|
| Status |
Public on May 20, 2019 |
| Title |
ProliHH organoid_c-MYC |
| Sample type |
SRA |
| |
|
| Source name |
ProliHH organoids which were transfected with c-MYC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: proliferating hepatocytes
culture time: Cultured primary hepatocytes
mutation: c-MYC over-expression
culture time: 10d
|
| Treatment protocol |
ProliHH organoids were transfected with c-MYC and RAS oncogenes following the same protocol of transfection in hiHep organoids.
|
| Growth protocol |
ProliHH organoids were cultured following the published protocol (Zhang et al, Cell Stem Cell, 2018).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of different groups of ProliHH 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_R18065338LR01-L577
Genes.counts-ProliHH organoids.txt
|
| 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: Genes.counts-ProliHH organoids.txt: Counts for each sample (without running and mapping together with hiHep organoids)
|
| |
|
| Submission date |
Jan 09, 2019 |
| 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 |
SAMN10719980 |
| SRA |
SRX5236303 |
