BioTuring Browser: making published single-cell data really accessible

Single-cell sequencing technologies have brought up an unprecedented level of resolution to omics studies with extremely detailed views into individual cells’ expression patterns. With the emergence of drop-based sequencing methods, the resolution now even comes with scale and efficiency. In a single experiment, scientists can now profile hundreds of thousands of cells, or even 2 million cells at a time (Cao et. al., 2019), and generate a huge amount of single-cell data, providing valuable inputs for biological research and breakthroughs.

However, huge amounts of single-cell data generated are posing major challenges for hosting, accessing, visualization and analysis. Although multiple repositories are available (eg.: Gene Expression Omnibus by NCBI, EBI, Human Cell Atlas, etc.), single-cell sequencing datasets are currently provided in different formats. Given the increasing size of the data, it is extremely challenging to explore many single-cell datasets at a time because of such variability in formats, and expensive computational resources to process. We are lucky to have some nice visualization portals at hand, thanks to the authors of the data, yet these portals are separate from one another, making it uneasy to combine multiple single-cell datasets for meta-analysis.

To address the challenges, we developed a single-cell data portal and standardized analytics dashboard in BioTuring Single-cell Browser, enabling any biologists to easily access, reanalyze, combine, and discover valuable stories from published single-cell datasets on their laptop.

The single-cell data portal in BioTuring Single-cell Browser

3D UMAP of 1.3 million cells from the mouse organogenesis cell atlas (MOCA) (Cao et al., 2019) in BioTuring Single-cell Browser

A curated database of more than 3.4 million cells, ready for downstream analyses

Our curated database in BioTuring Single-cell Browser is currently hosting more than 3.4 million cells from 12 different tissues and 59 latest high-impact single-cell studies, including the mouse organogenesis cell atlas by Cao and colleagues (2019), mouse retinal cell atlas (Clark et al., 2019) and the liver cell atlas (MacParland et al., 2018). The datasets are increasing exponentially in number, all ready for exploring in a few clicks, with interactive visualizations, and state-of-the-art analytics.

