WebAtlas pipeline for integrated single cell and spatial transcriptomic data
Single cell and spatial transcriptomics illuminate complementary features of tissues. However, the online dissemination and exploration of multi-modal datasets is challenging. We introduce the WebAtlas pipeline for user-friendly sharing and interactive navigation of integrated datasets. WebAtlas unifies commonly used atlassing technologies into the cloud-optimised Zarr format and builds on Vitessce to enable remote data navigation. We showcase WebAtlas on the developing human lower limb to cross-query cell types and genes across single cell, sequencing- and imaging-based spatial transcriptomic data.
- Contact
- Tong Li, David Horsfall, Daniela Basurto-Lozada
- Release
- 28 April 2023
- Lab
- Haniffa Lab, Bayraktar Lab, Teichmann Lab
- Dataset
- Lower Limb dataset & scRNA-seq Human Developmental Immune dataset:
Sarah A. Teichmann, Teichmann Lab.
Wellcome Sanger Institute, Hinxton, UK & University of Cambridge
seqFish Mouse Embryo dataset:
Shila Ghazanfar & John C. Marioni, Marioni Lab.
Cancer Research UK Cambridge Institute & European Bioinformatics Institute & Wellcome Sanger Institute, Hinxton, UK
Xenium Adult Human Brain & Adult Human Breast Cancer, Visium Adult Human Breast Cancer datasets:
10XGenomics
MERSCOPE Human Breast Cancer dataset:
MERSCOPE FFPE Human Immuno-oncology Data Release
- Tissue
- Brain, Breast, Embryo, Fetal Bone Marrow, Fetal Gut, Fetal Kidney, Fetal Liver, Fetal Mesenteric Lymph Node, Fetal Skin, Fetal Spleen, Fetal Thymus, Fetal lower limb, Yolk Sac
- Assay
- 10X Visium, 10x 3' v2, 10x 5' v1, 10x Visium, 10x Visium CytAssist, 10x Xenium, In Situ Sequencing, MERSCOPE, seqFISH
- Disease
- Alzheimer's, Breast Cancer, Breast Cancer (T2N1M0, ER+/HER2+/PR−), Glioblastoma Multiforme (GBM), None, Stage II-B
- Organism
- Homo sapiens, Mus musculus
Integrated Lower Limb Datasets
10x 3' v2
In Situ Sequencing
10x 3' v2
In Situ Sequencing
10x 3' v2
In Situ Sequencing
10x 3' v2
In Situ Sequencing
10x 3' v2
In Situ Sequencing
In Situ Sequencing
10x Visium
In Situ Sequencing
Individual Lower Limb Datasets
Integrated SeqFISH Mouse Embryo Datasets
seqFISH
Xenium Datasets
MERSCOPE Datasets
Visium Datasets
scRNA-seq Datasets
Fetal Gut
Fetal Kidney
Fetal Liver
Fetal Mesenteric Lymph Node
Fetal Skin
Fetal Spleen
Fetal Thymus
Yolk Sac
10x 3' v2
Reproducibility
Reproducibility is a major principle underpinning the scientific method. We make publicly available the raw data and analysis scripts associated with each collection.
- Code Repository
- https://github.com/haniffalab/webatlas-pipeline
- Reproducibility
- https://zenodo.org/record/7863308
