti_CD3e_CD28

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

46.5

7. B6_y_naive_none

196

75.1

8. CAST_o_naive_anti_CD3e_CD28

27.7

9. CAST_o_naive_none

26.3

10. CAST_y_naive_anti_CD3e_CD28

16.4

11. CAST_y_naive_none

12.9

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)

2414

377.9

1. Lin-CD34+CD38+CD45RA-CD90+_QUARTZ-Seq

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

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)

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

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)

2089

252.1

1. old_C57BL6_LTHSC

384

57.8

2. old_C57BL6_MPP

192

3. old_C57BL6_STHSC

384

49.4

4. old_DBA_LTHSC

140

7.9

5. old_DBA_MPP

4.1

6. old_DBA_STHSC

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

4.5

12. young_DBA_STHSC

3.6

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)

660

240.9

1. CMP

39.9

2. Gfi1-GFP_GMP

18.7

3. Gfi1-_GMP

19.4

4. GMP

136

51.3

5. Irf8-GFP_GMP

15.1

6. Irf8_KO_GMP

14.7

7. LK_CD34

20.4

8. LSK

41.6

9. Gfi1-_Irf8-_GMP

19.9

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)

293

210.6

1. MHCII_high_Ceacam1

29.9

2. MHCII_high_Tspan8

36.2

3. MHCII_high

163

115.6

4. MHCII_low

28.9

E-MTAB-2512

T helper 2 (Th2) cells

Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.

Mahata ... Teichmann
Cell Reports 2014

Mus musculus (mm10)

190.2

Th2

190.2

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)

288

185.3

1. 8wk_WT

2. BL6_HSC

24.4

3. Mut_HSC

75.8

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)

652

184.4

1. F_Circulation_EGFP-high

13.6

2. F_Circulation_EGFP-low

4.6

3. F_Kidney_EarlyEnriched

16.9

4. F_Kidney_EGFP-high

7.8

5. F_Kidney_EGFP-low

8.9

6. O_Kidney_EGFP-high

188

65.7

7. O_Kidney_EGFP-low

188

66.8

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)

272

157.9

1. day_0

35.7

2. day_14

110

62.2

3. day_49

112

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)

768

129.4

1. ILC2

768

129.4

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)

420

118

1. empty

1.5

2. GMP

140

36.6

3. LMPP

128

35.4

4. MLP

147

42.5

GSE67120

Several mouse cell populations closely related to HSC formation

Tracing haematopoietic stem cell formation at single-cell resolution.

Zhou ... Liu
Nature 2016

Mus musculus (mm10)

181

115.3

1. Adult_HSC

18.6

2. E12_FL

11.1

3. E14_FL

11.2

4. EC

12.5

5. T1CD201neg

15.3

6. T1

14.6

7. T2_CD41low

16.5

8. T2

15.4

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)

1061

109

1. WT

516

2. MTKO

545

59.1

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)

892

105

1. Tcell.ex.vivo

347

58.5

2. Tcell.in.vivo.D136

7.9

2. Tcell.in.vivo.D15

472

38.5

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)

35242

94.8

1. Cerebellum_5XFAD_CD45+_Alzheimer_disease_6_months

2280

6.3

2. Cerebellum_C57BL_CD45+_Alzheimer_disease_6_months

1520

3. Cortex_5XFAD_CD45+_Alzheimer_disease_6_months

2280

6.4

4. Cortex_C57BL_CD45+_Alzheimer_disease_6_months

1520

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

16. Whole_brain_C57BL_CD45+_Alzheimer_disease_6_months

6080

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

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)

23808

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

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

14. myeloid_spleen_GFP+BFP+CD3-TCRb-CD19-NK-1.1-Ly6g-+LPS_in_vivo_mix_BFP

2304

7.9

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)

460

1. bled_HSC

13.8

2. HSC

221

43.1

3. bled_MPP1

4. MPP1

123

10.2

ERP005546

Activated T helper cells

No Publication

... The Wellcome Trust Sanger Institute
2016

Mus musculus (mm10)

262

82.7

1. mesLN

100

22.1

2. spleen

162

60.6

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)

