Project description:We compared gene expression patterns between the occipital cortex tissues of four male and four female individuals in three species: an ape (human, Homo sapiens), an Old World monkey (macaque; Macaca fascicularis), and a New World monkey (marmoset; Callithrix jacchus). To do so, we hybridized cDNA from each sample (n = 24) to a human cDNA microarray that contains 46,128 probes. (Human 46k cDNA, http://www.biotech.kth.se/molbio/microarray/). We used a loop hybridization study design restricted to within-species comparisons only, in which we co-hybridized on each slide samples from the opposite sex.
Project description:Though the rhesus monkey is one of the most valuable non-human primate animal models for various human diseases because of its manageable size and genetic and proteomic similarities with humans, proteomic research using rhesus monkeys still remains challenging due to the lack of a complete protein sequence database and sufficient proteomic information. In this project, proteomic profiling of multiple organ tissues, 9 male and 11 female were performed in an automated, high-throughput manner employing annotated UniProtKB human database. Based on the success of this alternative interpretation of MS data, the list of proteins identified from total 12 organs of male and female subjects will benefit future rhesus monkey proteome research.
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
Project description:Experiment with 32 hybridizations, using 16 samples of species [Homo sapiens], using 32 arrays of array design [Affymetrix Custom Array - NuGO_Hs1a520180], producing 32 raw data files and 1 transformed and/or normalized data files.
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.
Project description:Experiment with 6 hybridizations, using 30 samples of species [Homo sapiens], using 6 arrays of array design [Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]], producing 6 raw data files and 6 transformed and/or normalized data files.
Project description:Search for SNPs associated with the pharmacogenomic profile of Benzidazole adverse reactions in Chagas Disease Homo sapiens patients.
Project description:Five HCMV (+) CRC tissues detected by PCR were selected for RNA-seq. GEPs were pre-processed by Cutadapter and FastQC to remove jointed reads and low-quality reads. Tophat (v.2.0.0) was used to compare the sequences with Homo sapiens and HCMV genomes. The GEPs of HCMV was determined by Integrated Genomics Viewer (IGV) and Partek® Genomics Suite™ (version 6.5 beta, Partek Inc., St. Louis, MO, USA).
