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Series GSE167193 Query DataSets for GSE167193
Status Public on Jun 06, 2023
Title Next Generation Sequencing Facilitates Quantitative Analysis of transcriptome profiling (RNA-seq) of E17.5 cortex from offspring derived from control and preeclampsia mothers
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) of E17.5 cortexes of offspring from control and preeclampsia mother mice.
Methods: E17.5 cortex mRNA profiles of offspring from control and preeclampsia mother mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the E17.5 cortexes of offspring from control and preeclampsia mother mice with BWA workflow and 34,115 transcripts with TopHat workflow. R
Conclusions: Our study represents the first detailed analysis of E17.5 cortical transcriptomes, with biologic replicates, generated by mRNA-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 tissue. We conclude that mRNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
Overall design E17.5 cortical mRNA profiles of offspring from Control (Con) and preeclampsia (PE) mother mice were generated by deep sequencing, in quadruplication, using HiSeq X Ten
Web link
Contributor(s) Liu X, Zhao W
Citation(s) 37290815
Submission date Feb 22, 2021
Last update date Sep 05, 2023
Contact name Wen-Long Zhao
Organization name The International Peace Maternity and Child Health Hospital
Street address Guangyuan road 145#
City Shanghai
ZIP/Postal code 200030
Country China
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (8)
GSM5098819 Control-cortex-1
GSM5098820 Control-cortex-2
GSM5098821 Control-cortex-3
BioProject PRJNA703836
SRA SRP307465

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Supplementary file Size Download File type/resource
GSE167193_All.counts.txt.gz 451.0 Kb (ftp)(http) TXT
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