{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Grace Hirzel"],"organism":["Junonia coenia"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15925"],"description":["Changes in sensory gene expression may underly seasonal changes in behavior. To accompany other research on seasonal changes in coloration and  behavior  in the seasonally plastic common buckeye butterfly Junonia coenia, we examined how gene expression in eyes differs between wild butterflies caught in summer and fall. We collected animals in 2019, 2020, and 2021 in the central United States. The samples consisted of three males and three females from each season: Summer (June/July) and Fall (late September/October) that had wing colors appropriate for previously described seasonal morphs (i.e. light in summer and dark in fall). We dissected eye tissue from butterfly heads and purified RNA prior to sending samples to Novogene for cDNA Library prep and RNA-Sequencing. We used DESeq2 for subsequent analysis.  We found gene expression correlated to sex, season, and interactions between sex and season.  Eye tissues from dark fall animals and light summer animals exhibit different patterns of expression in many genes including visual system development genes, pigmentation genes, and clock genes. This change in gene expression accompanies changes in basking behavior and wing color and indicates that J. coenia undergoes changes to its visual system depending on the seasonal environment."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - We sent purified RNA samples to Novogene for cDNA library prep (polyA enrichment).","Sequencing - Novogene completed paired-end 150 bp sequencing (NovaSeq PE150 on NovaSeq6000, Illumina) on samples.","Sample Collection - In 2019, 2020, and 2021 we caught wild butterflies in Summer (June/July) and Fall (late September/October) in Arkansas, USA grasslands. Butterflies were caught in the 90 minute period before and after solar noon and were decapitated within 5 minutes of capture. Heads were immediately placed in 1000 μL RNALater (Invitrogen) and placed on ice. We took collected heads back to the lab and stored them at 4° C overnight before transferring to -20° C.","Nucleic Acid Extraction - Tissue was homogenized with mortar and pestle and purified with Nucleopsin minikits (Machery-Nagel)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - We aligned mRNA sequencing reads (~33M-70M per sample) to the  J. coenia transcriptome (Fandino et al., 2024) with the program Salmon (Patro et al., 2017) for downstream differential expression analysis.","Data Transformation - Salmon provided raw counts for later analysis with DESeq2 in R."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Junonia coenia"],"pubmed_title":["Synchronous seasonal plasticity in colouration, behaviour, and visual gene expression in a wild butterfly population"],"pubmed_authors":["Chance Powell","Erica Westerman","Robert Reed","Grace E. Hirzel, Noah K. Brady, Keity J. Farfán-Pira, Chance A. Powell, Robert D. Reed, Erica L. Westerman","Grace Hirzel","Noah Brady"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq of eye tissue from a seasonally plastic temperate butterfly","description":"Changes in sensory gene expression may underly seasonal changes in behavior. To accompany other research on seasonal changes in coloration and  behavior  in the seasonally plastic common buckeye butterfly Junonia coenia, we examined how gene expression in eyes differs between wild butterflies caught in summer and fall. We collected animals in 2019, 2020, and 2021 in the central United States. The samples consisted of three males and three females from each season: Summer (June/July) and Fall (late September/October) that had wing colors appropriate for previously described seasonal morphs (i.e. light in summer and dark in fall). We dissected eye tissue from butterfly heads and purified RNA prior to sending samples to Novogene for cDNA Library prep and RNA-Sequencing. We used DESeq2 for subsequent analysis.  We found gene expression correlated to sex, season, and interactions between sex and season.  Eye tissues from dark fall animals and light summer animals exhibit different patterns of expression in many genes including visual system development genes, pigmentation genes, and clock genes. This change in gene expression accompanies changes in basking behavior and wing color and indicates that J. coenia undergoes changes to its visual system depending on the seasonal environment.","dates":{"release":"2025-10-24T00:00:00Z","modification":"2026-05-31T00:25:20.825Z","creation":"2025-10-24T16:34:17.056Z"},"accession":"E-MTAB-15925","cross_references":{"ENA":["ERP183000"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"],"doi":["10.1111/1365-2435.70215"]}}