{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Juraj Kokavec"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15117"],"description":["This RNA sequencing experiment is part of the study ”Global RNA expression analysis of patient samples identified potential diagnostic biomarkers specific for peritoneal, ovarian and deep endometriosis.” Endometriosis is a chronic, often progressive condition affecting approximately 10% of reproductive-aged women worldwide.. Endometriosis presents with a wide range of manifestations, from asymptomatic lesions discovered incidentally to severe cases. It is primarily classified based on its localization and histopathology, with three main subtypes: superficial peritoneal endometriosis, ovarian endometriosis, and deep endometriosis. Despite its prevalence and impact, diagnosis remains challenging—typically delayed by up to a decade and reliant on invasive procedures such as laparoscopy. Therefore there is a significant need to develop less-invasive and more accurate diagnostic approaches. Here we aimed to complement the existing biomarker landscape by conducting RNA sequencing of endometrial tissue samples from patients with various types of endometriosis (ovarian, deep, and peritoneal) and healthy controls and have identified distinct gene expression profiles across subtypes and revealed notable differences in immune cell composition within the lesions."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - 1µg of DNase I-treated RNA isolated from tissues was used for poly-A mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Paired-end libraries were prepared using the NEBNext Ultra II Directional RNA Library Kit with NEBNext multiplex index oligos for Illumina (Dual Index Primers Set 1) (New England Biolabs).","Nucleic Acid Extraction - Frozen tissues were grinded with mortar and pestle and the total RNA was isolated with Trizol reagent following manufacturer's protocol.","Sample Collection - Endometriotic tissues as well as samples of healthy endometrium were harvested laparoscopically at the time of the operation and immediately flash frozen in liquid nitrogen and stored in deep freeze until processing.","Sequencing - RNA sequencing was performed using the Illumina NovaSeq 6000 platform with NovaSeq 6000 S1 Reagent Kit version 1.5 (total 138 sequencing cycles). Cluster generation and sequencing were conducted using the patterned flow cell technology of the NovaSeq platform. Paired-end sequencing (P7 index: 8 cycles ,P5 index: 8 cycles, Read1: 70 cycles , Read2: 52 cycles) was aimed at an average 30 million reads per library to ensure sufficient read depth and coverage."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Juraj Kokavec","Radoslav Janoštiak"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of human endometrial tissue","description":"This RNA sequencing experiment is part of the study ”Global RNA expression analysis of patient samples identified potential diagnostic biomarkers specific for peritoneal, ovarian and deep endometriosis.” Endometriosis is a chronic, often progressive condition affecting approximately 10% of reproductive-aged women worldwide.. Endometriosis presents with a wide range of manifestations, from asymptomatic lesions discovered incidentally to severe cases. It is primarily classified based on its localization and histopathology, with three main subtypes: superficial peritoneal endometriosis, ovarian endometriosis, and deep endometriosis. Despite its prevalence and impact, diagnosis remains challenging—typically delayed by up to a decade and reliant on invasive procedures such as laparoscopy. Therefore there is a significant need to develop less-invasive and more accurate diagnostic approaches. Here we aimed to complement the existing biomarker landscape by conducting RNA sequencing of endometrial tissue samples from patients with various types of endometriosis (ovarian, deep, and peritoneal) and healthy controls and have identified distinct gene expression profiles across subtypes and revealed notable differences in immune cell composition within the lesions.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2026-01-18T22:49:37.59Z","creation":"2025-05-06T15:50:18.151Z"},"accession":"E-MTAB-15117","cross_references":{"ENA":["ERP172303"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}