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Series GSE136165 Query DataSets for GSE136165
Status Public on Mar 03, 2020
Title Efficient Identification of Multiple Pathways: RNA-Seq Analysis of Livers from 56Fe Ion Irradiated Mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Background: mRNA interactions with each other and other signaling molecules define different biological pathways and functions. Researchers have been investigating various tools to analyze these types of interactions. In particular, gene co-expression network methods have proved useful in finding and analyzing these molecular interactions. Many different analytical pipelines to identify these interactions networks have been proposed with the aim of identifying an optimal partition of the network where the individual modules are neither too small to make any general inference or too large to be biologically interpretable. Results: In this study, we propose a new pipeline to perform gene co-expression network analysis. The proposed pipeline uses WGCNA, a widely used software to perform different aspects of gene co-expression network analysis and modularity maximization algorithm to analyze novel RNA-Seq data to understand the effects of low-dose 56Fe ion irradiation on the formation of hepatocellular carcinoma in mice. The network results along with experimental validation show that using WGCNA combined with Modularity provide a more biologically interpretable network in our dataset. Our pipeline showed better performance than the existing clustering algorithm in WGCNA in finding modules and identified a module with mitochondrial subunits that are supported by mitochondrial complex assay. Conclusions: We present a pipeline that can reduce the problem of parameter selection with the existing algorithm in WGCNA for comparable RNA-Seq datasets which may assist in future research to discover novel mRNA interactions and their downstream molecular effects.
Overall design C57BL16 males were placed into 2 treatment groups and received the following irradiation treatments at Brookhaven National Laboratories (Long Island, NY): 600 MeV/n 56Fe (0.2 Gy), and no irradiation. Left liver lobes were collected at 30, 60, 120, 270, and 360 days post-irradiation, flash frozen and stored at -80°C until they could be processed for RNA-Seq. Livers were sampled by taking two 40-micron thick slices using a cryotome at -20°C. This allowed multiple sampling of the tissue without the tissue going through multiple freeze/thaw cycles. Total RNA was isolated from the liver slices using RNAqueousTM Total RNA Isolation Kit (ThermoFisher Scientific, Waltham, MA) and rRNA was removed via Ribo-ZeroTM rRNA Removal Kit (Illumina, San Diego, CA) prior to library preparation with the Illumina TruSeq RNA Library kit. Samples were sequenced in a paired-end 50 base format on an Illumina HiSeq 1500. Reads were aligned to the mouse GRCm38 reference genome using the STAR alignment program, version 2.5.3a, with the recommended ENCODE options.[34] The -quantMode GeneCounts option was used to obtain read counts per gene based on the Gencode release M14 annotation file.[35] Total number of reads used in analysis varies between 23-35 millions of reads.
Contributor(s) Nia AM, Barnette BL, Ullrich RL, Emmett MR
Citation(s) 32192433, 34769236
Submission date Aug 21, 2019
Last update date Feb 08, 2022
Contact name Anna Nia
Organization name University of Texas Medical Branch
Department Biochemistry and Molecular Biology
Lab Mark R. Emmett
Street address 301 University Blvd
City Galveston
State/province TX
ZIP/Postal code 77555
Country USA
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (30)
GSM4041974 H2
GSM4041975 H3
GSM4041976 H4
BioProject PRJNA561415
SRA SRP219043

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

Supplementary file Size Download File type/resource
GSE136165_Expression_Data.csv.gz 1.4 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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