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| Status |
Public on Aug 28, 2018 |
| Title |
Genome-wide transcriptomic profiling of cardiomyocyte differentiation from human ES cells and iPS cells under exposure to sublethal of isotretinoin (RNA-seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In this study, isotretinoin (INN)-induced alternations in transcriptome during caidiomyocyte differentiation derived from human hESCs and hiPSCs were investigated. H1-hESC and C15-hiPSC were differentiated to caidiomyocytes under exposure to sublethal level of INN, and cells were collected at day 0 (undifferentiated cellsl) day 2 (mesoderm) and day 6 (cardiac progenitors) for genome-wide transcriptomic profiling by RNA-seq.
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| Overall design |
H1-hESC and C15-hiPSC were grown in 12-well plates with Essential 8 medium (Thermo Fisher Scientific), and the cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific) under exposure to 25nM of isotretinoin (INN). At day 0, 2 and 6 during the differentiation period (before the medium-change on that day), and cells were collected using Accutase (Thermo Fisher Scientific), and then store in -80C till RNA isolation. For each cell line and each time-point, cells from two independent differentiation wells were used as two biological replicates. RNA-seq libriries were constructed using ScriptSeq™ v2 RNA-Seq Library Preparation kit (Epicentre Biotechnologies), and then sequenced by a HiSeq 4000 sequencer (Illumina) with 2 X 101 cycles. RNA-seq fastq data were aligned with Tophat (version 2.0.9) to GRCh39/hg19 Homo sapiens reference genome from the UCSC Genome Browser. The human gene symbols and their raw counts were calculated using HTSeq (version 0.6.1p1) package in Python with GRCh39/hg19 Homo sapiens gtf file. Differential gene-expression analysis was performed using edgeR package in R, and the normalization was performed using a trimmed mean of M-values (TMM) method.
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| Contributor(s) |
Liu Q, Snyder M |
| Citation(s) |
30154523 |
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| Submission date |
Aug 20, 2016 |
| Last update date |
Oct 11, 2022 |
| Contact name |
Qing Liu |
| E-mail(s) |
liuqingcell@gmail.com
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| Organization name |
Clemson University
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| Department |
Biological Sciences
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| Lab |
Qing Liu
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| Street address |
Jordan Hall
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| City |
Clemson |
| State/province |
SC |
| ZIP/Postal code |
29634 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (24)
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| This SubSeries is part of SuperSeries: |
| GSE85881 |
ES cells and iPS cells under exposure to sublethal of isotretinoin |
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| Relations |
| BioProject |
PRJNA339624 |
| SRA |
SRP082460 |
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