 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 12, 2017 |
| Title |
hHep |
| Sample type |
SRA |
| |
|
| Source name |
induced hHep
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hESCs-derived hepatic lineage cells
|
| Treatment protocol |
infected with HCVcc
|
| Growth protocol |
hESC H9 cells were passaged and grown for 1 day in MTeSR (Stem Cell), then cultured in KM (23) with Activin A (100 ng/ml) and Wnt3a (50 ng/ml) for 4 days to induce cells to definitive endoderm (DE) cells. The DE cells were differentiated in HM, Wnt3a (50 ng/ml), FGF4 (30 ng/ml), retinoic acid (RA, 0.1 μM) for 6 days to achieve lineage restrictions to hHpSCs. The hHBs were obtained by treating the hHpSCs with the HM, FGF4 (30 ng/ml), BMP4 (25 ng/ml) and HGF (25 ng/ml) for another 6 days. Finally differentiation to hepatocytes was achieved with HM with HGF (25 ng/ml), OSM (10 ng/ml) and dexamethasone (Dex, 0.1 μM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA (Qiagen, Cat#: 74004) were extracted according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.The library was sequenced using Illumina HiSeq X ten.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Paired-end reads were mapped against the UCSC GRCh38 reference by Tophat with stringent parameters: --coverage-search --microexon-search --b2-very-sensitive. Only unique mapping reads were retained for normalization purposes. Read counts of each gene were summarized using HTSeq version 0.6.1p1. DESeq2 was used to normalize read counts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts of each gene for each sample
|
| |
|
| Submission date |
Jul 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
yi wang |
| E-mail(s) |
lisa7825@163.com
|
| Phone |
861066931545
|
| Organization name |
Beijing Institute of Transfusion Medicine
|
| Street address |
27(9) Taiping Road
|
| City |
Beijing |
| ZIP/Postal code |
100850 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE101133 |
Human ES Cell-derived Hepatoblasts are an Optimal Lineage Stage for HCV Infection |
|
| Relations |
| BioSample |
SAMN07341754 |
| SRA |
SRX2995217 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
