biostudies-arrayexpressNils Jonathan TrostCallithrix jacchusscikit-learn (0.20.1), scrublet (0.2), Seurat (4.3.0.1), rliger (1.0.1)Cellranger (6.0.2)https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15025This study used droplet-based snATAC-seq to profile gene expression of 45,103 nuclei in the developing marmoset female and male gonads across several timepoints during development, from gestational day (GD) 92 until 3 weeks after birth (wo). Embryos were collected via hysterotomy. A specialized veterinarian performed all surgical procedures, including anesthesia and analgesia. Additionally, postnatal samples from newborn and 3weeks-old marmoset were collected following euthanasia. Single-cell barcoding and library preparation were performed using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).biostudies-arrayexpressLibrary Construction - Single-cell barcoding and library preparation were performed using Chromium Single Cell 3' Reagent Kits (v3 chemistry) and the Chromium Controller instrument (10x Genomics), following the manufacturer's protocols. The cDNA was amplified using 12 PCR cycles. The Qubit Fluorometer (Thermo Fisher Scientific) was used to quantify the libraries, and the average fragment size was assessed using a Fragment Analyzer.Sequencing - Sequencing of the libraries was carried out on the Illumina NextSeq 500/550 (RRID:SCR_016381; 28 cycles for Read 1, 8 cycles for i7 index, 56 cycles for Read 2).Sample Collection - Frozen tissue was homogenized on ice in a buffer containing sucrose, KCl, MgCl2, Tris-HCl (pH 8), IGEPAL, DTT, Murine RNase Inhibitor, SUPERase-In, and cOmplete Protease Inhibitor Cocktail. The tissue was disrupted by trituration and/or using a micropestle. After a brief incubation, unlysed tissue debris was removed by low-speed centrifugation (100g for 1 minute at 4°C). The supernatant was then centrifuged at 400g for 4 minutes to separate the nuclei (pellet) from the supernatant. Nuclei were washed once or twice in the homogenization buffer and resuspended in a storage buffer containing sucrose, KCl, MgCl2, Tris-HCl (pH 8), Murine RNase Inhibitor, SUPERase-In, and cOmplete Protease Inhibitor Cocktail. If needed, the nuclei were filtered using 40 µm Flowmi strainers. Nuclei concentration was determined by staining with Hoechst DNA dye or propidium iodide and counting on a Countess II FL Automated Cell Counter. Following the nuclei count, approximately 15,000 nuclei from each nuclei suspension were used for generating snRNA libraries. For early marmoset gonad samples (GD74 and GD80), around 5,000 nuclei were use for library generation due to the small size of the gonads at these stages.Nucleic Acid Extraction - RNA was extracted from the cytoplasm extracts or nuclei suspensions by mixing them with RLT buffer (supplemented with 40 mM DTT) and 100% ethanol in a 2:7:5 ratio. The RNA was then purified using the RNeasy Micro Kit from Qiagen. The quality of the extracted RNA was assessed using a Fragment Analyzer (Advanced Analytical), and all samples had RNA quality numbers (RQN) above 8.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Barcodes corresponding to nuclei were distinguished from empty droplets by clustering them by their number of reads and the fraction of intronic UMIs with a Bayesian Gaussian mixture model (using scikit-learn 0.20.1 in python 3.6.6), choosing the cluster with the centroid at the highest fraction of intronic UMIs and largest number of reads. Doublets were removed using scrublet (0.2), keeping barcodes with a doublet score < 0.5. Seurat (4.3.0.1) was used to filter the doublets further, keeping nuclei with at least 300 unique genes expressed, and less than 20,000 UMIs. rliger (1.0.1) was used to normalize and integrate the data following the protocol provided by the author of the package and using default parameters.Sequence Alignment - Raw sequencing data were demultiplexed to fastq format using cellranger mkfastq (6.0.2). The reads were corrected for sequencing errors and aligned to the marmoset genome (CalJac4) using cellranger count (6.0.2) to generate position sorted bam files.UnknownTranscriptomicsGenomicsProteomicsChromium 10xNextSeq 550single nucleus RNA sequencingCallithrix jacchusNils Jonathan TrostfalsesnRNA-seq of developing marmoset female and male gonads across developmentThis study used droplet-based snATAC-seq to profile gene expression of 45,103 nuclei in the developing marmoset female and male gonads across several timepoints during development, from gestational day (GD) 92 until 3 weeks after birth (wo). Embryos were collected via hysterotomy. A specialized veterinarian performed all surgical procedures, including anesthesia and analgesia. Additionally, postnatal samples from newborn and 3weeks-old marmoset were collected following euthanasia. Single-cell barcoding and library preparation were performed using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).2025-06-30T00:00:00Z2025-04-10T16:33:25.313Z2025-04-10T16:33:25.313ZE-MTAB-15025ERP171491E-MTAB-15021E-MTAB-15028E-MTAB-15024EFO_0002944EFO_0004170EFO_0004917EFO_0009809EFO_0005518EFO_0003816EFO_0004184