503

77.3

1. dNTPase_KO_1h_conditioned_LPS

1.26

2. dNTPase_KO_1h_conditioned

1.45

3. dNTPase_KO_1h_standard_LPS

2.29

4. dNTPase_KO_1h_standard

2.63

5. dNTPase_KO_8h_conditioned_LPS

3.47

6. dNTPase_KO_8h_conditioned

2.83

7. dNTPase_KO_8h_standard_LPS

2.89

8. dNTPase_KO_8h_standard

2.11

9. KO_1h_conditioned_LPS

1.81

10. KO_1h_conditioned

1.55

11. KO_1h_standard_LPS

2.81

12. KO_1h_standard

2.5

13. KO_8h_conditioned_LPS

1.99

14. KO_8h_conditioned

2.14

15. KO_8h_standard_LPS

2.22

16. KO_8h_standard

1.25

17. WT_1h_conditioned_LPS

4.5

18. WT_1h_conditioned

8.54

19. WT_1h_standard_LPS

5.23

20. WT_1h_standard

5.16

21. WT_8h_conditioned_LPS

4.34

22. WT_8h_conditioned

5.71

23. WT_8h_standard_LPS

4.53

24. WT_8h_standard

4.05

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)

567

1. BCL6_Ad5

2. BCL6_FV

12.8

3. WT_Ad5

190

22.8

4. WT_FV

185

19.5

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)

958

63.9

1. Day0

5.9

2. Day8

190

12.9

3. Day10

6.3

4. Day12

5.9

5. Day14

2.9

6. control

7.7

7. BCR_ABL

288

22.2

GSE77740

LMPP isolated from the bone marrow of 4mo and 14mo wild-type C57BL/6J female mice

Progressive alterations in multipotent hematopoietic progenitors underlie lymphoid cell loss in aging

Young ... Trowbridge
JEM 2016

Mus musculus (mm10)

167

63.5

1. LMPP_4_month

19.2

2. LPMM_14_month

44.3

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)

648

60.2

1. ILC1

127

12.7

2. ILC2

139

13.9

3. ILC3

308

27.6

4. NK

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)

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

GSE74596

Mouse Va14 iNKT thymocyte subsets

Innate-like functions of natural killer T cell subsets result from highly divergent gene programs

Engel ... Kronenberg
Nature Immunology 2016

Mus musculus (mm10)

203

51.7

1. NKT0

10.5

2. NKT1

10.3

3. NKT17

8.1

4. NKT2

22.9

E-MTAB-4825

Mouse B cells early class switching of IgE

Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE

Wu ... Rada
JEM 2016

Mus musculus (mm10)

213

50.2

1. GFP_female

10.9

2. GFP_male

3. neg_female

4. Tom_female

7.8

5. Tom_male

14.5

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)

278

1. spleen_10_month

14.3

2. spleen_3_month

182

35.7

GSE60297

Mature (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)

174

mhcIIhi4wk-wildtype

174

GSE72857

Bone marrow myeloid progenitors

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors.

Paul ... Amit
Cell 2015

Mus musculus (mm10)

10260

48.7

1. Cebpa_control

1140

6.4

2. Cebpa_KO

2280

11.4

3. Cebpe_control

380

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

GSE61533

Haematopoietic 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)

32.1

HSC

32.1

GSE70657

Young (2-3 months) and old (20-25 months) mouse HSCs

Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cell

Grover ... Nerlov
Nature Communications 2016

Mus musculus (mm10)

135

31.9

1. young

16.5

2. old

15.4

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)

4468

30.1

1. B_cell

0.6

2. CD8+CD86-

1.4

3. CD8+CD86+

0.9

4. CD8+pDC

0.1

5. CD8-CD4+ESAM+

1.9

6. CD8-pDC

1.9

7. GC_B_cell

8. CD11c+

701

13.4

9. CD11c+_LPS

1528

10. CD11c+_PBS

1528

3.6

11. monocyte_or_neutrophil

0.6

12. NK_cell

0.4

13. splenocyte

0.5

GSE85527

CD8+ 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 diabetes

Long ... Linsley
Science Immunology 2016

Homo sapiens (hg19)

219

29.2

1. 927496_TIGIT-KLRG1-

4.9

2. 927496_TIGIT+KLRG1+

4.8

3. 928616_TIGIT-KLRG1-

4.9

4. 928616_TIGIT+KLRG1+

4.9

5. 930954_TIGIT-KLRG1-

5.6

6. 930954_TIGIT+KLRG1+

GSE65528

Macrophages at 4 time points after Salmonella exposure

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.

