TIVelo datasets

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.

本数据集可用于复现《TIVelo：基于聚类水平轨迹推断的RNA速率估算》一文中的实验结果。配套脚本与Notebook可在https://github.com/cuhklinlab/TIVelo获取。本数据集均为公开可获取版本，且均已通过scVelo标准预处理流程（https://scvelo.readthedocs.io/en/stable/VelocityBasics.html）处理。
1. endocrinogenesis_day15_processed.h5ad：该胰腺内分泌发生数据集可从基因表达汇编（Gene Expression Omnibus，GEO）获取，登录号为GSE132188。本数据集为经过scVelo标准预处理流程后的版本。
2. 10X43_1_processed.h5ad：该齿状回发育数据集可从GEO获取，登录号为GSE95753。本数据集选取了P12与P35两个时间点的数据，并经过scVelo标准预处理流程。
3. erythroid_lineage_processed.h5ad：该小鼠原肠胚形成（红系）数据集可从阵列表达数据库（ArrayExpress）获取，登录号为E-MTAB-6967。本数据集为经过scVelo标准预处理流程后的版本。
4. oligo_lite_processed.h5ad：该小鼠后脑（少突胶质细胞）数据集可从Kharchenko实验室官网https://pklab.med.harvard.edu/ruslan/velocity/oligos/下载。本数据集为经过scVelo标准预处理流程后的版本。
5. Hindbrain_GABA_Glio_processed.h5ad：该小鼠后脑（GABA能神经元、胶质细胞）数据集可从GEO获取，登录号为GSE118068。其处理后的loom文件可通过DeepVelo的Figshare资源获取：https://doi.org/10.6084/m9.figshare.24716592.v1。本数据集为经过scVelo标准预处理流程后的版本。
6. organoids_processed.h5ad：该肠道类器官数据集可从GEO获取，登录号为GSE128365。本数据集为经过scVelo标准预处理流程后的版本。
7. retina_processed.h5ad：该小鼠视网膜发育数据集可从GEO获取，登录号为GSM3466902。本数据集为经过scVelo标准预处理流程后的版本。
8. scNT_processed.h5ad：该scNT-seq神经元KCl刺激数据集可从GEO获取，登录号为GSE141851。本数据集为经过scVelo标准预处理流程后的版本。
9. reprogramming_processed.h5ad：该小鼠胚胎成纤维细胞重编程数据集可从GEO获取，登录号为GSE99915。本数据集为经过scVelo标准预处理流程后的版本。
10. adata_fucci_rpe1_processed.h5ad 与 adata_fucci_u2os_processed.h5ad：RPE1-FUCCI与U2OS-FUCCI数据集可分别从veloVI的Figshare资源获取：https://doi.org/10.6084/m9.figshare.22773776.v1 与 https://doi.org/10.6084/m9.figshare.22773761.v1。本数据集为经过scVelo标准预处理流程后的版本。
11. MouseBrain.h5ad 与 MouseBrain_atac.h5ad：该10x Genomics的小鼠胚胎脑组织数据集可在10x官网https://www.10xgenomics.com/resources/datasets/fresh-embryonic-e-18-mouse-brain-5-k-1-standard-1-0-0获取。本数据集为经过MultiVelo标准预处理流程（https://multivelo.readthedocs.io/en/latest/MultiVelo_Fig2.html）后的版本。
12. DentateGyrus_processed.h5ad：该齿状回发育数据集可从GEO获取，登录号为GSE95753。本数据集为经过scVelo标准预处理流程后的版本。

搜集汇总

背景与挑战

背景概述

TIVelo数据集是一个生物信息学数据集集合，包含多个经过scVelo标准预处理的单细胞RNA测序数据，用于支持RNA速度估计和轨迹推断研究。这些数据覆盖了多种生物过程和研究领域，如胰腺发育、神经元刺激反应等，并附有对应的GitHub代码库链接。