List of indexed datasets

Total Single-cell RNA-seq studies in BBrowser

TitleIDSpecie# cells
A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cellsSinger2016mouse1061
Massively parallel single-nucleus RNA-seq with DroNc-seqhabib2017_2human14963
Shared and distinct transcriptomic cell types across neocortical areastasic2018mouse11430
Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma.GSE123139human64967
Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain - EntoPedunculardropviz.EntoPeduncularmouse27927
GSE121645_age - Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State ChangesGSE121645_agemouse85254
A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortexzhong2018human2394
Neutrophils escort circulating tumour cells to enable cell cycle progressionGSE109761_huhuman327
Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell typeboldog2018human914
Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - BC09-01-vdjbc09_1_vdjhuman7096
Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell SequencingZheng2017human5063
Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockadeIshizuka2018mouse8838
Highly parallel genome-wide expression profiling of individual cells using nanoliter dropletsmacosko2015mouse49300
Longitudinal single-cell RNA sequencing of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchySharma2018human1302
Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain - Cortex_noRep5_POSTERIORonlydropviz.Cortex_noRep5_POSTERIORonlymouse115990
Single-cell RNA-seq analysis of infiltrating neoplastic cells at the migrating front of human glioblastomadarmanis2017human3588
GSE121645_saline - Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State ChangesGSE121645_salinemouse13309
Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populationssonya2018human8444
Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypesromanov2017mouse3077
An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomicsAngelidis2018mouse14578
Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancerGSE103322mouse5902
Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain - GlobusPallidusdropviz.GlobusPallidusmouse86453
Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain - Striatumdropviz.Striatummouse90470
Composition of the Colonic Mesenchyme and the Nature of its Plasticity in Inflammatory Bowel DiseaseGSE114374human9271
Global characterization of T cells in non-small-cell lung cancer by single-cell sequencingxinyi2018human11840
Neutrophils escort circulating tumour cells to enable cell cycle progressionGSE109761_mmmouse109
Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumorsyoung2018human95682
Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell SpecificationMouseRetinamouse102830
Single-cell profiling of the myeloid landscape identifies cell subsets with distinct fates during neuroinflammationGSE118948mouse4509
Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell typeboldog2018_2mouse1679
Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain - SubstantiaNigradropviz.SubstantiaNigramouse66346
Temporal tracking of microglia activation in neurodegeneration at single-cell resolutionmathys2017mouse2208
Single-cell reconstruction of the early maternal--fetal interface in humansventotormo2018human64734
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seqzeisel2015mouse3488
Massively parallel single-nucleus RNA-seq with DroNc-seqhabib2017mouse13313
The bone marrow microenvironment at single-cell resolutionGSE108892-GSE108891mouse20094
Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brainlake2016human3042
Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomicsharris2018mouse3662
A molecular atlas of cell types and zonation in the brain vasculaturevanlandewijck2018mouse3186
Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - BC01-08GSE114725human28690
Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - BC09-11GSE114727human28690
The single-cell transcriptional landscape of mammalian organogenesisMOCA_2Mmouse1331984
The bone marrow microenvironment at single-cell resolutionGSE108892-GSE118436mouse23029
Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myelomaAdit2018human40065
Dissecting cell-type composition and activity-dependent transcriptional state in mammalian brains by massively parallel single-nucleus RNA-seqhu2017mouse18194
A unique microglia type associated with restricting development of Alzheimer’s diseaseHadas2017human37248
Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain - Cerebellumdropviz.Cerebellum_ALTmouse59309
Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain - Thalamusdropviz.Thalamusmouse124239
Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain - Hippocampusdropviz.Hippocampusmouse131953
GSE121645_percoll - Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State ChangesGSE121645_percollmouse15281
Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and ImmunityGSE116256human15281
Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris (FACS)TabulaMuris_facsmouse40494
Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris (droplet)TabulaMuris_dropletmouse40494
Colonic epithelial cell diversity in health and inflammatory bowel diseaseGSE116222human11167
Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory ResponseGSE109564-GSE114156human8784
Comparative analysis and refinement of human PSC-derived kidney organoid differentiation with single-cell transcriptomicsGSE118184human89333
Mapping the Mouse Cell Atlas by Microwell-SeqMCAmouse378824
Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and SpeciesGSE127465_humanhuman53179
Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and SpeciesGSE127465_mousemouse15915

UMAP of mouse retinal cell atlas (Clark et al., 2019) in BioTuring Single-cell Browser. See how we reanalyzed the dataset and explored a hybrid population expressing rod and cone markers here.

What can you do in BioTuring Single-cell Browser?

Here’s to name major analyses available for published single-cell data in BioTuring Browser:

  • Interactively visualize up to 1.3 million cells in 2D/3D t-SNE and UMAP
  • Find marker genes and predict cell types in real time
  • Explore sub-clusters of any cell types
  • Study compositional changes across conditions
  • Find differentially expressed genes
  • Pair clonotype data from TCR repertoire sequencing with expression data
  • Combine multiple published single-cell datasets or pair published data with your in-house data

Differential expression analysis for T cells in tumor and normal breast tissues (Azizi et al., 2018)

With BioTuring Single-cell Browser, we hope to foster extensive peer review and collaboration, as well as transparency in science. Access to published single-cell data repository is currently free of charge.

Explore now

BioTuring Single-cell Browser is now available at bioturing.com/product/bbrowser for Windows, MacOS, Ubuntu and Centos 7.

For more video tutorials:

 

References:

Cao, Junyue, et al. “The single-cell transcriptional landscape of mammalian organogenesis.” Nature 566.7745 (2019): 496.

Clark, Brian S., et al. “Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification.” Neuron (2019).

MacParland, Sonya A., et al. “Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations.” Nature communications 9.1 (2018): 4383.

Azizi, Elham, et al. “Single-cell map of diverse immune phenotypes in the breast tumor microenvironment.” Cell 174.5 (2018): 1293-1308.

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