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Dataset View [GSE65364]

SeriesGSE65364
TitleSingle Cell triple omics sequencing reveals genetic and epigenetic heterogeneity in hepatocellular carcinoma
Year2016
CountryChina
ArticlePeng J,Huang Y,Tang F,Wen L,Wu X,Zhu P,Hu B,Li X,Cao C,Guo H,Hou Y.Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas.Cell research.2016 Mar
PMID26902283
Bio ProjectBioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA273802
SraSRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP052901
Overall Desgin6 single human HepG2 cell line cells were sequenced using the newly developed scTrio-seq, other 2 HepG2 cells were sequenced using scRNA-seq and other 2 HepG2 cells were sequenced using scRRBS as technique control. 6 single mouse embryonic stem cells (mESCs) were sequenced using the newly developted scTrio-seq. Meanwhile, two scRNA-seq and two scRRBS were also completed using two mESCs separately. 26 single cells from hepatocellular carcinoma were sequenced using scTrio-seq to analyze the regulation relations between three omics of cancer cells.
SummarySingle cell genome, DNA methylome, and transcriptome sequencing has been achieved separately. However, to analyze the regulation of RNA expression by genetic and epigenetic factors within an individual cell, it is necessary to analyze these omics simultaneously from the same single cell. Here we developed a single cell triple omics sequencing technique- scTrio-seq, to analyze the genome, DNA methylome, and transcriptome concurrently of a mammalian cell.
Experimental ProtocolThe RNA and DNA of each single cell were separated and extracted by Trio-seq.; For RNA seq and genome DNA seq data, we constructed the sequencing libraries using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L). RRBS libraries were constructed using RRBS protocol as described in 2013 (Guo et al. 2013)
Data processingIllumina CASAVA version 1.8 were used to the basecalling.; Adapter sequence and low-quality sequences were trimmed.; For RNA seq data, TopHat (version 2.0.10) were used for sequence alignment to human hg19 genome. Gene expression level (FPKM) were calculated using Cufflinks (version 2.1.1).; For RRBS data, Bismark were used for sequence alignment to human (hg19) genome, and metlevel of each CpG site were calculated manually.; For gDNA seq data, bwa were used for sequence alignment to the human (hg19) genome, and the depth for each 10M window were calculated by summing the sequencing depth of all the positions in each window.; Genome_build: hg19
Illumina CASAVA version 1.8 were used to the basecalling.; Adapter sequence and low-quality sequences were trimmed.; For RNA seq data, TopHat (version 2.0.10) were used for sequence alignment to mouse mm9 genome. Gene expression level (FPKM) were calculated using Cufflinks (version 2.1.1).; For RRBS data, Bismark were used for sequence alignment to mouse mm9 genome, and metlevel of each CpG site were calculated manually.; For gDNA seq data, bwa were used for sequence alignment to the mouse (mm9) genome, and the depth for each 10M window were calculated by summing the sequencing depth of all the positions in each window.; Genome_build: mm9
PlatformGPL11154;GPL16791;GPL17021;GPL20795
Public OnPublic on Mar 01 2016

Cell Groups

Differential Expression Gene List

KEGG GO Others   

Gene SymbolEnsembl IDFDR
RPL8ENSG000001610165.5464767868414e-08
PGK1ENSG000001021446.53623449796027e-08
ID3ENSG000001173186.85259732327368e-08
VTNENSG000001090726.85259732327368e-08
AP5M1ENSG000000537707.0599624790514e-08
MTHFD2ENSG000000659119.87076857277618e-08
TM4SF4ENSG000001699031.08226744199051e-07
CLUENSG000001208851.08226744199051e-07
RARRES2ENSG000001065381.21971805967012e-07
APOC3ENSG000001102451.22407281406746e-07
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