Avraham ... Hung
Cell 2015

Mus musculus (mm10)

192

27.8

1. time_0

3.7

2. time_2.5

3. time_2.5_pHrodo

2.2

4. time_2.5_pHrodo_GFP

5. time_4

3.6

6. time_4_pHrodo

4.1

7. time_4_pHrodo_GFP

3.6

8. time_8

9. time_8_pHrodo

2.4

10. time_8_pHrodo_GFP

2.3

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)

2701

26.4

1. gut_ILC

1282

9.4

2. gut_ILC_GF

1108

13.7

3. gut_ILC_NoGFP

311

3.3

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)

316

23.8

1. Eng_BM-HSC

2.9

2. Eng_ES-HSC

1.5

3. ESC

3.8

4. FL_HSC

15.5

GSE60781

Macrophage DC progenitor (MDP), common DC progenitor (CDP), and pre-DC

Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow

Schlitzer ... Ginhoux
Nature Immunology 2015

Mus musculus (mm10)

251

22.1

1. MDP

7.7

2. CDP

7.2

3. Pre-DC

7.2

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)

21312

22.1

1. CMP

1282

1.5

2. GMP

215

1.7

3. HSC

123

1.7

4. Lin-CD34-CD164high

592

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

E-MTAB-4619

CD4 T-helper cells from 3 sites, 5 days after Nippostrongylus brasiliensis infection

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation

Proserpio ... Teichmann
Genome Biology 2016

Mus musculus (mm10)

210

21.5

1. mediastinal_lymph_nodes

7.2

2. mesenteric_lymph_nodes

6.3

3. lung

GSE64002

Hematopoietic stem and progenitor cells from bone marrow cells

Inflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors.

Haas ... Essers
Cell Stem Cell 2015

Mus musculus (mm10)

18.7

1. cd150minus

10.4

2. cd150plus

8.3

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)

957

17.7

1. blood_DC

164

3.4

2. blood_pre-cDC

341

3.8

3. CB_pre-cDC

452

10.4

GSE84789

Normal and tumor infiltrating B-cells

Multiparametric profiling of non-small-cell lung cancers reveals distinct immunophenotypes

Lizotte ... Wong
JCI Insight 2016

Homo sapiens (hg19)

192

1. Normal

6.3

2. Tumor

9.7

GSE100911

Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish. SuperSeries: GSE100913

Dissecting? hematopoietic? and renal? cell? heterogeneity? in? adult? zebrafish? at? single-cell? resolutionusing? RNA? sequencing.

Tang ... Langenau
J Exp Med 2017

Danio rerio (GRCz10)

246

1. cd41_GFPlow

3.2

2. lck_GFP

1.9

3. lck_GFP_rag1

3.2

4. mpx_EGFP

1.7

5. rag2_GFP

2.4

6. Runx123_GFP

2.6

GSE74923

Lymphocytic leukemia cell line (L1210) and CD8 T cells

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.

Kimmerling ... Manalis
Nature Communications 2016

Mus musculus (mm10)

194

14.6

1. Lymphocytic leukemia cell line (L1210)

4.7

2. CD8 T cells

106

GSE83142

Dormant (LRC) vs. dividing (non-LRC) cells or drug treated vs. non-treated cells from two PDX ALL Samples

Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia

Ebinger ... Jeremias
Cancer Cell 2016

Homo sapiens (hg19)

185

14.3

1. ALL-265_non-LRC

5.5

2. ALL-265_LRC

1.9

3. ALL-199_non-treated

2.7

4. ALL-199_VCR_Cyclo

4.1

5. BCR-ABL

0.06

GSE65529

Macrophages at 4 time points after LPS exposure

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.

Avraham ... Hung
Cell 2015

Mus musculus (mm10)

12.7

1. time_0

2.4

2. time_4_No_No

2.2

3. time_4_No_Yes

1.8

4. time_4_Yes_No

3.9

5. time_4_Yes_Yes

2.4

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)

8385

12.7

1. NK

8385

12.7

CD14+ Monocytes

CD14+ Monocytes enriched from fresh PBMCs.

