Skip to main content

Table 1 Protein acceleration datasets and parameters

From: Protein velocity and acceleration from single-cell multiomics experiments

DatasetCITE-seqREAP-seqECCITE-seq ctrlECCITE-seq CTCL10X 1k10X 10k
RNA dataGSM2695381GSM2685238GSM3596095GSM3596100See MethodsSee Methods
Protein dataGSM2695382GSM2685243GSM3596096GSM3596101See MethodsSee Methods
Alignment softwareCell Ranger 2.2Cell Ranger 1.3Cell Ranger 3.0Cell Ranger 3.0kallisto 0.46kallisto 0.46
Counting softwarevelocyto 0.17velocyto 0.17velocyto 0.17velocyto 0.17kallisto 0.46kallisto 0.46
Reference genomeGRCh38hg19hg19hg19GRCh38GRCh38
Cell count17803158508453177097855
Velocity genes117213385916671114920
Antibodies104149491717
Velocity proteins716111278
Cell types found544355
Imputation k4008008008005050
Clustering methodMVPRVPRVPMVPMVPMVP
EmbeddingPC2/3 and t-SNEt-SNEt-SNEt-SNEt-SNEt-SNE
  1. MVP ModularityVertexPartition, RVP RBERVertexPartition, PCA principal component, t-SNE t-Stochastic Neighbor Embedding