Table 1 Comparison between SUM-seq and other ATAC and RNA single-cell methods

From: Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics

Method

Platform

Multiplexing capacity

Estimated cost

Throughput

Sensitivity

Public accessions

SUM-seq

Combination plate based and microfluidic

Yes, combination of plate-based and microfluidic indexing

<0.05€ per cell

Ultra-high;

>50,000 profiles per microfluidic channel

High;

average genes per cell: 2,058 (K562)

Average fragments per cell: 5,164 (K562)

 

10x Multiome

Microfluidic

No

~0.35€ per cell

High;

~10,000 profiles per microfluidic channel

K562: 11,693 (ATAC), 13,228 (RNA)

High;

average genes per cell: 2,515

Average fragments per cell: 9,258

K562 ATAC: ERR9847049

K562 RNA:

ERR9847050

SNARE-seq2

Microfluidic

No

<0.1€ per cell

Low;

K562: 198 (ATAC),

355 (RNA)

Low;

average genes per cell: 361

Average fragments per cell: 595

K562 ATAC: SRR8528319

K562 RNA:

SRR8528318

Paired-seq

Plate based

No

<0.05€ per cell

Ultra-high; (1.51 million nuclei barcoded; sublibrary sequenced);

HEK293T: 1,357 (ATAC), 1,283 (RNA)

Low;

average genes per cell: 536

Average fragments per cell: 1,506

HEK293T ATAC: SRR8980188

HEK293T RNA: SRR8980189

ISSAAC-seq

Microfluidic and plate based possible

No

~0.2€ per cell

High (microfluidic);

K562: 5,700 (ATAC),

5,159 (RNA)

High;

average genes per cell: 2,522

Average fragments per cell: 6,789

K562 ATAC:

ERR9847051

K562 RNA: ERR9847052

Smart3-ATAC

Plate based

Theoretically possible, but limited in throughput

>0.25€ per cell

Low;

time-course mouse gastrulation: 3,196 single sorted cells

High;

average UMIa per cell: 46,501

Average fragments per cell: N/A

N/A

SHARE-seq

Plate based

Yes, plate based

<0.05€ per cell

Ultra-high;

K562: 5,219 (ATAC), 7,754 (RNA)

Low;

average genes per cell: 241

Average fragments per cell: 352

K562 ATAC: SRR10428394

K562 RNA: SRR10428405

scCAT-seq

Plate based

Theoretically possible, but limited in throughput

>0.25€ per cell

Low;

K562: 176 (ATAC),

74 (RNA)

High;

average genes per cell: 10,173

Average fragments per cell: 212,991

SRP136421

MultiPerturb-seq

Microfluidic

Yes, combination of plate-based and microfluidic indexing

<0.05€ per cell

Not reported

Very low;

average genes per cell: 83

Average fragments per cell: 681

PRJNA1160410

  1. aGenes per cell not reported.
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