|
| Status |
Public on Feb 12, 2017 |
| Title |
VK2-2 |
| Sample type |
SRA |
| |
|
| Source name |
hESCs-derived hepatocytes with VK2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ESC-derived hepatocytes
treatment: VK2
|
| Treatment protocol |
hESCs-derived hepatocytes were treated with 10 μM SB203580 or 50μM Vitamin K2.
|
| Growth protocol |
Human ESCs were passaged with Accutase (Sigma) and plated at a density of 100,000 cells/cm2 in mTeSR with 10 μM Y27632 (Selleck) on Matrigel (BD), Laminin (BD), and collagen IV (BD) (3:1:1) mixed gel coated-plate (Corning). In the restriction of definitive endoderm (DEs) stage (S1), cells were cultured for 24 hrs in RPMI with B27 supplement (1:50, Gibco), 100 ng/ml Activin A and 3 μM CHIR99021, and then treated with 100 ng/ml Activin A for 2 days. In the hepatic specification stage to get hepatic stem cells (S2), the culture medium was replaced with RPMI (Gibco) supplemented with B27 supplement (1:50), 20 ng/ml BMP4 and 10 ng/ml FGF2 for 5 days. And in stage III of hepatic maturation, cells were cultured in Hepatocyte Culture Medium (HCM, Lonza) with 20 ng/ml HGF, 10 ng/ml OSM and 1 μM dexamethasone for 10-15 days. During stages II and III, cells are fed every 48 hr. The final stage was also carried out with 10 μM SB203580 (Selleck) or 50μM Vitamin K2 (Sigma).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA (Qiagen, Cat#: 74004) were extracted according to manufacturer’s instructions.
mRNA was reverse transcribed and amplified by REPLI-g Single Cell Kit (cat#. 150063). The library was sequenced using Illumina Hiseq platform.
|
| |
|
| 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 raw read counts of each gene for each sample
|
| |
|
| Submission date |
Dec 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinhua Qin |
| E-mail(s) |
qinjinhuarhea@126.com
|
| Organization name |
Beijing Institute of Transfusion
|
| Street address |
Taiping Road
|
| City |
Beijing |
| ZIP/Postal code |
100850 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE76098 |
Connexin 32-mediated cell-cell communication is essential for hepatic differentiation from human embryonic stem cells |
|
| Relations |
| BioSample |
SAMN04348500 |
| SRA |
SRX1488627 |
