Supporting data for "Full-length single cell RNA-seq applied to a viral human cancer: Applications to HPV expression and splicing analysis in HeLa S3 cells".

Dataset type: Transcriptomic
Data released on November 09, 2015

Wu L; Zhang X; Zhao Z; Wang L; Li B; Li G; Dean M; Yu Q; Wang Y; Lin X; Rao W; Mei Z; Li Y; Jiang R; Yang H; Li F; Xie G; Xu L; Wu K; Zhang J; Chen J; Wang T; Kristiansen K; Zhang X; Li Y; Yang H; Wang J; Hou Y; Xu X (2015): Supporting data for "Full-length single cell RNA-seq applied to a viral human cancer: Applications to HPV expression and splicing analysis in HeLa S3 cells". GigaScience Database. http://dx.doi.org/10.5524/100160

DOI10.5524/100160

Viral infection causes multiple forms of human cancer, and human papillomavirus (HPV) infection is the primary factor in cervical carcinomas. Single-cell RNA-seq studies highlight the tumor heterogeneity of most cancers, but virally induced tumors have not been studied. HeLa is a well characterized HPV+ cervical cancer cell line. We developed a new high-throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip. Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells, 40 of which were randomly selected to perform single-cell RNA sequencing. On the basis of this data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in terms of gene expression, alternative splicing, and gene fusions. Furthermore, by co-expression analysis we can identify a high diversity of HPV-18 gene expression and splicing at the single-cell level. In addition to providing a characterization of the transcriptome of HeLa S3 cells at the single-cell level, our study demonstrates the power of single-cell RNA-seq analysis of virally infected cells and cancers.

Additional details

Read the peer-reviewed publication(s):

Wu, L., Zhang, X., Zhao, Z., Wang, L., Li, B., Li, G., … Xu, X. (2015). Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells. GigaScience, 4(1). doi:10.1186/s13742-015-0091-4

Accessions (data included in GigaDB):

BioProject: PRJNA301652





File NameSample IDData TypeFile FormatSizeRelease Date 
Expression dataEXCEL1.01 MB2015-11-09
Expression dataEXCEL5.72 MB2015-11-09
TextTEXT0.88 KB2015-11-09
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Date Action
November 9, 2015 Dataset publish
November 9, 2015 Dataset size updated from : 104857600 bytes
December 4, 2015 Manuscript Link added : 10.1186/s13742-015-0091-4
December 4, 2015 Link added : BioProject:PRJNA301652
December 4, 2015 Additional file HeLa.PE.expression.merge.xls.gz added
December 4, 2015 Additional file HeLa.SE.expression.merge.xls.gz added
December 4, 2015 Additional file README.txt added