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens (hg38)

2612

8.2

1. cd14

2612

8.2

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)

1920

7.5

1. lung

768

2.8

2. tumor

1152

4.6

GSE70798

Wildtype and AireKO thymic epithelial cells

Aire controls gene expression in the thymic epithelium with ordered stochasticity.

Meredith ... Benoist
Nature Immunology 2015

Mus musculus (mm10)

200

4.4

1. Aire_KO_AireGFP

100

2.2

2. WT_AireGFP

100

2.2

GSE98048

Single-cell comparison of vehicle (control) and HDAC inhibitor (ricolinostat)-treated tumor infiltrating T cells and macrophages

Synergistic 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)

192

1.3

1. Macrophage_ACY1215

0.3

2. Macrophage_Vehicle

0.3

3. Tcell_ACY1215

0.3

4. Tcell_Vehicle

0.4

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

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

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

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

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

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

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

AML027 Post-transplant BMMCs

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

3965

AML027 Pre-transplant BMMCs

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

3933

AML035 Post-transplant BMMCs

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

909

AML035 Pre-transplant BMMCs

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

3592

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

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

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

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

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

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

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

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

E-MTAB-4850

Transcriptomic profiling of antigen-specific T cells at the single-cell level after clearance of hepatitis C virus

Impact of sequencing depth and read length on single cell RNA sequencing data: lessons from T cells

Rizzetto ... Luciani
bioRxiv 2017

Homo sapiens

In Process

Fresh 68k PBMCs (Donor A)

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

68579

Frozen BMMCs (Healthy Control 1)

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

1985

Frozen BMMCs (Healthy Control 2)

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

2472

Frozen PBMCs (Donor A)

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

2900

Frozen PBMCs (Donor B)

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

7783

Frozen PBMCs (Donor C)

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

9519

GSE80212

Single-cell RNA-Seq Identifies A Highly Functional Dendritic Cell Subset In HIV-1 Elite Controllers

Gayo-Martin ... Yu
2017

Homo sapiens

In Process

151

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

GSE92495

Profile 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 musculus

In Process

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

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

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

GSE99068

RNA 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 Homeostasis

Theurich ... Bruning
Cell Metab. 2017

Homo sapiens; Mus musculus

In Process

Jurkat Cells

Massively parallel digital transcriptional profiling of single cells.

Zheng ... Bielas
Nat Commun 2017

Homo sapiens

In Process

3258

E-MTAB-4850

Transcriptomic profiling of antigen-specific T cells at the single-cell level after clearance of hepatitis C virus

Impact of sequencing depth and read length on single cell RNA sequencing data: lessons from T cells

Rizzetto ... Luciani
bioRxiv 2017

Homo sapiens

In Process

GSE80212

Single-cell RNA-Seq Identifies A Highly Functional Dendritic Cell Subset In HIV-1 Elite Controllers

no article

Gayo-Martin ... Yu
2017

Homo sapiens

In Process

151

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

Human cell Atlas

The hematopoietic system

The Human Cell Atlas Bone Marrow Single-Cell Interactive Web Portal

Hay ... Salomonis
Exp Hematol 2018

Homo sapiens

In Process

GSE100501

DNA sequencing of both mRNA and antibodies in a single workflow in human PBMCs and na?ve CD8+ T cells that were costimulated with either 1) aCD3 and aCD28 or 2) aCD3, aCD28 and aCD27

Multiplexed quantification of proteins and transcripts in single cells

Peterson ... Klappenbach
Nat Biotechnol 2017

Homo sapiens

In Process

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

GSE112903

Droplet-based scRNAseq on sorted mouse pLN CD45- CD31- cells from uninfected mice and mice at day 15 post-infection with LCMV-Armstrong

Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity

Rodda ... Cyster
Immunity 2018

Mus musculus

In Process

GSE106973

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

141

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

GSE104054

Single cells from the specific immune niches in the lymph node and spleen

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

Medaglia ... Amit
Science 2017

Mus musculus

In Process

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

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

GSE103967

Transcriptional profiling of single cells from the stroma of mouse thymus

Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells

Bornstein ... Amit
Nature 2018

Mus musculus

In Process

GSE103968

Transcriptional profiling of single cells from the stroma of mouse thymus

Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells

Bornstein ... Amit
Nature 2018

Mus musculus

In Process

GSE119562

Natural Killer cell heterogeneity in humans and mice

High-Dimensional Single-Cell Analysis Identifies Organ-Specific Signatures and Conserved NKCell Subsets in Humans and Mice

Crinier ... Vivier
Immunity 2018

Homo sapiens; Mus musculus

In Process

GSE111664

Drop-seq analysis of bleomycin-treated and control mouse lung single-cell suspensions

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

Aran ... Bhattacharya
Nat Immunol 2019

Mus musculus

In Process

E-MTAB-7142

Drop-seq analysis of bleomycin-treated and control mouse lung single-cell suspensions

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

Aran ... Bhattacharya
Nat Immunol 2019

Mus musculus

In Process

GSE118948

CD45+ cells isolated from different CNS compartments (including leptomeninges, perivascular space and parenchyma, and choroid plexus) and Ly6Chigh and Ly6Clow monocytes from blood

Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation.

Jord?o ... Prinz
Science 2019

Mus musculus

In Process

GSE124731

Lymphocyte innateness defined by transcriptional states reflects a balance between proliferationand effector functions.

Gutierrez-Arcelus ... Brennan
Nat Commun 2019

Homo sapiens

In Process

GSE122846

Single, live, CD3+CD8a–TCR??–CD4+/– T-cells from one human fetal intestines

Memory CD4+ T cells are generated in the human fetal intestine

Li ... Koning
Nat Immunol 2019

Homo sapiens

In Process

GSE116256

Bone marrow aspirates of five healthy control donors, 16 AML patients at diagnosis, and 19 matched samples during treatment

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

van Galen ... Bernstein
Cell 2019

Homo sapiens

In Process

GSE125044

single cells from pathogen-injected mouse auricular lymph nodes

Single-Cell Analysis of Diverse Pathogen Responses Defines a Molecular Roadmap for Generating Antigen-Specific Immunity

Blecher-Gonen ... Amit
Cell Syst 2019

Mus musculus

In Process

EGAS00001003363

Single-cell transcriptional profiling of immune cells from human melanoma tumors and several matching pbmc samples

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

Li ... Amit
Cell 2019

Homo sapiens

In Process

GSE128985

Time course RNA-seq profiling in sorted endothelial, epithelial, immune, and mesenchymal-derived cells from E16.5, E18.5, P7 and P28 wild-type C57BL6 mice

Whitsett ... Xu
2019

Mus musculus

In Process

GSE108892

SubSeries: GSE108891, GSE118436

The bone marrow microenvironment at single-cell resolution

Tikhonova ... Aifantis
Nature 2019

Mus musculus

In Process

GSE111731

Parallel host-pathogen transcriptional dynamics using sorted subpopulations and single, Candida albicans infected macrophages

Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single macrophages infected with Candida albicans

Mu?oz ... Cuomo
Nat Commun 2019

Candida albicans; Mus musculus

In Process

GSE127465

scRNAseq of RBC-depleted cells from non-small cell lung tumor and from blood of 7 patients. ScRNAseq of CD45-positive cells from lungs of 2 healthy mice and 2 lung tumor-bearing mice

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

Zilionis ... Klein
Immunity 2019

Homo sapiens; Mus musculus

In Process

GSE127005

Single cell transcriptomic analysis (InDrops) of mouse mesenchymal stromal cells (mSCs or FAPs, fibro-adipogenic progenitors) isolated from lymph node, muscle and visceral adipose tissue

Distinct immunocyte-promoting and adipocyte-generating stromal components coordinate adipose tissue immune and metabolic tenors

Spallanzan ... Mathis
Science Immunology 2019

Mus musculus

In Process

GSE128855 (GSE128854 )

single-cell atlas of mouse brain macrophages

A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shapedby ontogeny and tissue environment

Van Hove ... Movahedi
Nat Neurosci. 2019

Mus musculus

In Process

GSE111898

SubSeries: GSE111894, GSE111896