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Series GSE118542 Query DataSets for GSE118542
Status Public on Aug 01, 2021
Title RNA-seq Quantitative Analysis of Wild Type and Kcnh2-/- day4 cells derived from rESCs
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. To understand how ERG1 executes its function during differentiation, we performed RNA-seq experiments in Kcnh2-/- and wild-type rEBs at day 4
Methods: RNA profiles of day 4 wild type (WT) and Kcnh2-/- rEBs were generated by deep sequencing, in duplicate, using Illumina Hiseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 35 million sequence reads per sample to the rat genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Kcnh2−/− rESC with TopHat workflow. RNA-seq datashows 211 differentially expressed gene with a fold change ≥2 and p value <0.01, in which 109 genes were downregulated and 102 genes were upregulateds.Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.Based on GO enrichment analysis results, the deletion of Kcnh2 resulted in the impaired heart development and cell differentiation by inhibiting the expression of heart related genes. KEGG enrichment analysis of all differentially expressed genes yielded the enrichment for several cell differentiation signaling pathways, like PI3K-Akt signaling pathway and Wnt signaling pathway, which is consistent with the experiment results.
Conclusions: Our study represents the detailed analysis of transcriptomes of Kcnh2-/- vs. WT rat embryonic stem cell, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
Overall design MRNA profiles of day 4 wild type (WT) and Kcnh2-/- rEBs were generated by deep sequencing, in duplicate, using Illumina Hiseq.
Contributor(s) Wang D, Wang Y
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Submission date Aug 14, 2018
Last update date Aug 02, 2021
Contact name Luying Peng
Phone +86-21-65983617
Organization name Tongji University
Department School of Medicine
Lab Key Laboratory of Arrhythmias, Ministry of Education
Street address 1239 Siping Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200092
Country China
Platforms (1)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (4)
GSM3332221 EB4_Kcnh2_WT rep1
GSM3332222 EB4_Kcnh2_WT rep2
GSM3332223 EB4_Kcnh2_KO rep1
BioProject PRJNA485980
SRA SRP157921

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Supplementary file Size Download File type/resource
GSE118542_RAW.tar 2.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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