Datasets for evaluating SCEMENT: Scalable and Memory Efficient Integration of Large-scale Single Cell RNA-sequencing Data
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): 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
- Georgia Institute of Technology United States
citations This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).0 popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.Average influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).Average impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.Average
Citations provided by BIP!Popularity provided by BIP!