|
| Status |
Public on Jul 24, 2016 |
| Title |
RNA-seq-hiEndoPC3 |
| 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 |
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 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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. The "README.txt" file on the series record contains annotations for the processed data file.
|
| |
|
| 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 |
GPL16791 |
| Series (2) |
| GSE58557 |
Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules [gene expression] |
| GSE69706 |
Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules |
|
| Relations |
| BioSample |
SAMN03766257 |
| SRA |
SRX1054527 |
