Silk-Ovarioids: Establishment and characterization of human ovarian primary cells 3D-model system

The samples in the dataset are connected to a study focusing on establishment of a long-term stable three-dimensional (3D) model of human primary ovarian cells for toxicological research. These samples are collected from patients undergoing elective abdominal surgery. The cortex and medulla were separated and dissociated into single-cell suspension using mechanical and enzymatic methods, followed by culture in 2D and 3D systems. In total 75 samples are included in the dataset (36 samples from cortex and 39 from medulla). Among these samples, 29 tissue samples were used as reference in the comparison of 2D culture vs tissue and 3D culture vs tissue. 16 samples from 2D culture were used as the reference in the comparison of 3D vs 2D. The rest 30 samples were from 3D culture (Silk-Ovarioid). RNA extraction of tissues and 2D cultured cells was performed using RNeasy Mini Kit (Qiagen, Germany). Total RNA of Silk-Ovarioids samples was extracted using RNeasy Micro Kit (Qiagen, Germany). Only samples with RIN values > 9 were used for library preparation. Libraries were prepared using Illumina Stranded mRNA Prep Ligation protocol (Illumina, USA) using 10 ng RNA as input. Pooled libraries were sequenced on Illumina NovaSeq 6000 platform. Fastq files were mapped to human genome GRCh38 using STAR (version 2.7.10b). subread package (version 2.0.1) was used to align the bam files using featureCount function. After import the raw data matrix into Rstudio, technical replicates were collapsed using DESeq2 collapseReplicates function. GRCh38 (Homo_sapiens.GRCh38.108.chr.gtf) was used for mapping and alignment. The dataset consists of 150 files in fastq format, compressed with GNUzip (gzip), one file in txt format and one file in xlsx format. The total size of the dataset is approximately 400 GB.