Mapping the developing human immune system across organs

Data processing and analysis scripts for fetal immune atlas (OA link).

Repository contents

• src contains scripts and notebooks used for data processing and analysis.
• metadata: contains metadata relevant for sample and cell annotations, pointers to raw and processed data, color palettes and groupings.
• tutorials: contains tutorials for model re-use (details here)

Data and metadata pointers

Browse all processed datasets, models and annotations at https://developmental.cellatlas.io/fetal-immune.

Primary tissue gene expression data

For primary tissue samples, gene expression count matrices from scRNA-seq (10X Genomics 3' and 5') are available as AnnData objects in .h5ad format for the full dataset (including stromal, immune and low quality cells), and 7 lineage subsets. In all objects adata.X stores gene counts corrected for background expression using CellBender.

Cell-level metadata, including cell type annotations, are stored in adata.obs and can be downloaded in .csv format here (note: here cell type annotations are stored in column anno_lvl_2_final_clean). Sample-level metadata, including matching between scRNA-seq and scVDJ-seq libraries, can be downloaded in .csv format here.

Primary tissue spatial transcriptomics data

Gene expression count matrices in .h5ad format and high-resolution images in .tiff format can be downloaded from the data portal (see section Spatial Datasets). Here cell type results for cell type deconvolution analysis with cell2location are stored in adata.obsm.

Primary tissue scVDJ-seq data

Combined gene expression and antigen-receptor sequencing data is available in .h5ad format (see section VDJ Datasets). Here adata.obs stores the data from the antigen-receptor libraries using the data structure used by scirpy and dandelion. To match scRNA-seq and scVDJ-seq library IDs, see sample metadata file.

In addition, contig files for all libraries generated by 10X Genomics cell-ranger and dandelion can be downloaded as tarballs (abTCR) (BCR)

In vitro derived T cells gene expression data

For in vitro derived T cells from Artificial Thymic Organoid protocols the gene expression count matrix from scRNA-seq (10X genomics 3') is available in .h5ad (download). Sample-level metadata can be found here.

Raw sequencing data

Raw sequencing libraries are deposited in ArrayExpress

• scRNA-seq libraries: raw data for libraries generated for this study are deposited under accession E-MTAB-11343. Raw data for libraries published in previous studies can be found in the following data repositories:
  • ArrayExpress E-MTAB-7407 (Popescu et al. 2019)
  • HCA data coordination platform (Stewart et al. 2019)
  • ArrayExpress E-MTAB-9389 (Jardine, Webb et al. 2021)
  • ArrayExpress E-MTAB-8901 (Elmentaite et al. 2020)
  • ArrayExpress E-MTAB-8142 (Reynolds et al. 2021)
  • ArrayExpress E-MTAB-8581 (Park et al. 2020)
• Visium libraries: E-MTAB-11341
• scVDJ libraries (all libraries): E-MTAB-11388).

smFISH data

The imaging data for detection of immune cell progenitors in fetal tissues can be found on the BioImage Archive (S-BIAD515)

Model re-use tutorials

Trained models for integrated embedding with scVI and cell type annotation with CellTypist can be downloaded through our data portal. We provide the following tutorials to explain how to use these models for contextualization and fast analysis of new data:

• Mapping query data to fetal immune reference with scArches
• Automatic cell type annotation from fetal immune reference with CellTypist

Citation

If you use this data or code for your work, please cite

Suo C., Dann E., et al. (2022). Mapping the developing human immune system across organs. Science, 376(6597), https://doi.org/10.1126/science.abo0510

@article{suoMappingDevelopingHuman2022,
  title = {Mapping the Developing Human Immune System across Organs},
  author = {Suo, Chenqu and Dann, Emma and Goh, Issac and Jardine, Laura and Kleshchevnikov, Vitalii and Park, Jong-Eun and Botting, Rachel A. and Stephenson, Emily and Engelbert, Justin and Tuong, Zewen Kelvin and Polanski, Krzysztof and Yayon, Nadav and Xu, Chuan and Suchanek, Ondrej and Elmentaite, Rasa and Dom{\'i}nguez Conde, Cecilia and He, Peng and Pritchard, Sophie and Miah, Mohi and Moldovan, Corina and Steemers, Alexander S. and Mazin, Pavel and Prete, Martin and Horsfall, Dave and Marioni, John C. and Clatworthy, Menna R. and Haniffa, Muzlifah and Teichmann, Sarah A.},
  year = {2022},
  journal = {Science},
  volume = {376},
  number = {6597},
  publisher = {{American Association for the Advancement of Science}},
  doi = {10.1126/science.abo0510},
}

Contact

For any questions, please post an issue in this repository or contact by email ed6<at>sanger.ac.uk or cs42<at>sanger.ac.uk.