Project description:Single cell RNA-seq samples from 3 species across a differentiation from induced pluripotent stem cells to neural progenitor cells were generated to study gene expression evolution. Briefly, previously generated urinary stem cell derived iPSCs of 3 human (Homo sapiens) individuals (3 clones), 1 gorilla (Gorilla gorilla) individual (2 clones) and fibroblast derived cynomolgus macaque (Macaca fascicularis) iPSCs of 2 individuals (4 clones) (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). Single cell RNA-seq libraries from differentiation days 0, 1, 3, 5, 7, 9 were generated using mcSCRB-seq protocol (Bagnoli et al. 2018).
Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 7,359 nuclei in gorilla adult testis. This dataset includes three samples from three different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
Project description:RNA sequencing (RNA-seq) was used to annotate chimpanzee, gorilla, gibbon, and marmoset genome and transcript isoforms in adult testis. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
Project description:To compare chromatin accessibility across three primate species, between wild-type (WT) and genetically modified induced pluripotent stem cell (iPSC) lines, and between the iPSC state and neural precursor cells (NPCs) derived from these iPSCs, we generated ATAC-seq data from nine primate samples. The samples included two gorilla WT iPSC samples and one gorilla KRAB-dCas9 iPSC sample (all from the same individual), one orangutan WT iPSC sample, one orangutan KRAB-dCas9 iPSC sample and two orangutan NPC samples (from two different individuals), and one cynomolgus macaque WT iPSC sample and one cynomolgus macaque KRAB-dCas9 iPSC sample (from the same individual). The gorilla and orangutan iPSCs were derived from urinary stem cells (Geuder et al. 2021), while the cynomolgus macaque iPSCs were derived from skin-fibroblasts. The KRAB-dCas9 iPS cell lines were created by stably integrating dox-inducible KRAB-dCas9-HA-P2A-mCherry construct at the AAVS1 locus (Edenhofer et al. 2024). NPCs were obtained by the directed differentiation of iPSCs via dual-SMAD inhibition (Chambers et al. 2009; Ohnuki et al. 2014). ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.