Single Cell Gene Expression Datasets

Low Throughput Demonstration (LT v3.1 Chemistry)

Chromium Next GEM Single Cell 3’ LT v3.1 (referred to as low throughput or LT) is a low throughput, cost-effective solution for smaller-scale and pilot studies for profiling whole transcriptome and cell surface proteins at the single cell level for hundreds to a thousand cells per sample. For comparison, both LT and corresponding standard throughput datasets are provided below.

Cell Ranger 6.0.0

• 1k 1:1 Mixture of Human HEK293T and Mouse NIH3T3 Cells, 3’ LT v3.1
• 1k 1:1 Mixture of Human HEK293T and Mouse NIH3T3 Cells, 3’ v3.1
• 10k 1:1 Mixture of Human HEK293T and Mouse NIH3T3 Cells, 3’ v3.1
• 1k Human PBMCs with TotalSeq-B Human TBNK Antibody Cocktail, 3’ LT v3.1
• 1k Human PBMCs with TotalSeq-B Human TBNK Antibody Cocktail, 3’ v3.1
• 10k Human PBMCs with TotalSeq-B Human TBNK Antibody Cocktail, 3’ v3.1
• 750 Sorted Nuclei from Human Brain, 3’ LT v3.1
• 7.5k Sorted Nuclei from Human Brain, 3’ v3.1
• 750 Sorted Cells from Human Invasive Ductal Carcinoma, 3’ LT v3.1
• 7.5k Sorted Cells from Human Invasive Ductal Carcinoma, 3’ v3.1
• 200 Sorted Cells from Human Glioblastoma Multiforme, 3’ LT v3.1
• 2k Sorted Cells from Human Glioblastoma Multiforme, 3’ v3.1

CellPlex Demonstration - Raji Jurkat Mixture (v3.1 Chemistry)

10k 1:1 Mixture of Raji and Jurkat Cells Multiplexed, 2 CMOs.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 10k 1:1 Mixture of Raji and Jurkat Cells Multiplexed, 2 CMOs - Inputs/Library
• 10k 1:1 Mixture of Raji and Jurkat Cells Multiplexed, 2 CMOs - Raji
• 10k 1:1 Mixture of Raji and Jurkat Cells Multiplexed, 2 CMOs - Jurkat

CellPlex Demonstration - Lung Carcinoma (Unstained) (v3.1 Chemistry)

5k A549, Lung Carcinoma Cells, No Treatment Transduced with a CRISPR Pool.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 5k A549, Lung Carcinoma Cells, No Treatment Transduced with a CRISPR Pool - Inputs/Library
• 5k A549, Lung Carcinoma Cells, No Treatment Transduced with a CRISPR Pool - No Treatment

CellPlex Demonstration - Lung Carcinoma (v3.1 Chemistry)

30k A549, Lung Carcinoma Cells, Treatments Transduced with a CRISPR Pool, Multiplexed, 6 CMOs.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 30k A549, Lung Carcinoma Cells, Treatments Transduced with a CRISPR Pool, Multiplexed, 6 CMOs - Inputs/Library
• 30k A549, Lung Carcinoma Cells, Treatments Transduced with a CRISPR Pool, Multiplexed, 6 CMOs - No Treatment
• 30k A549, Lung Carcinoma Cells, Treatments Transduced with a CRISPR Pool, Multiplexed, 6 CMOs - DZNep
• 30k A549, Lung Carcinoma Cells, Treatments Transduced with a CRISPR Pool, Multiplexed, 6 CMOs - Trichostatin A
• 30k A549, Lung Carcinoma Cells, Treatments Transduced with a CRISPR Pool, Multiplexed, 6 CMOs - Valproic Acid
• 30k A549, Lung Carcinoma Cells, Treatments Transduced with a CRISPR Pool, Multiplexed, 6 CMOs - Kinetin
• 30k A549, Lung Carcinoma Cells, Treatments Transduced with a CRISPR Pool, Multiplexed, 6 CMOs - Resveratrol

CellPlex Demonstration - DTC (v3.1 Chemistry)

