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Series GSE189591 Query DataSets for GSE189591
Status Public on Nov 24, 2022
Title m6A sequencing analysis of chicken hepatic mRNA under normal and LPS stimulated conditions
Organism Gallus gallus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Here, the m6A modification patterns in chicken liver at the acute stage of LPS-stimulated inflammation and at the normal state were explored via m6A and RNA sequencing and bioinformatics analysis. A total of 7815 m6A peaks distributed in 5066 genes were identified in the normal chicken liver, and were mostly located in the CDS, 3’UTR region and around the stop codon. At 2 h after the LPS intraperitoneal injection, the m6A modification pattern changed, and showed 1200 different m6A peaks. The hyper- and hypo-m6A peaks were differentially located, with the former mostly located in the CDS region and the later in the 3’UTR and in the region near the stop codon. The hyper- or hypo methylated genes were enriched in different GO ontrology and pathways. Co-analysis revealed a significantly positive relationship between the fold change of m6A methylation level and the relative fold change of mRNA expression. Moreover, protein and protein interaction analysis showed that genes with altered m6A methylation and mRNA expression levels were clustered in processes involved in lipid metabolism, immune response, DNA replication and protein ubiquitination. CD18 and SREBP-1 were the two hub genes clustered in the immune process and lipid metabolism, respectively. Hub gene AGPAT2 was suggested to link the immune response and lipid metabolism clusters in the PPI network. This study presented the first m6A map of broiler chicken liver at the acute stage of LPS induced inflammation. The findings may shed lights on the possible mechanisms of m6A-mediated lipid metabolism disorder in inflammation.
 
Overall design Examination of the m6A modification in hepatic mRNA of boilers under normal and LPS stimulated conditions
 
Contributor(s) Guo F, Zhang Y, Ma J
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Submission date Nov 26, 2021
Last update date Nov 24, 2022
Contact name Yanhong Zhang
E-mail(s) yuhui0906@126.com
Phone 15993051780
Organization name Henan institute of science and technology
Street address 90, Huanlan road
City Xinxiang
State/province Henan
ZIP/Postal code 453003
Country China
 
Platforms (1)
GPL23499 Illumina HiSeq 4000 (Gallus gallus)
Samples (8)
GSM5704241 hepatic mRNA-control 1
GSM5704242 hepatic mRNA-control 2
GSM5704243 hepatic mRNA-LPS 1
Relations
BioProject PRJNA783797
SRA SRP348015

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Supplementary file Size Download File type/resource
GSE189591_4_genes_fpkm_expression.txt.gz 1.7 Mb (ftp)(http) TXT
GSE189591_Control_IPVSControl_input_peak.txt.gz 1.1 Mb (ftp)(http) TXT
GSE189591_Treat_IPVSTreat_input_peak.txt.gz 856.0 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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