Update README.md

README.md

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-### Analysis notebooks and data used in the manuscript: <br>
-***"Gene-level alignment of single cell trajectories"*** <br>
-**Authors**: Dinithi Sumanaweera†, Chenqu Suo†, Ana-Maria Cujba, Daniele Muraro, Emma Dann, Krzysztof Polanski, Alexander S. Steemers, Woochan Lee, Amanda J. Oliver, Jong-Eun Park, Kerstin B. Meyer, Bianca Dumitrascu, Sarah A. Teichmann* <br><br>
-Available at: [https://www.biorxiv.org/content/10.1101/2023.03.08.531713v3](https://doi.org/10.1101/2023.03.08.531713 ) (bioRxiv Preprint)
+### Analysis notebooks and data used in the manuscript: ***"Gene-level alignment of single cell trajectories"*** <br>
+[https://www.biorxiv.org/content/10.1101/2023.03.08.531713v3](https://doi.org/10.1101/2023.03.08.531713 ) (bioRxiv Preprint)
+
+Available datasets:
+
+1. Simulated trajectories using Gaussian Processes
+2. Simulated perturbations using the mouse pancreas development dataset from CellRank (https://github.com/theislab/cellrank)
+3. Negative control simulated dataset generated using the published script of Laidlaw et al (2023) at https://github.com/No2Ross/TrAGEDy  
+4. Anndata objects of the PAM/LPS treated Murine bone marrow-dreived dendritic cell dataset of Shalek et al. (2014) compiled from the datafiles at https://github.com/shenorrLabTRDF/cellAlign
+5. Preprocessed and analysed Healthy/IPF datasets <br>(original raw data of Adams et al. (2020) downloaded from GEO: GSE136831)
+6. Preprocessed and analysed Pan fetal reference datasets <br> (original raw data of Suo et al. (2022) downloaded from https://developmental.cellatlas.io/fetal-immune)
+7. Preprocessed and analysed Artificial thymic organoid datasets <br> (raw sequencing data available from ArrayExpress: E-MTAB-12720)
+
+Large data objects are available at: https://zenodo.org/records/11182400