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Series GSE208778 Query DataSets for GSE208778
Status Public on Jul 03, 2023
Title Reduced representation bisulfite sequencing of equine sarcoid andhorse skin samples
Organism Equus caballus
Experiment type Methylation profiling by high throughput sequencing
Summary DNA methylation is a key mechanism in transcription regulation, and aberrant methylation is a common and important mechanism in tumor initiation, maintenance, and progression. To find genes that are aberrantly regulated by altered methylation in horse sarcoids, we used reduced representation bisulfite sequencing (RRBS) accompanied by RNA sequencing (RNA-Seq) for methylome (whole genome DNA methylation sequencing) and transcriptome profiling, respectively. We found that the DNA methylation level was generally lower in lesion samples than in controls. In the analyzed samples, a total of 14,692 differentially methylated sites (DMSs) in the context of CpG (where cytosine and guanine are separated by a phosphate), and 11,712 differentially expressed genes (DEGs) were identified. The integration of the methylome and transcriptome data suggests that aberrant DNA methylation may be involved in the deregulation of expression of the 493 genes in equine sarcoid. Furthermore, enrichment analysis of the genes demonstrated the activation of multiple molecular pathways related to extracellular matrix (ECM), oxidative phosphorylation (OXPHOS), immune response, and disease processes that can be related to tumor progression. The results provide further insight into the epigenetic alterations in equine sarcoids and provide a valuable resource for follow-up studies to identify biomarkers for predicting susceptibility to this common condition in horses.
Overall design RRBS sequencing of 12 equine tissues and 12 skin controls was performed using the Illumina NextSeq 500/550 platform.
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Contributor(s) Semik-Gurgul E, Szmatoła T, Pawlina-Tyszko K, Gurgul A
Citation(s) 37211255
Submission date Jul 21, 2022
Last update date Jul 04, 2023
Contact name Ewelina Semik-Gurgul
Organization name National Research Institute of Animal Production
Department Department of Animal Molecular Biology
Lab Laboratory of Genomics
Street address Krakowska 1
City Balice
ZIP/Postal code 32083
Country Poland
Platforms (1)
GPL21401 Illumina NextSeq 500 (Equus caballus)
Samples (24)
GSM6369220 sc65L
GSM6369221 sc67L
GSM6369222 sc71L
BioProject PRJNA860988

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE208778_RAW.tar 649.9 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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