|
Status |
Public on Jul 24, 2016 |
Title |
RNA-seq-hiEndoPC-Hep2 |
Sample type |
SRA |
|
|
Source name |
hepatoctes induced by differentiation of hiMEPs
|
Organism |
Homo sapiens |
Characteristics |
cell type: hepatoctes induced by differentiation of hiMEPs
|
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.
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|
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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.
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|
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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 |
SAMN03766261 |
SRA |
SRX1054531 |