Datasets for evaluating SCEMENT: Scalable and Memory Efficient Integration of Large-scale Single Cell RNA-sequencing Data

This resource contains pre-processed A. thaliana root , the H. sapiens aortic valve datasets, PBMC Covid atlas and public 10x datasetse used in the paper, SCEMENT: Scalable and Memory Efficient Integration of Large-scale Single Cell RNA-sequencing Data. The raw datasets provided in the links below are pre-processed for quality control with respect to both cells and genes. 

A. thaliana datasets are sourced from the following locations at Single-cell Gene expression Atlas and Gene Expression Omnibus (GEO):

1. E-GEOD-121619 : https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-121619/results
2. E-GEOD-152766 : https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-152766/results
3. E-GEOD-158761 :   https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-158761/results
4. E-GEOD-123013 : https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-123013/results

H. sapiens datasets are obtained from the NCBI database : https://www.ncbi.nlm.nih.gov/bioproject/PRJNA562645/ 

1. GSE152766: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152766
2. GSE158761: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158761

All COVID atlas datasets are from: http://covid19.cancer-pku.cn . covid_atlas_data1.zip contains the h5ad files and covid_atlas_data2.zip contains the Seurat rds files.

PBMC datasets are from the following public sources:

References for the Datasets :

1. H. sapiens dataset: Kang Xu, Shangbo Xie,Yuming Huang,Tingwen Zhou, Ming Liu, Peng Zhu, Chunli Wang, Jiawei Shi, Fei Li,Frank W. Sellke and Nianguo Dong (2020) Cell-Type Transcriptome Atlas of Human Aortic Valves Reveal Cell Heterogeneity and Endothelial to Mesenchymal Transition Involved in Calcific Aortic Valve Disease.
2. E-GEOD-152766: Shahan R, Hsu C, Nolan TM, Cole BJ, Taylor IW et al. (2020) A single cell Arabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants.
3. E-GEOD-121619: Jean-Baptiste K, McFaline-Figueroa JL, Alexandre CM, Dorrity MW, Saunders L et al. (2019) Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana.
4. E-GEOD-123013: Ryu KH, Huang L, Kang HM, Schiefelbein J. (2019) Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells.
5. E-GEOD-158761: Gala HP, Lanctot A, Jean-Baptiste K, Guiziou S, Chu JC et al. (2020) A single cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana.
6. COVID Atlas Reference: Xianwen Ren, Wen Wen, Xiaoying Fan et.al. (2021) COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas
7. PBMC data are downloaded from respective links