Single Cell Gene Expression Datasets

Targeted Demonstration (v3.1 Chemistry)

Cell Ranger 4.0.0

• PBMCs from a Healthy Donor: Whole Transcriptome Analysis
• PBMCs from a Healthy Donor: Targeted, Immunology Panel
• PBMCs from a Healthy Donor: Targeted-Compare, Immunology Panel
• Hodgkin's Lymphoma, Dissociated Tumor: Whole Transcriptome Analysis
• Hodgkin's Lymphoma, Dissociated Tumor: Targeted, Gene Signature Panel
• Hodgkin's Lymphoma, Dissociated Tumor: Targeted-Compare, Gene Signature Panel
• Hodgkin's Lymphoma, Dissociated Tumor: Targeted, Immunology Panel
• Hodgkin's Lymphoma, Dissociated Tumor: Targeted-Compare, Immunology Panel
• Hodgkin's Lymphoma, Dissociated Tumor: Targeted, Pan-Cancer Panel
• Hodgkin's Lymphoma, Dissociated Tumor: Targeted-Compare, Pan-Cancer Panel

Single vs Dual Indexing Demonstration (v3.1 Chemistry)

Cell Ranger 4.0.0

• 10k Peripheral blood mononuclear cells (PBMCs) from a healthy donor, Single Indexed
• 10k Peripheral blood mononuclear cells (PBMCs) from a healthy donor, Dual Indexed
• 1k 1:1 Mixture of Human HEK293T and Mouse NIH3T3 Cells, Single Indexed
• 1k 1:1 Mixture of Human HEK293T and Mouse NIH3T3 Cells, Dual Indexed
• 10k 1:1 Mixture of Human HEK293T and Mouse NIH3T3 Cells, Single Indexed
• 10k 1:1 Mixture of Human HEK293T and Mouse NIH3T3 Cells, Dual Indexed
• 10k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells, Single Indexed
• 10k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells, Dual Indexed
• 1k Human PBMCs Stained with a Panel of TotalSeq B Antibodies, Single Indexed
• 1k Human PBMCs Stained with a Panel of TotalSeq B Antibodies, Dual Indexed
• 10k A375 Cells Transduced with (1) Non-Target and (1) Target sgRNA, Single Indexed
• 10k A375 Cells Transduced with (1) Non-Target and (1) Target sgRNA, Dual Indexed

Chromium Connect Demonstration (v3.1 Chemistry)

Cell Ranger 3.1.0

• Peripheral blood mononuclear cells (PBMCs) from a healthy donor - Chromium Connect (channel 1)
• Peripheral blood mononuclear cells (PBMCs) from a healthy donor - Manual (channel 1)
• Peripheral blood mononuclear cells (PBMCs) from a healthy donor - Chromium Connect (channel 5)
• Peripheral blood mononuclear cells (PBMCs) from a healthy donor - Manual (channel 5)
• Aggregate of 8 Chromium Connect channels and 8 manual channels

Chromium Next GEM Demonstration (v3.1 Chemistry)

Cell Ranger 3.0.2

• 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v3 chemistry)
• 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (Next GEM)
• 1k 1:1 mixture of fresh frozen human (HEK293T) and mouse (NIH3T3) cells (v3 chemistry)
• 1k 1:1 mixture of fresh frozen human (HEK293T) and mouse (NIH3T3) cells (Next GEM)
• 5k 1:1 mixture of fresh frozen human (HEK293T) and mouse (NIH3T3) cells (Next GEM)
• 10k 1:1 mixture of fresh frozen human (HEK293T) and mouse (NIH3T3) cells (Next GEM)
• 5k Cells from a combined cortex, hippocampus and subventricular zone of an E18 mouse (v3 chemistry)
• 5k Cells from a combined cortex, hippocampus and subventricular zone of an E18 mouse (Next GEM)
• 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (v3 chemistry)
• 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (Next GEM)

Cell Ranger 3.1.0

• 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (v3 chemistry)
• 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (Next GEM)

Chromium Demonstration (v3 Chemistry)

Cell Ranger 3.0.0

• 1k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein
• 10k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein
• 10k Cells from a MALT Tumor - Gene Expression and Cell Surface Protein
• 1k PBMCs from a Healthy Donor (v2 chemistry)
• 1k PBMCs from a Healthy Donor (v3 chemistry)
• 10k PBMCs from a Healthy Donor (v3 chemistry)
• 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (v2 chemistry)
• 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (v3 chemistry)
• 5k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (v3 chemistry)
• 10k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (v3 chemistry)
• 1k Brain Cells from an E18 Mouse (v2 chemistry)
• 1k Brain Cells from an E18 Mouse (v3 chemistry)
• 10k Brain Cells from an E18 Mouse (v3 chemistry)
• 1k Heart Cells from an E18 mouse (v2 chemistry)
• 1k Heart Cells from an E18 mouse (v3 chemistry)
• 10k Heart Cells from an E18 mouse (v3 chemistry)

