|
| Status |
Public on May 20, 2019 |
| Title |
hiHep_3D_GFP_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
hiHep organoids which were infected with GFP-Replicate2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiHep hepatocyte-like cells
mutation: GFP_Control
culture time: 16 days
|
| Growth protocol |
hiHep organoids consisted of hiHep cells. Organoids were formed by aggregating 5x105 hiHep cells in 24-well nonattachment plate. Lentiviruses of different oncogenes were transfected to hiHep organoids the time we seeded cells and the second infection was operated 4 days later. We changed half medium every day.hiHep cells were transdifferentiated from UCFs according to the published protocol(Huang, et al, Cell Stem Cell, 2014).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of different groups of hiHep cells was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Sample_R17001343LR01
|
| Data processing |
Low quality reads were trimmed. The remained reads were aligned to the human genome (Ensemble GRCh38.84) using Tophat2
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks using default parameters for gene expression levels
The counts expression profiles were normalized by Cuffnorms
Genome_build: Ensemble GRCh38.84
Supplementary_files_format_and_content: Tab-delimited text files include counts for each sample
|
| |
|
| Submission date |
Jun 15, 2018 |
| Last update date |
May 20, 2019 |
| Contact name |
Lulu Sun |
| E-mail(s) |
sunlulu2014@sibcb.ac.cn
|
| Organization name |
Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
|
| Street address |
320 Yueyang Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE115853 |
Organoids derived from directly reprogrammed human hepatocytes for modeling liver cancer initiation |
|
| Relations |
| BioSample |
SAMN09429662 |
| SRA |
SRX4220855 |
