{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Charlotte Soneson"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15330"],"description":["Accessing endometrial tissue during the early phases of the menstrual cycle is challenging. With this experiment we are capturing the dynamic epithelial cell states after breakdown using endometrial organoids (EOs) subjected to the in vitro menstrual cycle (IVMC) protocol. EOs are collected for scRNAseq analysis before breakdown (Hormonal Withdrawal 48h), 12h after breakdown (Post-breakdown 12h), 24h after breakdown (Post-breakdown 24h), 48h after breakdown (Post-breakdown 48h) as well as 24h (E2 differentiation 24h) and 48h after estrogen treatment (E2 differentiation 48h)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - Endometrial organoid cultures were first dissociated into single cells which were cultured until organoid formation. To mimic the proliferative phase, organoids were then primed with 500 nM β-estradiol (E2) for 48 h followed by treatment with 80 μM progesterone, 100 μg/ml cAMP and 100 mg/ml prolactin in the presence of 500 nM β-estradiol for four additional days to simulate the secretory phase. Hormonal treatment was then withdrawn for 48h, and organoids were collected for scRNAseq (Hormonal Withdrawal 48h).  Organoids were then subjected to mechanical breakdown with automatic (300 times) and manual (100 times) pipetting. Organoid fragments were then replated and maintained without hormones for 48h to simulate the post-breakdown phase. Organoids were collected at post-breakdown 12h, post-breakdown 24h and post-breakdown 48h. Finally, organoids were re-exposed to E2 for another 48h to simulate the transition back to the proliferative phase and they were collected at E2-differentiation 24h and E2-differentiation 48h for scRNAseq.","Sample Collection - Endometrial organoids were derived from biopsies of women in the secretory phase of the cycle undergoing IVF at the Bourn Hall Fertility Clinic with approval from East of England Cambridge Central Research Ethics Committee (17/EE/01551 IRAS 225205). The transfer and use of all the endometrial tissue samples together with the established endometrial organoid cultures for this study are authorized under a Material Transfer Agreements (MTA) between the University of Cambridge and the Friedrich Miescher Institute for Biomedical Research (Agreements No. G119629 and G108313). Endometrial organoids from donors B050, B066 and B080 were used for this experiment.  They were subjected to the in vitro menstrual cycle (IVMC) protocol. Organoids were dissociated into single cells and alive cells were FACS sorted at the following timepoints: before breakdown (hormonal withdrawal 48h), 12h after breakdown (post-breakdown 12h), 24h after breakdown (post-breakdown 24h), 48h after breakdown (post-breakdown 48h). Estrogen was re-introduced, and samples were collected at 24h (E2 differentiation 24h) and 48h after estrogen treatment (E2 differentiation 48h).","Sequencing - Samples were sequenced using Illumina Novaseq S1 2x56bp","Growth Protocol - Endometrial organoids were grown at 37°C in a humidified atmosphere of 5% CO2. They were cultured in Matrigel (Corning, 356231) droplets supplemented with endometrial organoid medium (EOM).  The medium was refreshed every 2-3 days, and the organoids were passaged at an average ratio of 1:3 every 5-7 days. The organoid suspension was centrifuged for 6 minutes at 600×g between passaging steps. The passaged organoid pellet was resuspended in ice cold Matrigel droplets, allowed to solidify at 37°C for 15-30 minutes, and covered with EOM.","Nucleic Acid Extraction - The nucleic acid extraction was performed following the manufacturer's instructions (Chromium Single Cell 3’ v3.1, 10X Genomics)","Library Construction - The libraries were constructed following the manufacturer's instructions (Chromium Single Cell 3’ v3.1, 10X Genomics)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Quantifications from alevin-fry were imported into R using the loadFry() function from the fishpond R package. The 'spliced' and 'ambiguous' counts were added up to form the count matrix.","Sequence Alignment - The human genome sequence (GRCh38.primary_assembly.genome.fa) and transcript annotation (gencode.v38.annotation.gtf) files were downloaded from GENCODE release 38 (https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/). Coordinates for transcripts and introns were extracted from the gtf file using the getFeatureRanges function from the eisaR R package v1.6.0, with arguments featureType = c(\\\"spliced\\\", \\\"intron\\\"), intronType = \\\"separate\\\", flankLength = 50, joinOverlappingIntrons = TRUE, collapseIntronsByGene = TRUE, keepIntronInFeature = TRUE. Sequences for the extracted features were obtained using the extractTranscriptSeqs function from the GenomicFeatures package v1.46.1, and a splici index was generated using Salmon v1.6.0 with the k-mer length set to 23. A feature-to-gene map was created using the getTx2Gene function from the eisaR package, adding an extra column indicating the feature type (spliced or unspliced). scRNA-seq data were quantified using Salmon v1.9.0 and alevin-fry v0.8.0, in USA (unspliced-spliced-ambiguous) mode. alevin-fry was run with parameters `-d fw --knee-distance` (for the generate-permit-list subcommand) and `--resolution cr-like-em --use-mtx` (for the quant subcommand)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Hans-Rudolf Hotz","Margherita Turco","Charlotte Soneson","Konstantina Nikolakopoulou"],"additional_accession":[]},"is_claimable":false,"name":"Single cell RNA sequencing of endometrial organoids in the IVMC protocol","description":"Accessing endometrial tissue during the early phases of the menstrual cycle is challenging. With this experiment we are capturing the dynamic epithelial cell states after breakdown using endometrial organoids (EOs) subjected to the in vitro menstrual cycle (IVMC) protocol. EOs are collected for scRNAseq analysis before breakdown (Hormonal Withdrawal 48h), 12h after breakdown (Post-breakdown 12h), 24h after breakdown (Post-breakdown 24h), 48h after breakdown (Post-breakdown 48h) as well as 24h (E2 differentiation 24h) and 48h after estrogen treatment (E2 differentiation 48h).","dates":{"release":"2026-04-28T00:00:00Z","modification":"2026-04-28T01:01:55.133Z","creation":"2025-07-07T15:26:52.6Z"},"accession":"E-MTAB-15330","cross_references":{"ENA":["ERP174885"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}