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Series GSE188111 Query DataSets for GSE188111
Status Public on Jun 30, 2023
Title Genome-wide transcriptomic profiling of cardiomyocyte differentiation from Wild-type and PERK-KO H1 hESCs [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Cardiac development involves large-scale rearrangements of the proteome. How the developing cardiac cells maintain the integrity of the proteome during the rapid lineage transition remains unclear. Here we show that proteotoxic stress visualized by the misfolded protein aggregates appears during early cardiac differentiation of human embryonic stem cells (hESCs) and is resolved by activation of the PERK branch of the unfolded protein response (UPR). PERK depletion increases misfolded protein accumulation, leading to pluripotency exit defect and impaired mesendoderm specification of hESCs. Mechanistically, we found that PERK safeguards cardiogenesis through its conserved downstream effector ATF4, which subsequently activates a novel transcriptional target WARS1, to cope with the differentiation-induced proteotoxic stress. Our results indicate that protein quality control represents a previously unrecognized core component of the cardiogenic regulatory network. Broadly, these findings provide a framework for understanding how UPR is integrated into the developmental program by activating the PERK-ATF4-WARS1 axis.
Overall design Undifferentiated hESCs cultured in E8 medium were dissociated into single cell suspension by Accutase (Stem Cells Technology, 7920) and reseeded onto Matrigel-coated 24-well plate at a density of 105 cells/per well in E8 medium containing 10 μM Y-27632. When reached ~80% confluence 2-3 days after plating, CM differentiation was initiated by switching to the cardiac differentiation medium (DMEM/F-12 (Gibco, 11330032) supplemented with 50 U ml-1 Penicillin-Streptomycin (Gibco, 15070063), Chemically Defined Lipid Concentrate (1:100, Gibco, 11905031), 10.7 μg ml-1 holo-Transferrin human (Sigma, T0665), 71 μg ml-1 L-Ascorbic acid (Sigma, A8960), 14 ng ml-1 Sodium selenite (Sigma, S5261)) and renewed every day. 5 μM CHIR99021 (Selleck, S1263) and 3 μM IWP2 (Selleck, S7085) was added into the cardiac differentiation medium from days 0-1 and days 2-5, respectively. 3 μg ml-1 Heparin was added into the cardiac differentiation medium from days 1-7. 20 μg ml-1 Insulin (Sigma, 91077C) was added into the cardiac differentiation medium from day 7 onward. The medium was changed daily until day 7 and renewed every 2-3 days from day 7 onward. At day 0, 2 and 6 during the differentiation period, and cells were collected using using the NucleoZol reagent. mRNA libraries were prepared using the VAHTS® mRNA-seq V2 Library Prep Kit for Illumina from Vazyme and sequenced on an Illumina HiSeq 2000 with 150 bp paired-end reads by GENEWIZ.
Contributor(s) Cheng W, Cao N
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Submission date Nov 04, 2021
Last update date Jun 30, 2023
Contact name Weisheng Cheng
Organization name Sun yat-sen University
Street address 2nd Zhongshan Road
City Guangzhou
ZIP/Postal code 510080
Country China
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (36)
GSM5670253 H1_Day0_rep1
GSM5670254 H1_Day0_rep2
GSM5670255 H1_Day0_rep3
This SubSeries is part of SuperSeries:
GSE188123 RNA-seq and ChIP-seq studies of cardiomyocyte differentiation from H1 hESCs
BioProject PRJNA777808
SRA SRP344521

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE188111_RAW.tar 85.9 Mb (http)(custom) TAR (of TXT)
GSE188111_Raw_gene_counts_matrix.txt.gz 2.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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