Project description:1075 members of the Lothian Birth Cohort 1936 (LBC1936) were sequenced using the Illumina HiSeq X platform. The LBC1936 are a relatively healthy cohort of 1091 individuals who underwent cognitive and medical testing at a mean age of 69.5 (SD=0.8) years. They have since undergone four further waves of testing, approximately three years apart.
Project description:We collected ten embryonic stages covering cleavage, blastula, gastrula, somite, and late stages until hatching. We also collected two adult tissue samples, including ovary and testis. 13 samples were sequenced using the illumina short-read sequencing platform.
Project description:Phospho-ribosome associated RNAs were immunopurified using the antibodies against phospho-S6. The purified RNAs were converted to cDNAs, which were sequenced in Illumina HiSeq platform. Vomeronasal organs were extracted from male CD-1 animals exposed to either pup cues or fresh bedding.
Project description:The goal of this study is to identify genomic signatures predicitve of cell-of-origin in acute myeloid leukemia Cryopreserved leukemic bone marrow samples were thawed, and 50,000 bulk leukemia (GFP+) cells were sorted by FACSAria (BD). Samples were placed at 37oC and 5% CO2 in IMDM plus 10% fetal calf serum for 30 minutes, then harvested, washed with 1X PBS, and ATAC-seq libraries were prepared. Quantitative PCR using the Library Quantitation kit (Kapa Biosystems) was used to estimate library concentrations. Libraries were sequenced on the Illumina HiSeq 2000 platform generating 2x150bp paired end reads at a sequencing depth of ~30-50 million reads per sample. Libraries were sequenced on the Illumina HiSeq 2000 platform.
Project description:The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions, such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours amongst others. The metabolites of H. hemerocallidea have been identified in several studies. More recently, the terpenoids of the plant have been identified. However, the biochemical pathways and the enzymes involved in the production of metabolites have not been characterised. In this study, total RNA extracted from the corm, leaf and flower tissues of H. hemerocallidea was sequenced on the Illumina HiSeq 2500 platform. A total of 143,549 transcripts were assembled de novo using Trinity and 107,131 transcripts were functionally annotated between the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues was sequenced using LC-MS/MS, revealing aspects of secondary metabolism and serving as data validation for the transcriptome. Functional annotation led to the identification of numerous terpene synthases such as nerolidol synthase, germacrene D synthase and cycloartenol synthase amongst others. Transcripts were also annotated to encode for the terpene phytoalexin momilactone A synthase. Differential expression analysis using edgeR identified 946 transcripts differentially expressed between the three tissues and revealed that the leaf upregulates linalool synthase compared to the corm and the flower tissues. The transcriptome as well as the proteome of Hypoxis hemerocallidea presented here provide a foundation for future research.