DOI: 10.5281/zenodo.11521688
title: Datasets for evaluating SCEMENT: Scalable and Memory Efficient Integration of Large-scale Single Cell RNA-sequencing Data

description: 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):



E-GEOD-121619 : https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-121619/results

E-GEOD-152766 : https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-152766/results

E-GEOD-158761 :   https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-158761/results

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/ 



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

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:




Dataset Name
Chemistry Version
Web Link


10k Human PBMCs, 3' v3.1, Chromium X
v3.1
https://www.10xgenomics.com/datasets/10k-human-pbmcs-3-ht-v3-1-chromium-x-3-1-high


20k Human PBMCs, 3' HT v3.1, Chromium X
v3.1
https://www.10xgenomics.com/datasets/20-k-human-pbm-cs-3-ht-v-3-1-chromium-x-3-1-high-6-1-0


10k Human PBMCs, 3' v3.1, Chromium Controller
v3.1
https://www.10xgenomics.com/datasets/10k-human-pbmcs-3-v3-1-chromium-controller-3-1-high


Healthy PBMC Chromium Connect (channel 1)
v3.1
https://www.10xgenomics.com/datasets/peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-chromium-connect-channel-1-3-1-standard-3-1-0


Healthy PBMC Chromium Connect (channel 5)
v3.1
https://www.10xgenomics.com/datasets/peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-chromium-connect-channel-5-3-1-standard-3-1-0


10k PBMCs from a Healthy Donor (v3 chemistry)
v3.0
https://www.10xgenomics.com/datasets/10-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0


1k PBMCs from a Healthy Donor (v2 chemistry)
v2.0
https://www.10xgenomics.com/datasets/1-k-pbm-cs-from-a-healthy-donor-v-2-chemistry-3-standard-3-0-0


1k PBMCs from a Healthy Donor (v3 chemistry)
v3.0
https://www.10xgenomics.com/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0


Fresh 68k PBMCs (Donor A)
v1.0
https://www.10xgenomics.com/datasets/fresh-68-k-pbm-cs-donor-a-1-standard-1-1-0


Frozen PBMCs (Donor A)
v1.0
https://www.10xgenomics.com/datasets/frozen-pbm-cs-donor-a-1-standard-1-1-0


Frozen PBMCs (Donor B)
v1.0
https://www.10xgenomics.com/datasets/frozen-pbm-cs-donor-b-1-standard-1-1-0


Frozen PBMCs (Donor C)
v1.0
https://www.10xgenomics.com/datasets/frozen-pbm-cs-donor-c-1-standard-1-1-0


PBMCs from a Healthy Donor: Whole Transcriptome Analysis
v3.1
https://www.10xgenomics.com/datasets/pbm-cs-from-a-healthy-donor-whole-transcriptome-analysis-3-1-standard-4-0-0


PBMC 600K
v1
https://www.ebi.ac.uk/gxa/sc/experiments/E-HCAD-4/downloads


GSM4560071
v2.0
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4560071


GSM4560074
v2.0
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4560074


GSM4560070
v2.0
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4560070




References for the Datasets :



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.

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.

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.

E-GEOD-123013: Ryu KH, Huang L, Kang HM, Schiefelbein J. (2019) Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells.

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.

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

PBMC data are downloaded from respective links