biostudies-arrayexpressJoel Martinez-MirallesHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15939Human retinal pigment epithelial (RPE) cells were treated with the sesquiterpene lactones α-cyclocostunolide (α-C) or Grosheimin to investigate their effects on primary cilium structure and associated signaling pathways. Sesquiterpene lactones (SLs) are plant-derived metabolites known for diverse pharmacological activities. Previous studies have shown that certain SLs can alter primary cilium morphology; however, their impact on ciliary signaling remains unclear. This dataset explores the transcriptional changes induced by α-C and Grosheimin in RPE cells. RNA sequencing was performed to identify gene expression changes related to ciliogenesis, microtubule organization, and Hedgehog (Hh) signaling. These data contribute to understanding how structurally distinct SLs modulate ciliary function and may inform future studies on ciliopathies and tumor biology.biostudies-arrayexpressSequencing - Sequencing of the prepared libraries was carried out on an Illumina NextSeq 500 platform using a MID-output flow cell with 150 total cycles, generating paired-end reads of 2 × 75 base pairs. The sequencing run was monitored and analyzed through Illumina’s BaseSpace Seq Hub, which reported excellent data quality metrics. Specifically, 93% of the total bases achieved a Phred quality score of Q30 or higher, indicating highly accurate base calling and minimal sequencing error rates.Sample Collection - RPE cells from two 12-well plates per experimental condition were carefully harvested using a sterile cell scraper. The collected cells were immediately lysed in RLT buffer supplied with the RNeasy Mini Kit (Qiagen, catalog number 74104) to ensure optimal RNA stabilization and preservation for subsequent extraction and downstream molecular analyses.Nucleic Acid Extraction - Samples suspended in RLT buffer were thoroughly vortexed to ensure complete cell lysis and homogenization. The lysates were then purified using column-based RNA extraction according to the manufacturer’s protocol. Following the first cleanup step, samples were treated with RNase-free DNase (Qiagen, catalog number 79254) to remove genomic DNA contamination, then subjected to a second column cleanup to ensure highly pure RNA.Growth Protocol - RPE cells were grown at 37 °C in 5% CO 2 in DMEM/F-12. Media was supplemented with L-glutamine, sodium pyruvate, 10% FBS (Fetal Bovine Serum, Gibco), 100 U/mL penicillin, 100 µg/mL streptomycin, and 3 µg/mL ciprofloxacin (NORMON laboratories). RPE cells were seeded at 70,000 cells/well in 12-well plates, and experiments were performed after 24h. Cilia were induced by incubating cells for 24 h in media supplemented with 0.5% FBS (starvation).Sample Treatment - SLs were administered concurrently with the 0.5% FBS-containing media to the cells, achieving a final working concentration of 10 µM for each compound. As the test compounds were initially prepared as DMSO stock solutions, an equivalent volume of DMSO alone was included as the control condition to account for any potential effects of the solvent.Library Construction - RNA quality and integrity were carefully assessed to confirm suitability for sequencing. A total of 150 ng of RNA from each sample was used to prepare libraries following the Illumina Stranded mRNA Prep Ligation protocol. Libraries were quality-checked using TapeStation DNA High Sensitivity D1000 assay and quantified using Qubit™ DNA HS Assay. Library sizes were approximately 270-290 bp.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - The quality of the raw FASTQ files was assessed using FASTQC. Reads were subsequently aligned to the human reference genome assembly GRCh38/hg38 using the STAR aligner.Data Transformation - After sequencing reads were aligned to the reference genome, first-strand paired-end fragments were quantified for each gene using the featureCounts software. Subsequently, raw fragment counts were normalized to account for sequencing depth and gene length, and Transcripts Per Million (TPM) values were calculated for each gene. These TPM values provided standardized measures of gene expresión.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNAHomo sapiensJoel Martinez-MirallesElena RealesfalseNew insights into the molecular actions of Grosheimin, Costunolide, α- and β- Cyclocostunolide on primary cilia structure and Hedgehog signalingHuman retinal pigment epithelial (RPE) cells were treated with the sesquiterpene lactones α-cyclocostunolide (α-C) or Grosheimin to investigate their effects on primary cilium structure and associated signaling pathways. Sesquiterpene lactones (SLs) are plant-derived metabolites known for diverse pharmacological activities. Previous studies have shown that certain SLs can alter primary cilium morphology; however, their impact on ciliary signaling remains unclear. This dataset explores the transcriptional changes induced by α-C and Grosheimin in RPE cells. RNA sequencing was performed to identify gene expression changes related to ciliogenesis, microtubule organization, and Hedgehog (Hh) signaling. These data contribute to understanding how structurally distinct SLs modulate ciliary function and may inform future studies on ciliopathies and tumor biology.2025-11-20T00:00:00Z2026-05-27T14:06:24.756Z2025-10-30T15:48:11.24ZE-MTAB-15939ERP183406EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969