Transcriptome sequencing analysis of FFPE prostate tissue
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ABSTRACT: Transcriptome sequencing data were generated for four fresh prostate needle biopsies at the Australian Genome Research Facility, Australia, on the NovaSeq 6000 using the TruSeq stranded mRNA sample preparation. Samples were run in duplicate and 20 million, 100 base pair (bp) single end reads were generated for each. Data were accessed for transcript level expression and differential expression between two EZH2 rs78589034 variant carriers and two non-variant carriers.
Project description:The Australian Chronic Allograft Dysfunction (AUSCAD) study is an ongoing single centre cohort study at Westmead hospital in Australia. In this section of the study, we aimed to identify biomarkers for chronic allograft dysfunction in kidney transplant recipients. Our study recruited 136 patients, each having protocol renal allograft biopsies taken pre transplantation.
Project description:The Australian Chronic Allograft Dysfunction (AUSCAD) study is an ongoing single centre cohort study at Westmead hospital in Australia. In this section of the study, we aimed to identify biomarkers for allograft rejection in kidney transplant recipients, 3-months after their transplant. Our study recruited 123 patients, each having protocol renal allograft biopsies taken 3-months post transplantation.
Project description:We used our newly ultra deep sequence data and bioinformatics to re-annotate P. xylostella genome for high confidence miRNAs with the correct 5p and 3p arm features. Furthermore, the whole genome was screened to identify potential miRNA binding sites using three target-predicting algorithms. Totally, 203 mature miRNAs were annotated, including 33 novel miRNAs. Two geographical populations of Diamondback moth larvae from Queensland (Gatton) and South Australia (Waite) were collected and reared on the cabbage plant at the University of Queensland in Australia. Total RNA was extracted from fifteen 3rd instar larval samples using Triazol® following the manufacturerâs protocol (Life Technologies). The small RNA libraries were generated from both populations with three biological replicates using the Illumina Truseq small RNA preparation kit at the Australian Genome Research Facility (AGRF-Melbourne, Australia). The purified cDNA libraries were sequenced on Illumina HiSeq and raw sequencing reads (50 nt) were obtained using Illuminaâs Sequencing Control Studio software.
Project description:The Australian Chronic Allograft Dysfunction (AUSCAD) study is an ongoing single centre cohort study at Westmead hospital in Australia. In this section of the study, we aimed to identify biomarkers for rejection phenotypes in kidney transplant recipients, 3-months after their transplant. Our study recruited 70 patients, each having whole blood taken at the time of their 3-month protocol biopsy.
Project description:Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach
Pedro A. Saa, Lars K. Nielsen*
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
*Corresponding author
Email: lars.nielsen@uq.edu.au
Reference methionine cycle model (i.e., true model) used for parameter estimation.
This model is almost entirely based on the kinetic reconstruction of Korendyaseva et al. (2008).
Korendyaseva TK, Kuvatov DN, Volkov Va, Martinov MV, Vitvitsky VM, Banerjee R, Ataullakhanov FI (2008) An allosteric mechanism for switching between parallel tracks in mammalian sulfur metabolism. Plos Comput Biol 4: e1000076
Project description:Genome-wide mRNA expression profiles of 70 primary gastric tumors from the Australian patient cohort. Like many cancers, gastric adenocarcinomas (gastric cancers) show considerable heterogeneity between patients. Thus, there is intense interest in using gene expression profiles to discover subtypes of gastric cancers with particular biological properties or therapeutic vulnerabilities. Identification of such subtypes could generate insights into the mechanisms of cancer progression or lay the foundation for personalized treatments. Here we report a robust gene-xpression-based clustering of a large collection of gastric adenocarcinomas from Singaporean patients [GSE34942 and GSE15459]. We developed and validated a classifier for the three subtypes in Australian patient cohort. Profiling of 70 primary gastric tumors on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. All tumors were collected with approvals from Peter MacCallum Cancer Center, Australia; the Research Ethics Review Committee; and signed patient informed consent.
Project description:Background: Constitutional MLH1 epimutations are characterized by monoallelic methylation of the MLH1 promoter throughout normal tissues, accompanied by allele-specific silencing. The mechanism underlying primary MLH1 epimutations is currently unknown. The aim of this study was to perform an in-depth characterization of constitutional MLH1 epimutations targeting the aberrantly methylated region around MLH1 and other genomic loci. Methods: Twelve MLH1 epimutation carriers, 61 Lynch syndrome patients and 41 healthy controls, were analyzed by Infinium Human Methylation 450K beadchip, and targeted molecular techniques were used to characterize the MLH1 epimutation in carriers and their inheritance pattern. Results: No nucleotide or structural variants were identified in-cis on the epimutated allele in ten carriers, in which intergenerational methylation erasure was demonstrated in two, suggesting primary type of epimutation. CNVs outside the MLH1 locus were found in two cases. EPM2AIP1-MLH1 CpG island was identified as the sole differentially methylated region in MLH1 epimutation carriers compared to controls. Conclusion: Primary constitutional MLH1 epimutations arise as a focal epigenetic event at the EPM2AIP1-MLH1 CpG island in the absence of cis-acting genetic variants. Further molecular characterization is needed to elucidate the mechanistic basis of MLH1 epimutations and their heritability/reversibility.
Project description:The immune responses generated by YF-17D by profiling 20,077 genes in 25 vaccine recipients were accessed at days 1, 3, 7, and 21 post-vaccination compared to pre-vaccination in PBMCs. The immune responses generated by YF-17D by profiling 20,077 genes in 25 vaccine recipients were accessed at days 1, 3, 7, and 21 post-vaccination compared to pre-vaccination in PBMCs. Keywords: time course
Project description:In the Greenlandic Inuit population, 17% are carriers of a nonsense TBC1D4 p.Arg684Ter variant. Homozygous variant carriers have impaired glucose tolerance and a 10-fold increased risk of type 2 diabetes. Here, we illuminate the consequences of lacking this muscle-specific long isoform of TBC1D4 during metabolic challenges in humans.
Project description:We collected 49 breast cancer FFPE needle biopsies from patients with different ER and HER2 receptor expression levels. TMT labeling quantitative proteomics were conducted. Potentially differential expressed proteins, which represented to different pathology groups, were studied.