|
| Status |
Public on Jul 24, 2016 |
| Title |
BS-seq-hiEndoPC1 |
| Sample type |
SRA |
| |
|
| Source name |
hiMEPs derived from GECs by reprogramming
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiMEPs derived from GECs by reprogramming
|
| Treatment protocol |
GECs, hiMEP-Heps and Fetal-Heps were collected after trypsinized with TrypLE. The hiMEPs were collected by manual picking.
|
| Growth protocol |
GECs were cultured in Kubota's medium. The hiMEPs were reprogrammed from GECs under advanced DMEM/F12 with 2μM Bay K 8644, 0.5μM Bix01294 , 0.04μM RG108, 2μM SB431542, with the support of feeder cells. The hiMEP-Heps were induced from hiMEPs under hepatic differentiation conditions and cultured in hepatocyte medium (Sciencell) with 25 ng/ml HGF (R&D), 1 μM Dexamethasone (Sigma), and 10 ng/ml OSM (R&D).Fetal-Heps were cultured in hepatocyte medium (Sciencell).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA(Qiagen, Cat#: 51306) were extracted according to manufacturer’s instructions.
The DNA was directed to bisulfite conversion using the EZ DNA methylation-Gold kit (Zymo Research) according to the instruction manual. The library was sequenced using illumina Hiseq platform.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Paired-end BS-seq reads were mapped against the reference by Bismark with stringent parameters: -n 2 -l 60 -e 100 -X 600. The overlapped part of paired reads is trimmed from one end to prevent counting twice from the same observation. For each CpG site, the number of CGs and the number of TGs were counted.
5mC level is calculated as the number of CGs divided by the sum of the number of CGs and the number of Tgs.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include 5mC level for each sample. The file "README-BSseq.txt.gz" (available on the series record) contains column header information for the processed data files.
|
| |
|
| Submission date |
Jun 09, 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 |
GPL20301 |
| Series (2) |
| GSE69705 |
Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules [DNA methylation] |
| GSE69706 |
Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules |
|
| Relations |
| BioSample |
SAMN03766265 |
| SRA |
SRX1054538 |
