Single-cell RNA-seq reveals lincRNA expression differences in Hela-S3 cells

Biotechnol Lett. 2017 Mar;39(3):359-366. doi: 10.1007/s10529-016-2260-7. Epub 2016 Nov 23.


Objective: To characterize transcriptome-wide lincRNAs of Hela-S3 cell line by analyzing RNA sequencing data to provide a foundation for further functional verification and clinical application of cervical carcinoma development.

Results: Single-cell RNA sequencing data of 37 Hela-S3 cells were analysed. On average, 511 lincRNAs were expressed in each cell. Comparing the expression difference of the lincRNAs and protein-coding genes, we found that lincRNAs expression displayed more cell specificity than that of protein-coding genes (t-test, P<2.2E-16). In co-expression network analysis, we identified seven modules and one of them was enriched in pathways of mitotic, packaging of telomere ends, and chromosome maintenance.

Conclusion: incRNAs are specifically expressed and form a network to perform function at single cell level. Their expression was more specific than that of protein-coding genes.

Keywords: Cervical carcinoma; Hela cell line; LincRNAs; RNA-seq.

MeSH terms

  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic*
  • Gene Regulatory Networks
  • HeLa Cells
  • Humans
  • Open Reading Frames / genetics
  • RNA, Long Noncoding / genetics*
  • RNA, Long Noncoding / metabolism
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*


  • RNA, Long Noncoding