Virus Dataset Detail

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Dataset Information
Accession GSE67848
Status 2016/9/22
Title Characterization of Type I Interferon pathway during Hepatic Differentiation of Human Pluripotent Stem Cells and hepatitis C virus infection
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Pluripotent stem cells are being actively studied as a cell source for regenerating damaged liver. For long term survival of engrafting cells in the body, not only do the cells have to execute liverspecific function but also withstand the physical strains and invading pathogens. The cellular innate immune system orchestrated by the interferon (IFN) pathway provides the first line of defense against pathogens. The objective of this study is to assess the innate immune function as well as to systematically profile the IFN-induced genes during hepatic differentiation of pluripotent stem cells. To address this objective, we derived endodermal cells (day 5 postdifferentiation), hepatoblast (day 15) and immature hepatocytes (day 21) from human embryonic stem cells (hESC). Day 5, 15 and 21 cells were stimulated with IFN-α and subjected to IFN pathway analysis. Transcriptome analysis was carried out by RNA sequencing. The results showed that the IFN-α treatment activated STAT-JAK pathway in differentiating cells. Transcriptome analysis indicated stage specific expression of classical and non-classical IFNstimulated genes (ISGs). Subsequent validation confirmed the expression of novel ISGs including RASGRP3, CLMP and TRANK1 by differentiated hepatocytes upon IFN treatment. Hepatitis C virus replication in hESC-derived hepatic cells induced the expression of ISGs – LAMP3, ETV7, RASGRP3, and TRANK1. The hESC-derived hepatic cells contain intact innate system and can recognize invading pathogens. Besides assessing the tissue-specific functions for cell therapy applications, it may also be important to test the innate immune function of engrafting cells to ensure adequate defense against infections and improve graft survival.
Samples
GSM ID Sample info Characteristics Description
GSM1657139 day 5 control sample - biological replicate #1 developmental stage:endodermal cells; control or ifn-treated:control; days of differentiation:5 01-day5-Cntrl-1
GSM1657140 day 5 control sample - biological replicate #2 developmental stage:endodermal cells; control or ifn-treated:control; days of differentiation:5 02-day5-Cntrl-2
GSM1657141 day 5 sample stimulated with human interferon-alpha A - biological replicate #1 developmental stage:endodermal cells; control or ifn-treated:IFN-treated; days of differentiation:5 03-day5-IFN-1
GSM1657142 day 5 sample stimulated with human interferon-alpha A - biological replicate #2 developmental stage:endodermal cells; control or ifn-treated:IFN-treated; days of differentiation:5 04-day5-IFN-2
GSM1657143 day 15 control sample - biological replicate #1 developmental stage:post differentiation hepatoblast; control or ifn-treated:control; days of differentiation:15 05-day15-Cntrl-1
GSM1657144 day 15 control sample - biological replicate #2 developmental stage:post differentiation hepatoblast; control or ifn-treated:control; days of differentiation:15 06-day15-Cntrl-2
GSM1657145 day 15 sample stimulated with human interferon-alpha A - biological replicate #1 developmental stage:post differentiation hepatoblast; control or ifn-treated:IFN-treated; days of differentiation:15 07-day15-IFN-1
GSM1657146 day 15 sample stimulated with human interferon-alpha A - biological replicate #2 developmental stage:post differentiation hepatoblast; control or ifn-treated:IFN-treated; days of differentiation:15 08-day15-IFN-2
GSM1657147 day 21 control sample - biological replicate #1 developmental stage:immature hepatocytes; control or ifn-treated:control; days of differentiation:21 09-day21-Cntrl-1
GSM1657148 day 21 control sample - biological replicate #2 developmental stage:immature hepatocytes; control or ifn-treated:control; days of differentiation:21 10-day21-Cntrl-2
GSM1657149 day 21 sample stimulated with human interferon-alpha A - biological replicate #1 developmental stage:immature hepatocytes; control or ifn-treated:IFN-treated; days of differentiation:21 11-day21-IFN-1
GSM1657150 day 21 sample stimulated with human interferon-alpha A - biological replicate #2 developmental stage:immature hepatocytes; control or ifn-treated:IFN-treated; days of differentiation:21 12-day21-IFN-2
Platform GPL16791  : Illumina HiSeq 2500 (Homo sapiens)
Literature 26702414  26313525  
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* p<0.05 ** p<0.01