Skip to main content

Table 1 Transcriptomic approaches for studying stem cells

From: Transcriptomic analysis of pluripotent stem cells: insights into health and disease

Objective Method Reference
DNA sequencing NGS [65]
mRNA expression analysis Microarray [58]
  RNA-seq [93]
miRNA expression analysis Microarray [11]
  RNA-seq [18]
lncRNA expression analysis Microarray [12, 13]
Identification of alternative splicing isoforms Microarray [22, 94]
  RNA-seq [95]
Mapping of protein-DNA binding ChIP-chip [9, 10, 24]
  ChIP-PET [23]
  ChIP-seq [15]
DNA methylation profiling BS-seq [68]
  MethylC-seq [68]
  DIP-seq [16]
Mapping of long-range chromatin interactions ChIA-PET [17]
  3C [29]
Identification of RNA-protein interactions RIP-seq [19]
  RIP and direct RNA quantification [14]
  1. BS-seq, bisulfite sequencing; ChIA-PET, chromatin interaction analysis with paired-end tag sequencing; ChIP-chip, chromatin immunoprecipitation on chip; ChIP-PET, chromatin immunoprecipitation with paired-end tag sequencing; ChIP-seq, chromatin immunoprecipitation and sequencing; DIP-seq, DNA immunoprecipitation and sequencing; MethylC-seq, methylcytosine sequencing; NGS, next-generation sequencing; RIP, RNA-binding protein immunoprecipitation; RIP-seq, RNA-binding protein immunoprecipitation and sequencing; RNA-seq, RNA sequencing; 3C, chromosome conformation capture.