30k Sorted DTC Multiplexed, 4 CMOs and Stained with a Panel of TotalSeq B Antibodies.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 30k Sorted DTC Multiplexed, 4 CMOs and Stained with a Panel of TotalSeq B Antibodies - Inputs/Library
• 30k Sorted DTC Multiplexed, 4 CMOs and Stained with a Panel of TotalSeq B Antibodies - Adenocarcinoma
• 30k Sorted DTC Multiplexed, 4 CMOs and Stained with a Panel of TotalSeq B Antibodies - NSCLC
• 30k Sorted DTC Multiplexed, 4 CMOs and Stained with a Panel of TotalSeq B Antibodies - Squamous Cell Carcinoma
• 30k Sorted DTC Multiplexed, 4 CMOs and Stained with a Panel of TotalSeq B Antibodies - Lung Cancer

CellPlex Demonstration - E18 Mouse Brain Cells (Unstained) (v3.1 Chemistry)

5k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 5k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells - Inputs/Library
• 5k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells - Brain Cells

CellPlex Demonstration - E18 Mouse Brain Cells (v3.1 Chemistry)

30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells Multiplexed, 12 CMOs.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells Multiplexed, 12 CMOs - Inputs/Library
• 30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells Multiplexed, 12 CMOs - Brain 1
• 30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells Multiplexed, 12 CMOs - Brain 2
• 30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells Multiplexed, 12 CMOs - Brain 3
• 30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells Multiplexed, 12 CMOs - Brain 4

CellPlex Demonstration - E18 Mouse Brain Nuclei (Unstained) (v3.1 Chemistry)

5k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 5k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei - Inputs/Library
• 5k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei - Brain Nuclei

CellPlex Demonstration - E18 Mouse Brain Nuclei (v3.1 Chemistry)

30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei Multiplexed, 12 CMOs.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei Multiplexed, 12 CMOs - Inputs/Library
• 30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei Multiplexed, 12 CMOs - Brain Nuclei 1
• 30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei Multiplexed, 12 CMOs - Brain Nuclei 2
• 30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei Multiplexed, 12 CMOs - Brain Nuclei 3
• 30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei Multiplexed, 12 CMOs - Brain Nuclei 4

CellPlex Demonstration - Human PBMCs (v3.1 Chemistry)

10k Human PBMCs Multiplexed, 2 CMOs.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 10k Human PBMCs Multiplexed, 2 CMOs - Inputs/Library
• 10k Human PBMCs Multiplexed, 2 CMOs - Human 1
• 10k Human PBMCs Multiplexed, 2 CMOs - Human 2

CellPlex Demonstration - Mouse PBMCs (v3.1 Chemistry)

10k Mouse PBMCs Multiplexed, 2 CMOs.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 10k Mouse PBMCs Multiplexed, 2 CMOs - Inputs/Library
• 10k Mouse PBMCs Multiplexed, 2 CMOs - Mouse 1
• 10k Mouse PBMCs Multiplexed, 2 CMOs - Mouse 2

CellPlex Demonstration - Rat PBMCs (v3.1 Chemistry)

10k Rat PBMCs Multiplexed, 2 CMOs.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 10k Rat PBMCs Multiplexed, 2 CMOs - Inputs/Library
• 10k Rat PBMCs Multiplexed, 2 CMOs - Rat 1
• 10k Rat PBMCs Multiplexed, 2 CMOs - Rat 2

CellPlex Demonstration - Monkey PBMCs (v3.1 Chemistry)

10k Monkey PBMCs Multiplexed, 2 CMOs.

The links below represent a single cellranger multi run.

Cell Ranger 6.0.0

• 10k Monkey PBMCs Multiplexed, 2 CMOs - Inputs/Library
• 10k Monkey PBMCs Multiplexed, 2 CMOs - Monkey 1
• 10k Monkey PBMCs Multiplexed, 2 CMOs - Monkey 2

Targeted Neuroscience Demonstration Data (v3 Chemistry)

Cell Ranger 4.0.0

• Human Glioblastoma Multiforme: 3’v3 Whole Transcriptome Analysis
• Human Glioblastoma Multiforme: 3’v3 Targeted, Neuroscience Panel

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