DOI: 10.6084/m9.figshare.27643494.v1
title: TIVelo datasets

description: The provided datasets can be used for reproducing the results in "TIVelo: RNA velocity estimation leveraging cluster-level trajectory inference". The corresponding scripts and notebooks can be found in https://github.com/cuhklinlab/TIVelo. All the datasets provided here are openly accessible, and are the version after scVelo standard preprocessing pipeline (https://scvelo.readthedocs.io/en/stable/VelocityBasics.html).

1. endocrinogenesis_day15_processed.h5ad: The pancreatic endocrinogenesis data is available in the Gene Expression Omnibus (GEO) under accession code GSE132188. The dataset provided here is the version after scVelo standard preprocessing pipeline.

2. 10X43_1_processed.h5ad: The dentate gyrus development data is available in GEO under accession code GSE95753. The dataset provided here is the version by selecting two time points (P12 and P35), and after scVelo standard preprocessing pipeline. 

3. erythroid_lineage_processed.h5ad: The mouse gastrulation (erythroid) data is available in ArrayExpress under accession code E-MTAB-6967. The dataset provided here is the version after scVelo standard preprocessing pipeline.

4. oligo_lite_processed.h5ad: The mouse hindbrain (Oligo) data can be downloaded from the website of Kharchenko Lab at https://pklab.med.harvard.edu/ruslan/velocity/oligos/. The dataset provided here is the version after scVelo standard preprocessing pipeline.

5. Hindbrain_GABA_Glio_processed.h5ad: The mouse hindbrain (GABA, Glial) data is available in GEO under accession code GSE118068. The processed loom files are available from Figshare of DeepVelo by: https://doi.org/10.6084/m9.figshare.24716592.v1. The dataset provided here is the version after scVelo standard preprocessing pipeline.

6. organoids_processed.h5ad: The intestinal organoid data is available in GEO under accession code GSE128365. The dataset provided here is the version after scVelo standard preprocessing pipeline.

7. retina_processed.h5ad: The mouse retina development data is available in GEO under accession code GSM3466902. The dataset provided here is the version after scVelo standard preprocessing pipeline.

8. scNT_processed.h5ad: The scNT-seq neuron KCl stimulation data is available in GEO under accession code GSE141851. The dataset provided here is the version after scVelo standard preprocessing pipeline.

9. reprogramming_processed.h5ad: The mouse embryonic fibroblast reprogramming data is available in GEO under accession code GSE99915. The dataset provided here is the version after scVelo standard preprocessing pipeline.

10. adata_fucci_rpe1_processed.h5ad and adata_fucci_u2os_processed.h5ad: The RPE1-FUCCI and U2OS-FUCCI data can be downloaded from Figshare of veloVI by: https://doi.org/10.6084/m9.figshare.22773776.v1 and https://doi.org/10.6084/m9.figshare.22773761.v1. The two datasets provided here are the version after scVelo standard preprocessing pipeline.

11. MouseBrain.h5ad and MouseBrain_atac.h5ad: The embryonic mouse brain data from 10x Genomics is available at 10x website: https://www.10xgenomics.com/resources/datasets/fresh-embryonic-e-18-mouse-brain-5-k-1-standard-1-0-0. The dataset provided here is the version after MultiVelo preprocessing pipeline: https://multivelo.readthedocs.io/en/latest/MultiVelo_Fig2.html. 

12. DentateGyrus_processed.h5ad: The dentate gyrus development data is available in GEO under accession code GSE95753. The dataset provided here is the version after scVelo standard preprocessing pipeline.