characteristics.text: 2025-11-20
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Hospital del Mar Research Institute
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS27170564
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-15939:Sample 6
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: hTERT-RPE1 
characteristics.characteristic: cell line
characteristics.text: Retinal pigment epithelium cell
characteristics.characteristic: cell type
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: 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. Not applicable. 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).  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. Raw sequencing data was generated in BCL (binary base call) format on the Illumina NextSeq 500. These BCL files were converted into FASTQ format using Illumina's BaseSpace Seq Hub. This process included base calling, filtering by quality and length, trimming of adapters, and de-multiplexing based on the unique indices of each sample. 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. 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.
characteristics.characteristic: description
characteristics.text: normal
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Retinal pigment epithelium
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: Sample 6
characteristics.characteristic: title