Project description:Indian rhesus macaque major histocompatibility complex (MHC) variation can influence the outcomes of transplantation and infectious disease studies. Frequently, rhesus macaques are MHC genotyped to identify variants that could account for unexpected results. Since the MHC is only one region in the genome where variation could impact experimental outcomes, strategies for simultaneously profiling variation in the macaque MHC and the remainder of the protein coding genome would be useful. Here we determine MHC class I and class II genotypes using target-capture probes enriched for MHC sequences, a method we term macaque exome sequence (MES) genotyping. For a cohort of 27 Indian rhesus macaques, we describe two methods for obtaining MHC genotypes from MES data and demonstrate that the MHC class I and class II genotyping results obtained with these methods are 98.1% and 98.7% concordant, respectively, with expected MHC genotypes. In contrast, conventional MHC genotyping results obtained by deep sequencing of short multiplex PCR amplicons were only 92.6% concordant with expectations for this cohort.

| S-EPMC6790296 | biostudies-literature

mitochondrial 12S rRNA sequences Cynomolgus macaque

Project description:mitochondrial 12S rRNA sequences Cynomolgus macaque

| PRJEB49348 | ENA

Atlas of Cynomolgus Macaque Hematopoiesis

Project description:Self-renewal and differentiation are inherent properties of hematopoietic stem cells that are necessary to support hematopoiesis. However, the underlying mechanisms, especially in human, remain unclear. Here, using the cynomolgus macaque as a surrogate model, we develop a new gating strategy to isolate with high purity transplantable cynomolgus HSCs and generated a single-cell transcriptomic map of cynomolgus HSCs and progenitor cells, that covers the gestational period not analyzed in human. We show that hematopoietic cells from the late-1st to early-3rd trimester fetal liver and late-2nd trimester and thereafter bone marrow has repopulating potential, closely mimicking humans. Unexpectedly however, we found unlike in human, cynomolgus HSCs express CD38 but not CD33, indicating that these cellular counterparts are molecularly distinct. Our transcriptomic analysis reveals the presence of a direct differentiation pathway from HSCs to megakaryocyte lineages, lineage-primed multipotent progenitors and also identified putative HSC surface markers. Taken together, our comprehensive dataset highlights not only the utility of cynomolgus monkeys as model systems to study hematopoiesis but also their potential for translational applications.

2024-04-26 | GSE262140 | GEO

Phased cynomolgus macaque assembly

Project description:High-quality phased assembly of the cynomolgus macaque genome

| PRJEB37906 | ENA

cynomolgus macaque miRNAs

Project description:Characterization of miRNAs distribution in cynomolgus macaque genome using small RNA sequencing

| PRJEB32837 | ENA

Infinium Monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis) RRBS-seq

Project description:Infinium 450K is a hybridization array designed for the human genome, but the relative conservation between the macaque and human genomes makes its use in macaques feasible. We used the Infinium450K array to assay twelve Cynomolgus macaque muscle biopsies and compared it to Reduced Representation Bisulphite Sequencing (RRBS) data generated on the same samples.

2014-06-05 | GSE53593 | GEO

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