Skip to main content

Table 1 Protein acceleration datasets and parameters

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

Dataset

CITE-seq

REAP-seq

ECCITE-seq ctrl

ECCITE-seq CTCL

10X 1k

10X 10k

RNA data

GSM2695381

GSM2685238

GSM3596095

GSM3596100

See Methods

See Methods

Protein data

GSM2695382

GSM2685243

GSM3596096

GSM3596101

See Methods

See Methods

Alignment software

Cell Ranger 2.2

Cell Ranger 1.3

Cell Ranger 3.0

Cell Ranger 3.0

kallisto 0.46

kallisto 0.46

Counting software

velocyto 0.17

velocyto 0.17

velocyto 0.17

velocyto 0.17

kallisto 0.46

kallisto 0.46

Reference genome

GRCh38

hg19

hg19

hg19

GRCh38

GRCh38

Cell count

1780

3158

5084

5317

709

7855

Velocity genes

1172

1338

591

667

1114

920

Antibodies

10

41

49

49

17

17

Velocity proteins

7

16

11

12

7

8

Cell types found

5

4

4

3

5

5

Imputation k

400

800

800

800

50

50

Clustering method

MVP

RVP

RVP

MVP

MVP

MVP

Embedding

PC2/3 and t-SNE

t-SNE

t-SNE

t-SNE

t-SNE

t-SNE

  1. MVP ModularityVertexPartition, RVP RBERVertexPartition, PCA principal component, t-SNE t-Stochastic Neighbor Embedding