Chromium Demonstration (v2 Chemistry)

Cell Ranger 2.1.0

• 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 6k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 12k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 4k PBMCs from a Healthy Donor
• 8k PBMCs from a Healthy Donor
• 9k Brain Cells from an E18 Mouse
• 1k Brain Cells from an E18 Mouse
• 1k Brain Nuclei from an E18 Mouse
• 2k Brain Nuclei from an Adult Mouse (>8 weeks)
• 2k Brain Cells from an E18 Mouse
• 2k Fixed Brain Cells from an E18 Mouse
• 2k Fixed (for 6 days at -80ºC) Brain Cells from an E18 Mouse
• 3k Pan T Cells from a Healthy Donor
• 4k Pan T Cells from a Healthy Donor
• Aggregate of t_3k and t_4k

Cell Ranger 2.0.1

• 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 1k Brain Cells from an E18 Mouse
• 1k Brain Nuclei from an E18 Mouse
• 2k Brain Nuclei from an Adult Mouse (>8 weeks)
• 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 6k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 12k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 4k PBMCs from a Healthy Donor
• 8k PBMCs from a Healthy Donor
• 9k Brain Cells from an E18 Mouse
• 3k Pan T Cells from a Healthy Donor
• 4k Pan T Cells from a Healthy Donor
• Aggregate of t_3k and t_4k

Cell Ranger 1.3.0

• 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 6k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 12k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 4k PBMCs from a Healthy Donor
• 8k PBMCs from a Healthy Donor
• 9k Brain Cells from an E18 Mouse
• 3k Pan T Cells from a Healthy Donor
• 4k Pan T Cells from a Healthy Donor
• Aggregate of t_3k and t_4k

Cell Ranger 1.2.0

• 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 6k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 12k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 4k PBMCs from a Healthy Donor
• 8k PBMCs from a Healthy Donor
• 9k Brain Cells from an E18 Mouse
• 3k Pan T Cells from a Healthy Donor
• 4k Pan T Cells from a Healthy Donor
• Aggregate of t_3k and t_4k

Chromium Megacell Demonstration (v2 Chemistry)

Cell Ranger 1.3.0

• 1.3 Million Brain Cells from E18 Mice

Cell Ranger 1.2.0

• 1.3 Million Brain Cells from E18 Mice

Chromium Demonstration (v1 Chemistry)

Cell Ranger 1.1.0

• 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 33k PBMCs from a Healthy Donor
• 3k PBMCs from a Healthy Donor
• 6k PBMCs from a Healthy Donor

Cell Ranger 1.0.0

• 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
• 3k PBMCs from a Healthy Donor

Single Cell 3' Paper: Zheng et al. 2017

Datasets for the paper Zheng et al, “Massively parallel digital transcriptional profiling of single cells” (previously deposited to biorxiv). We encourage you to download the data here, as the BAM files deposited in the SRA database have had the cell barcode tags removed. We are working with NCBI to resolve this issue. You can download the supplementary tables 1-6 here.

Cell Ranger 1.1.0

• 293T Cells
• 293T and 3T3 Cell Mixture
• 50%:50% Donor B: Donor C PBMC Mixture
• 50%:50% Jurkat:293T Cell Mixture
• 90%:10% Donor B: Donor C PBMC Mixture
• 99%:1% Donor B: Donor C PBMC Mixture
• 99%:1% Jurkat:293T Cell Mixture
• AML027 Post-transplant BMMCs
• AML027 Pre-transplant BMMCs
• AML035 Post-transplant BMMCs
• AML035 Pre-transplant BMMCs
• CD14+ Monocytes
• CD19+ B Cells
• CD34+ Cells
• CD4+ Helper T Cells
• CD4+/CD25+ Regulatory T Cells
• CD4+/CD45RA+/CD25- Naive T cells
• CD4+/CD45RO+ Memory T Cells
• CD56+ Natural Killer Cells
• CD8+ Cytotoxic T cells
• CD8+/CD45RA+ Naive Cytotoxic T Cells
• ERCC (1k GEMS, 1:10 Dilution)
• Fresh 68k PBMCs (Donor A)
• Frozen BMMCs (Healthy Control 1)
• Frozen BMMCs (Healthy Control 2)
• Frozen PBMCs (Donor A)
• Frozen PBMCs (Donor B)
• Frozen PBMCs (Donor C)
• Jurkat Cells