Awesome

Besca's publication results

This repository includes notebooks utilized to produce results for the publication on the Besca toolkit (https://github.com/bedapub/besca). Please find additional tutorials and documentation here: https://bedapub.github.io/besca/

To demonstrate how Besca can be applied to a wide variety of biological samples, we reprocessed publicly available single-cell data from ten studies:

Three datasets cover blood- and bone-marrow-derived hematopoietic cells:

• PBMC3k (https://doi.org/10.5281/zenodo.3948150) includes healthy peripheral blood mononuclear cell (PBMC) samples from one donor, a reference dataset often used in single-cell tutorials based on 10X Genomics data (https://www.10xgenomics.com/).
• Granja2019 (https://doi.org/10.5281/zenodo.3944753) includes bone marrow mononuclear cell (BMMCs) and PBMC samples from healthy donors (1). In addition to scRNA-seq, several protein markers were also probed by CITE-seq.
• Kotliarov2020 (https://doi.org/10.5281/zenodo.3938290) includes baseline PBMC samples from healthy donors, who were high and low responders to influenza vaccines (2). In addition to scRNA-seq, a high number of protein markers were also probed by CITE-seq.

Four datasets reveal the intestinal cell composition:

• Smillie2019 (https://doi.org/10.5281/zenodo.3960617) includes colon epithelium and lamina propria samples from healthy donors and ulcerative colitis patients (3).
• Martin2019 (https://doi.org/10.5281/zenodo.3862132) includes ileal lamina propria samples from Crohn’s disease patients (4).
• Haber2017 (https://doi.org/10.5281/zenodo.3935782) includes murine small intestine samples (5).
• Lee2020 (https://doi.org/10.5281/zenodo.3967538) includes tumor and non-malignant colon samples from colorectal cancer (CRC) patients (6).

Three datasets are pancreas-derived:

• Segerstolpe2016 (https://doi.org/10.5281/zenodo.3928276) includes pancreatic islet cells from healthy donors and type 2 diabetic patients (7).
• Peng2019 (https://doi.org/10.5281/zenodo.3969339) includes tumor and non-malignant pancreatic samples from pancreatic ductal adenocarcinoma (PDAC) and non-pancreatic tumor patients (8).
• Baron2016 (https://doi.org/10.5281/zenodo.3968315) includes pancreatic samples from healthy donors (9).

References:

1. Granja JM, Klemm S, McGinnis LM, Kathiria AS, Mezger A, Corces MR, et al. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nature Biotechnology. Nature Publishing Group; 2019;37:1458–65.
2. Kotliarov Y, Sparks R, Martins AJ, Mulè MP, Lu Y, Goswami M, et al. Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nature Medicine. Nature Publishing Group; 2020;26:618–29.
3. Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, et al. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. Cell. Elsevier; 2019;178:714-730.e22.
4. Martin JC, Chang C, Boschetti G, Ungaro R, Giri M, Grout JA, et al. Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy. Cell. Elsevier; 2019;178:1493-1508.e20.
5. Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, et al. A single-cell survey of the small intestinal epithelium. Nature. Nature Publishing Group; 2017;551:333–9.
6. Lee H-O, Hong Y, Etlioglu HE, Cho YB, Pomella V, Van den Bosch B, et al. Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer. Nature Genetics. Nature Publishing Group; 2020;52:594–603.
7. Segerstolpe Å, Palasantza A, Eliasson P, Andersson E-M, Andréasson A-C, Sun X, et al. Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes. Cell Metabolism. Elsevier; 2016;24:593–607.
8. Peng J, Sun B-F, Chen C-Y, Zhou J-Y, Chen Y-S, Chen H, et al. Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma. Cell Research. Nature Publishing Group; 2019;29:725–38.
9. Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, et al. A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. cels. Elsevier; 2016;3:346-360.e4.