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| Status |
Public on Feb 10, 2021 |
| Title |
Gene expression profiling in human induced pluripotent stem cell-derived cardiomyocytes(hiPS-CMs) after different topographic substrates stimulation |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: To induce hiPS-CMs maturation by using engineering technics, including culturing on the anisotropic pattern, has been widely explored. However, the underlying mechanisms of the benefits driven by the aligned topographic stimuli are still pending. To obtain insights into the underlying molecular pathways/signaling involved in the facilitation of hiPS-CMs maturation driven by specific topographic stimuli, we performed RNA-seq for the hiPS-CMs samples after culturing on the different patterns
Methods: hiPS-CMs cultured on the flat bottom 24-well plate (MS-80240; Sumilon)/random nanofiber substrate (NanoECM, 2401; Funakoshi)/aligned nanofiber substrate (NanoAligned, 2402; Funakoshi) for one week. Then the cells were harvested as Flat, Random, Align group samples. Total RNA was extracted using the RNeasy Plus mini kit (740990.250; Takara), the concentration of RNA was measured by using NanoDrop (2000/2000c Spectrophotometers, Thermo Fisher). The Illumina package bcl2fastq software was used for base-calling. The raw reads were mapped to the human reference genome sequences (GRCh38) using TopHat ver. 2.1.1 in combination with Bowtie2 ver. 2.3.4.1
Results: The principal component analysis(PCA) analysis revealed that the hiPS-CMs from flat and random patterns showed the most variance. And the differentially expressed genes (DEGs) were detected with theDESeq2 package, showed that the flat group samples occupied most of the enrichment gene expression. The enriched DEGs termed by Gene Ontology(GO) Biological Process revealed that the upregulated genes in flat group are mainly related to the regulation of cell movement, including extracellular matrix organization, cell adhesion, and cell migration. The well-known cardiac maturation markers such as MYH7 and TNNI3 showed significantly upregulated in align group, as well as cardiac structural(MLC2, TNNT2, GJA1), and calcium handling relevant genes( CASQ2, CAMK2B, CAV3) also showed a higher expression than that of in flat group. The most up-regulated gene sets related pathways in align group include cardiac development and heart morphogenesis, negative regulation of binding, and microtubule-based process. In contrast, the relative down-regulated gene enriched pathways in align group are mostly involved in KRT gene family, which also plays a role in cell movement
Conclusions: hiPS-CMs by culturing on the aligned pattern for a short-term have facilitated maturation of hiPS-CMs. The up-regulated gene sets in align group related to regulating cell cycle pathways. The genome-wide expression analysis provided insights into the underlying molecular pathways/signaling involved in the specific topographic stimuli induced maturation of hiPS-CMs
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| Overall design |
mRNA profiles of hiPS-CMs in flat, random, and align patterns
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| Contributor(s) |
Li J, Lee J |
| Citation(s) |
33659246 |
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| Submission date |
Dec 04, 2020 |
| Last update date |
Mar 11, 2021 |
| Contact name |
Jong-Kook LEE |
| E-mail(s) |
jkl.research@gmail.com
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| Phone |
+81-6-6210-8375
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| Organization name |
Osaka University Graduate School of Medicine
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| Department |
Cardiovascular Regenerative Medicine
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| Street address |
2-2 Yamada-oka
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| City |
Suita |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA682636 |
| SRA |
SRP295994 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE162707_gene_RPKM_edgeR_test_A2.xlsx |
3.3 Mb |
(ftp)(http) |
XLSX |
| GSE162707_gene_RPKM_edgeR_test_B.xlsx |
3.4 Mb |
(ftp)(http) |
XLSX |
| GSE162707_gene_RPKM_edgeR_test_C2.xlsx |
3.3 Mb |
(ftp)(http) |
XLSX |
| GSE162707_gene_norm_TCC.xlsx |
4.2 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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