Monkey metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA436633 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 | iProX
Project description:Goal: To identify small RNA associated with the decision of undifferentiated spermatogonia to commit to a pathway of differentiation. Methods: testis small RNA profiles of 6 juvenile wild-type rhesus monkeys (3 vehicle-treated; 3 gonadotropin treated) were generated by deep sequencing, in triplicate, using Ion Torrent. The sequence reads that passed filters were analyzed with miRDeep2, HTSeq counts and edgeR. qRT–PCR validation was performed using SYBR Green assays Results: We mapped about 3 million sequence reads per sample to the rhesus monkey genome (rheMac 2 and rheMac 8.0.1) and identified 932 small RNAs in the testes of wild type monkeys with Bowtie and miRDeep2 workflow. Approximately a combined 7% of unique transcripts showed differential expression between vehicle and gonadotropin treatment for 48 and 96h, with a fold change ≥1.5 and p value <0.05. Altered expression of 12 genes was confirmed with qRT–PCR, substantiating the RNA-seq findings. Conclusions: The testis transcriptome of the juvenile monkey contained 932 non coding smallRNA. Gonadotropin stimulation for 48 h resulted in the commitment of spermatogonia to differentiate and this was associated with the emergence of 51 differentially expressed genes. Funding support: NIH R01 HD072189 to Tony Plant
2019-08-08 | GSE118346 | GEO
Project description:Goal: To identify the genes associated with the decision of undifferentiated spermatogonia to commit to a pathway of differentiation. Methods: testis mRNA profiles of 10 juvenile wild-type rhesus monkeys (3 vehicle-treated; 6 gonadotropin treated) were generated by deep sequencing, in triplicate and quadruplicate, using Illumina NextSeq500. The sequence reads that passed filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We mapped about 45-55 million sequence reads per sample to the rhesus monkey genome (rheMac 8.0.1) and identified 26,813 transcripts in the testes of wild type monkeys with TopHat workflow. Approximately a combined 7% of unique transcripts showed differential expression between vehicle and gonadotropin treatment for 48 and 96h, with a fold change ≥1.5 and p value <0.05. Altered expression of 12 genes was confirmed with qRT–PCR, substantiating the RNA-seq findings. Conclusions: The testis transcriptome of the juvenile monkey contained 15,475 genes of which 15,174 were protein encoding genes or pseudogenes. Gonadotropin stimulation for 48 h resulted in the commitment of spermatogonia to differentiate and this was associated with the emergence of 1587 differentially expressed genes. Funding support: NIH R01 HD072189 to Tony Plant
2017-10-09 | GSE97786 | GEO
Project description:monkey feces microbiota and mild health symptoms
| PRJNA715597 | ENA
Project description:Embryonic stem cells (ESCs) may be able to cure or alleviate the symptoms of various degenerative diseases. However, unresolved issues regarding apoptosis, maintaining function and tumor formation mean a prudent approach should be taken towards advancing ESCs into human clinical trials. The rhesus monkey provides the ideal model organism for developing strategies to prevent immune rejection and test the feasibility, safety and efficacy of ESC-based medical treatments. Transcriptional profiling of rhesus ESCs provides a foundation for future pre-clinical ESC research using non-human primates as the model organism. In this research we use microarray, immunocytochemistry, real-time and standard RT-PCR to characterize and transcriptionally profile rhesus monkey embryonic stem cells. We identify 367 rhesus monkey stemness genes, we demonstrate the high level (>85%) of conservation of rhesus monkey stemness gene expression across five different rhesus monkey embryonic stem cell lines, we demonstrate that rhesus monkey ESC lines maintain a pluripotent undifferentiated state over a wide range of Pou5f1 (Oct-4) expression levels and we compare rhesus monkey, human and murine stemness genes to identify the key mammalian stemness genes. The supplementary tables list the genes that have been upregulated in each undifferentiated rhesus monkey embryonic stem cell line (GSM99998, GSM99999,GSM100000, GSM100001, GSM100002, GSM99965, GSM99966) in comparison analysis with the pooled differentiated embryonic stem cells (GSM99840). Supplemental Table 1 contains the comparison analysis for all 52,865 probe sets on the rhesus monkey gene chip, Supplemental Table 2 contains the rhesus monkey genes that were significantly upregulated (FC>3) in the ORMES-6 biological replicates, Supplemental Table 3 contains the rhesus monkey genes that were significantly upregulated (FC>3) in the pooled differentiated EBs and Supplemental Tables 4-8 represent genes that were significantly upregulated in ORMES 6A, 7, 9, 10 and 13 respectively. Supplemental Table 9 contains the RT-PCR primers used in this project. Keywords: Rhesus monkey embryonic stem cell microarray
2006-08-17 | GSE4446 | GEO
Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
2021-05-17 | PXD023186 | Pride
Project description:PINK1 protein is highly expressed in primate brains. CRISPR-Cas9-mediated depletion of PINK1in fetal and adult monkey brains causes severe neurodegeneration without affecting mitochondrial proteins and morphology.
2022-02-16 | PXD023520 | Pride