|
| Status |
Public on Mar 01, 2016 |
| Title |
scTrio_HepG2_1_RNA |
| 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 |
total RNA |
| 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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
single cell RNA seq
|
| 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 |
SAMN04414113 |
| SRA |
SRX1531576 |
