single-cell-benchmarking-resources

Collection of papers & tools focused on benchmarking methods and datasets for single-cell data analysis.

Benchmark study

Mereu, E., Lafzi, A., Moutinho, C., Ziegenhain, C., McCarthy, D. J., Álvarez-Varela, A., Batlle, E., Sagar, Grün, D., Lau, J. K., Boutet, S. C., Sanada, C., Ooi, A., Jones, R. C., Kaihara, K., Brampton, C., Talaga, Y., Sasagawa, Y., Tanaka, K., … Heyn, H. (2020). Benchmarking single-cell RNA-sequencing protocols for cell atlas projects. Nature Biotechnology, 38(6), 747–755. https://doi.org/10.1038/s41587-020-0469-4

Probst, V., Simonyan, A., Pacheco, F., Guo, Y., Nielsen, F. C., & Bagger, F. O. (2022). Benchmarking full-length transcript single cell mRNA sequencing protocols. BMC Genomics, 23(1), 860. https://doi.org/10.1186/s12864-022-09014-5

Yamawaki, T. M., Lu, D. R., Ellwanger, D. C., Bhatt, D., Manzanillo, P., Arias, V., Zhou, H., Yoon, O. K., Homann, O., Wang, S., & Li, C.-M. (2021). Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling. BMC Genomics, 22(1), 66. https://doi.org/10.1186/s12864-020-07358-4

Ziegenhain, C., Vieth, B., Parekh, S., Reinius, B., Guillaumet-Adkins, A., Smets, M., Leonhardt, H., Heyn, H., Hellmann, I., & Enard, W. (2017). Comparative Analysis of Single-Cell RNA Sequencing Methods. Molecular Cell, 65(4), 631-643.e4. https://doi.org/10.1016/j.molcel.2017.01.023

Chen, J., Cheung, F., Shi, R., Zhou, H., & Lu, W. (2018). PBMC fixation and processing for Chromium single-cell RNA sequencing. Journal of Translational Medicine, 16(1). doi:10.1186/s12967-018-1578-4

Chen, W., Zhao, Y., Chen, X., Yang, Z., Xu, X., Bi, Y., Chen, V., Li, J., Choi, H., Ernest, B., Tran, B., Mehta, M., Kumar, P., Farmer, A., Mir, A., Mehra, U. A., Li, J.-L., Moos, M., Xiao, W., & Wang, C. (2021). A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples. Nature Biotechnology, 39(9), 1103–1114. https://doi.org/10.1038/s41587-020-00748-9

Hornung, B. V. H., Azmani, Z., den Dekker, A. T., Oole, E., Ozgur, Z., Brouwer, R. W. W., van den Hout, M. C. G. N., & van IJcken, W. F. J. (2023). Comparison of Single Cell Transcriptome Sequencing Methods: Of Mice and Men. Genes, 14(12), 2226. https://doi.org/10.3390/genes14122226

Xie, Y., Chen, H., Chellamuthu, V. R., Lajam, A. bin M., Albani, S., Low, A. H. L., Petretto, E., & Behmoaras, J. (2024). Comparative Analysis of Single-Cell RNA Sequencing Methods with and without Sample Multiplexing. International Journal of Molecular Sciences, 25(7), 3828. https://doi.org/10.3390/ijms25073828

Dataset

PBMCs:

• Data set of PBMCs measured with CITE-seq (211,000 cells). First presented in the Seurat v4 paper: Hao et al, 2021, Cell 184, 3573-3587. https://doi.org/10.1016/j.cell.2021.04.048. Containing PBMC samples from 8 volunteers in an HIV vaccine trial, measured at 3 time points; resulting in 24 batches in this dataset.