Biotechnology Letters

, Volume 39, Issue 3, pp 359–366 | Cite as

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

  • Jie WangEmail author
  • Bhaskar Roy
Original Research Paper



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.


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.


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.


Cervical carcinoma Hela cell line LincRNAs RNA-seq 



We are grateful to Bo Li (BGI), Shiping Liu (BGI), Lei Xing (BGI) and Yan Wang (BISU) for a careful modification of the manuscript.

Supporting information

Supplementary Table 1—Summary of RNA-seq data and alignment.

Supplementary Table 2—The matrix of lincRNAs expression quantity in 37 Hela-S3 single cells.

Supplementary Table 3—The information of co-expression modules about 323 lincRNAs.

Supplementary Table 4—The GO and pathway annotation of co-expression modules.

Compliance with ethical standards

Conflict of interest

The authors have declared that they have no conflict of interest.


The authors have no commercial, proprietary, or financial interest in the products or companies described in this article.

Supplementary material

10529_2016_2260_MOESM1_ESM.xlsx (14 kb)
Supplementary Table 1 Summary of RNA-seq data and alignment (XLSX 13 kb)
10529_2016_2260_MOESM2_ESM.xlsx (578 kb)
Supplementary Table 2 The matrix of lincRNAs expression quantity in 37 Hela-S3 single cells (XLSX 577 kb)
10529_2016_2260_MOESM3_ESM.xlsx (16 kb)
Supplementary Table 3 The information of co-expression modules about 323 lincRNAs (XLSX 15 kb)
10529_2016_2260_MOESM4_ESM.xlsx (59 kb)
Supplementary Table 4 The GO and pathway annotation of co-expression modules (XLSX 59 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.BGI Education CenterUniversity of Chinese Academy of SciencesShenzhenChina
  2. 2.BGI-ShenzhenShenzhenChina
  3. 3.BGI Genomics Co. Ltd.ShenzhenChina

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