{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Lydia Alvarez Fernández"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15373"],"description":["A RPE cell model mimicking a mature RPE was used to investigate the potential anti-inflammatory effects of high-dose zinc supplementation in the context of AMD research. RPE cultures were exposed to inflammatory conditions induced by interleukin 1α (IL-1α) after a 14-day treatment with high doses of zinc. RNA sequencing was employed to examine the relationship between zinc homeostasis and transcriptional changes driven by supplementation and inflammation. By analyzing the effects of different zinc concentrations prior to IL-1α exposure, we explored the role of the Zn-metallothioneins complex in regulating inflammatory responses and cellular function. This study aims to provide valuable insights into potential therapeutic strategies for AMD that target zinc homeostasis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - The RNA of a total of 11 samples (3 biological replicates of each age, except for 25 weeks, with 2 biological replicates) was extracted using RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol","Sample Collection - After removing the culture media, lysis buffer was added on top of the cultures, then lysed cells were transferred to RNase-free eppendorf tubes.","Sequencing - RNA sequencing was performed in BGI Corporation (Beijing Genomics Institute, Shenzhen, China) using the platform BGISEQ-500. 100-bp paired-end reads were generated and the sequencing data were filtered using the software SOAPnuke [1], version v1.5.2 (https://github.com/BGI-flexlab/SOAPnuke), developed by BGI. This software removes the reads containing the adaptor, the reads whose N content is greater than 5% and the low-quality reads (more than 20% bases with Phred threshold score < 10). Alignment was performed using the software HISTAT2 [2] v2.0.4 (http://www.ccb.jhu.edu/software/hisat) to align the clean reads to the reference genome (GCF_000001405.38_GRCh38.p12) and check the quality of data. Bowtie 2 (v2.2.5) (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) [3] and RSEM (v1.2.12) (http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html) [4] were used to carried out the quantitative analysis through the reads count mapping to gene.  [1] Y. Chen et al., “SOAPnuke: a MapReduce acceleration-supported software for integrated quality  control and preprocessing of high-throughput sequencing data.,” Gigascience, vol. 7, no. 1, pp. 1–6, Jan. 2018, doi: 10.1093/gigascience/gix120. [2] D. Kim, B. Langmead, and S. L. Salzberg, “HISAT: a fast spliced aligner with low memory requirements.,” Nat. Methods, vol. 12, no. 4, pp. 357–360, Apr. 2015, doi: 10.1038/nmeth.3317. [3] B. Langmead and S. L. Salzberg, “Fast gapped-read alignment with Bowtie 2.,” Nat. Methods, vol. 9, no. 4, pp. 357–359, Mar. 2012, doi: 10.1038/nmeth.1923. [4] B. Li and C. N. Dewey, “RSEM: accurate transcript quantification from RNA-Seq data with or without a  reference genome.,” BMC Bioinformatics, vol. 12, p. 323, Aug. 2011, doi: 10.1186/1471-2105-12-323.","Library Construction - mRNA enrichment and purification was performed using oligo(dT) coupled to magnetic beads. cDNA library construction involved mRNA fragmentation, cDNA synthesis (generating first-strand cDNA with random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis), end-repair, A-tailing and adapter ligation, followed by PCR amplification, circularization and rolling circle amplification for DNA nanoball (DNB) generation, which harbored more than 300 copies of one molecule."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Data normalization to obtain differentially expressed genes was carried out using the DESeq2 package"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["BGISEQ-500"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_authors":["Lydia Alvarez Fernández"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of primary human fetal RPE cells (hfRPE) treated with IL1α, with and without prior high-dose zinc supplementation, compared to untreated controls","description":"A RPE cell model mimicking a mature RPE was used to investigate the potential anti-inflammatory effects of high-dose zinc supplementation in the context of AMD research. RPE cultures were exposed to inflammatory conditions induced by interleukin 1α (IL-1α) after a 14-day treatment with high doses of zinc. RNA sequencing was employed to examine the relationship between zinc homeostasis and transcriptional changes driven by supplementation and inflammation. By analyzing the effects of different zinc concentrations prior to IL-1α exposure, we explored the role of the Zn-metallothioneins complex in regulating inflammatory responses and cellular function. This study aims to provide valuable insights into potential therapeutic strategies for AMD that target zinc homeostasis.","dates":{"release":"2025-08-14T00:00:00Z","modification":"2025-07-21T11:12:18.737Z","creation":"2025-07-21T11:12:18.737Z"},"accession":"E-MTAB-15373","cross_references":{"ENA":["ERP176990"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0003816","EFO_0004184"]}}