{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Elias Bou Samra"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15371"],"description":["Global gene expression profile from skin of variable pigmentation to identify new biological pathways which could be involved in the pigmentation phenotype. We performed a next generation NGS RNA sequencing study on ex vivo epidermis with different levels of pigmentation. We used the ITA   to define skin pigmentation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Library preparation and RNA sequencing Library preparation and RNA-seq were carried out as described in the Illumina TruSeq stranded mRNA User Guide (Illumina inc., San Diego, CA, USA). Briefly, the first step in the workflow involved purifying the poly-A containing mRNA molecules from 600 ng of total RNA using poly-T oligos attached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. The cDNA fragments were then purified with Agencourt AMPure XP beads (Beckman Coulter, Missisauga, Ontario, Canada) and enriched with 13 cycles PCR to create the final cDNA library. cDNA quality was assessed on the TapeStation 2200 (Agilent technologies, Santa Clara, CA, USA) and the library was quantified using the Qbit 3.0 fluorimeter (ThermoFischer Scientific, Canada).","Nucleic Acid Extraction - Epidermis was separated from the dermis using NaBr (1h at 37°C), and RNA was isolated from the epidermis. Total RNA was isolated from the 21 samples with the RNeasy Mini kit (Qiagen, Germantown, MD, USA). Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 NanoLabChip reagent set (Agilent, Palo Alto, CA, USA) and the Nanodrop spectrophotometer.","Sample Collection - ex-vivo skin samples with variable skin color were used for the study. Normal human skin samples were obtained after breast reduction surgery from healthy women living in France","Sequencing - Equimolar amounts of each library were sequenced on a HiSeq 2500 (Illumina Inc., San Diego, CA, USA) instrument, for a 101-nucleotides paired-end sequencing."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Transcript annotation was performed using the Gencode database (v27). Transcript expression quantification was performed from the raw read data (raw counts) using Kallisto (v0.43.1) tool. To generate the normalized signals, raw count values were transformed into TPM (Transcript per Million) using Kallisto tool, or FPKM (Fragments Per Kilobase per Millions reads aligned) using R (v.3.4.0) scripts.","Data Transformation - Quality of raw reads was assessed using the FastQC (v0.11.2) and MultiQC (v1.3) quality control tools. Raw reads were of a very good quality; the scores were systematically located within the 30 to 40 score area."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500","HiSeq 2500 Illumina"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Elias Bou Samra"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq of human ex-vivo skin samples with variable skin color types","description":"Global gene expression profile from skin of variable pigmentation to identify new biological pathways which could be involved in the pigmentation phenotype. We performed a next generation NGS RNA sequencing study on ex vivo epidermis with different levels of pigmentation. We used the ITA   to define skin pigmentation.","dates":{"release":"2025-12-30T00:00:00Z","modification":"2025-12-30T02:02:09.447Z","creation":"2025-07-18T22:19:36.255Z"},"accession":"E-MTAB-15371","cross_references":{"ENA":["ERP176950"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}