Project description:This study is a high-level comparison of the embryonic brains of Homo sapiens, Macaca mulatta, and Mus musculus using scRNA-seq. This submission includes the novel Macaca mulatta scRNA-seq generated for this study between PCD40 and 100. The supplementary h5ad file contains the meta-atlas including processed data from all 3 species, with annotations from the publication.
Project description:Changes in gene transcription regulation are necessary for species to respond to changes in their environment. In particular, host-pathogen dynamics have been observed to entail rapid evolution of genes involved in the host innate immune system. Cytokines such as type I interferon alpha and beta trigger an antiviral cellular state controlled by members of the transcription factor families STAT and IRF. However, it remains poorly understood how gene transcription regulation has been rewired through evolutionary time to achieve species-specific interferon-controlled changes in gene expression. We generated nascent transcription (PRO-seq) datasets to determine the initial transcriptional response on lymphoblastoid cell lines derived from homo sapiens and macaca mulatta upon stimulation with interferon alpha2 to assess species-specific changes in gene regulation.
Project description:MicroRNAs are small non-coding RNAs that are critical in post-transcriptional regulation. According to the latest miRBase (v22), there are 617 annotated pre-miRNAs in Macaca mulatta, which is much less than 1917 in human, although both of these two species are primates. To improve the annotation of miRNAs in Macaca mulatta, we generated 12 small RNA profiles from 8 tissues and perform comprehensive analysis of these profiles. We identified 613 conserved pre-miRNAs that have not been reported in Macaca mulatta and 25 novel miRNAs. Furthermore, we identified 996 editing sites with significant editing levels from 250 pre-miRNAs after analyzing the 12 self-generated and 58 additional published sRNA-seq profiles from different types of organs or tissues. Our results show that the distribution of different miRNA editing types in Macaca mulatta is different from that in human brains. Particularly, there are much more small indel events in miRNAs of Macaca mulatta than in human brains. These results significantly increase our understanding of miRNAs and their editing events in Macaca mulatta.
Project description:Homo sapiens and Macaca fascicularis neural progenitor cell lines were transduced with a lentiviral MPRA (Massively Parallel Reporter Assay) library. MPRA barcode sequencing and RNA-seq was performed on the extracted RNA. RNA-seq data was used to confirm transcription factor expression.
Project description:Homo sapiens and Macaca fascicularis neural progenitor cell lines were transduced with a lentiviral MPRA (Massively Parallel Reporter Assay) library. MPRA barcode sequencing and RNA-seq was performed on the extracted RNA. MPRA data was used to compare activity of regulatory sequences across 75 mammalian species with a focus on primates and correlate these activities with the Phenotype of gyrencephaly.
Project description:Transposable elements (TE) account for more than 50% of human genome. It has been reported that some types of TEs are dynamically regulated in the reprogramming of human cell lines. However, it is largely unknown whether some TEs in Macaca mulatta are also regulated during the reprogramming of cell lines of monkey. Here, we systematically examined the transcriptional activities of TEs during the conversion of Macaca mulatta fibroblast cells to neuroepithelial stem cells (NESCs). Hundreds of TEs were dynamically regulated during the reprogramming of Macaca mulatta fibroblast cells. Furthermore, 60 Long Terminal Repeats (LTRs), as well as some integrase elements, of MacERV3 were transiently activated during the early stages of the conversion process. These LTRs were potentially bound by critical transcription factors for reprogramming, such as KLF4 and ETV5. These results suggest that the transcription of TEs are delicately regulated during the reprogramming of Macaca mulatta fibroblast cells. Although the family of ERVs activated during the reprogramming of fibroblast cells in Macaca mulatta are different from those in the reprogramming of human fibroblast cells, our results suggest that the activation of some ERVs is a conserved mechanism in primates for converting fibroblast cells to stem cells.
Project description:Homo sapiens fresh whole blood was infected with Candida parapsilosis. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Homo sapiens gene expression.
Project description:Homo sapiens fresh whole blood was infected with Candida albicans SC5314. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
