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Sample GSM1707685 Query DataSets for GSM1707685
Status Public on Jul 24, 2016
Title RNA-seq-hiEndoPC-Hep3
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.
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
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
BioSample SAMN03766262
SRA SRX1054532

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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