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Sample GSM2039758 Query DataSets for GSM2039758
Status Public on Mar 01, 2016
Title scTrio_HepG2_2_RRBS
Sample type SRA
 
Source name HepG2 cell line
Organism Homo sapiens
Characteristics cell line: HepG2
gender: Male
tissue: hepatocellular carcinoma
Treatment protocol HepG2 cells were digested with trypsin before single cell picking.
Growth protocol The HepG2 cell line were cultured in RPMI 1640 with 10% FBS, and digested with trypsin before single cell picking.
Extracted molecule genomic DNA
Extraction protocol The 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)
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model HiSeq X Ten
 
Description single cell RRBS
Data processing 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
 
Submission date Jan 14, 2016
Last update date May 15, 2019
Contact name Yu Hou
Organization name Peking University
Department School of life sciences
Lab Fuchou Tang
Street address No.5 Yiheyuan Street
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL20795
Series (1)
GSE65364 Single Cell triple omics sequencing reveals genetic and epigenetic heterogeneity in hepatocellular carcinoma
Relations
BioSample SAMN04414116
SRA SRX1531579

Supplementary file Size Download File type/resource
GSM2039758_scTrio_HepG2_2_RRBS.single.CpG.txt.gz 8.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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