Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 22,032 nuclei in the developing marmoset female and male gonads across several timepoints during development, from gestational day (GD) 74 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 3 weeks-old marmoset were collected following euthanasia. Single-cell barcoding and library preparation were performed using Chromium Single Cell 3' Reagent Kits (v3 chemistry) and the Chromium Controller instrument (10x Genomics). Sequencing of the libraries was carried out on the Illumina NextSeq 500/550 and initial data processing was performed using Cellranger.
Project description:This 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).
Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 22,032 nuclei in the developing human female and male gonads across several timepoints during prenatal development, from Carnegie Stage (CS) 17 until 21 weeks post conception (WPC). For most timepoints the study includes two biological replicates for each sex. Additionally, the study includes three technical replicates of a Klinefelter Syndrome (XXY karyotype) testis sample at 13WPC. Human prenatal tissue samples were provided by the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR) and obtained from elective terminations of pregnancy. The samples were classified according to a particular Carnegie stage or week post conception based on their external physical appearance and measurements. 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).
Project description:This study used droplet-based snRNA-seq to profile the gene expression of 127,371 nuclei in the developing human female and male gonads across eleven timepoints, from Carnegie Stage (CS) 14 until 21 weeks post conception (WPC). For most timepoints the study includes two biological replicates for each sex. Additionally, the study includes three technical replicates of a Klinefelter Syndrome (XXY karyotype) testis sample at 13WPC. Human prenatal tissue samples were provided by the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR) and obtained from elective terminations of pregnancy. The samples were classified according to a particular Carnegie stage or week post conception based on their external physical appearance and measurements. Single-cell barcoding and library preparation were performed using Chromium Single Cell 3' Reagent Kits (v3 chemistry) and the Chromium Controller instrument (10x Genomics). Sequencing of the libraries was carried out on the Illumina NextSeq 500/550 and initial data processing was performed using Cellranger.
Project description:Single cell transcriptomic analyses are increasingly being employed to study human developmental processes in the gonad to advance our understanding of human gametogenesis. However, to date, these analyses have primarily focused on germ cells, while the somatic niche has been largely overlooked. Moreover, a comparative transcriptomic analysis of both female and male early gonad development on the single cell level is currently lacking. We performed single cell RNA-Seq on whole human fetal gonads from first and second trimester, both from male and female. We define gene expression profiles, which include novel marker genes, of major gonadal somatic cell types and validate them on the protein level. We identify the genetic signature of early human male rete cells, both in male and in female gonads. Overall, our study provides an in-depth molecular characterization of both male and female somatic cell types in early fetal gonads.
Project description:We used deep sequencing to characterize 3 families of sRNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and focused on the sRNA fraction present in both male and female gonads. Of the sequences detected in the testes, 2.6% of piRNAs, 9% of miRNAs, and 10% of tRFs were also present in the ovaries. Notably, the majority of the shared piRNAs mapped to the introns of ribosomal RNAs and were derived from clustered loci. In addition, the most abundant miRNAs present in the ovaries and testes are conserved and are involved in many biological processes such as the regulation of homeobox genes, the control of cell proliferation, and carcinogenesis. Unexpectedly, we detected a novel sRNA type, the tRFs, which are 30–36-nt RNA fragments derived from tRNA molecules, in gonads