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Table 1 Overview of genome-wide high-throughput sequencing-based single-cell technologies

From: 4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?

Technology (single cell)

Information

Throughput (no. cells)

Strength

Limitation

Ref.

Year

RNA sequencing

Transcriptome

High (>1000)

Resolution

Low mRNA detection limit

[45, 46]

2009

Amplification bias

In situ RNA sequencing

Transcriptome with RNA localization

High (>1000)

Colocalization of locus and transcript

Time-consuming

[91, 92]

2014

Abundance of rRNA transcripts

Selective towards active gene

ChIP sequencing

Protein association with the genome

High (>1000)

Reduced cost of ChIP assay

Antibody-dependent

[40]

2015

Data sparsity/low coverage

Hi-C

Global chromatin contact maps

Low (<100)

Global view of the genome

Data sparsity/low coverage

[35]

2013

DamID

Lamina-associated domains

Medium (<200)

No need for antibody

Proximity assay

[36]

2015

    

Relative low resolution

  

ATAC sequencing

Genome accessibility

Medium (<500)

Resolution

Recovery of ATAC-seq DNA fragments

[38, 39]

2015

Bisulfite sequencing (BiS)

DNA methylation

Medium (<400)

Base resolution

DNA amplification before bisulfite conversion

[41, 43]

2014

Cost

Reduced-representation BiS

DNA methylation

Low (<100)

Sensitivity

Low coverage

[42, 44]

2013

  1. Abbreviations: ATAC assay for transposase-accessible chromatin, ChIP chromatin immunoprecipitation, rRNA ribosomal RNA