Project description:This collection represents whole transcriptome data for human islets that were stratified to high quality (Group 1), intermediary quality (Group 2) and poor quality (Group 3) islets (Wong WKM et al JCI Insight 2019).
Project description:With the aim to identify rare genetic variation involved in stroke recovery, this is a pilot study on extreme phenotypes of good and bad recovery.
Exome sequencing was performed on 41 and 49 samples in the bad and good recovery subset, respectively.
Rare Variant association Analysis was performed on the exome sequencing results.
Project description:The goal of this study was to associate metabolite changes with protection of human islets from cell death induced by the diabetogenic stress of inflammatory cytokines. Protection of human islet viability was accomplished via enhanced glucose metabolism using phospho-BAD mimicry peptide treatment.
Project description:Chromatin packaging in sperm protects it against DNA fragmentation, and the importance of proper chromatin packaging for boar fertility outcome has become increasingly evident. Little is known however about the molecular mechanisms underlying differences in sperm DNA fragmentation and an understanding of the genes controlling this sperm parameter could help in selecting the best boars for AI use. The aim of this study was to identify differentially expressed genes in testis of Norsvin Landrace and Duroc boars with good and bad sperm DNA fragmentation using transcriptome sequencing and to use the data for polymorphism search. RNA sequence reads were obtained using Illumina technology and mapped by TopHat using the Ensembl pig database. Differentially expressed genes and pathways were analyzed using the R Bioconductor packages edgeR and goseq respectively. Using a false discovery rate of 0.05, 309 and 375 genes were found displaying significant differences in expression level between the good and bad condition in Landrace and Duroc respectively. Of the differentially expressed genes, 72 were found in common for the two breeds. Gene ontology analysis revealed that terms common for the two breeds included extracellular matrix, extracellular region and calcium ion binding. Additionally, different metabolic processes were enriched in Landrace and Duroc, whereas immune response ontologies were found to be important in Landrace. SNP detection in Landrace/Duroc identified 53182/53931 variants in 10924/10748 transcripts and of these, 1573/1827 SNPs occurred in 189/241 unique genes that were also differentially expressed. Possible high impact variants were detected using SnpEff. Transcriptome sequencing identified differentially expressed genes and nucleotide variants related to differences in sperm DNA fragmentation, and functional annotation of the genes pointed towards important biochemical pathways. This study provides insights into the genetic network underlying this trait and is a first step towards using sperm DNA fragmentation for predicting boar fertility.
Project description:Gene-specific two-way ANOVA analysis for identification of candidate genes for processing quality, seed development, and interaction (quality x development) Gene expression data of two good chapatti making varieties, C306 and Lok1 and two poor chapatti making varieties, sonalika and WH291 at three seed development stages (7, 14, and 28 days after anthesis) were analyzed using gene-specific two-way ANOVA to parition varition in gene expression due to quality, seed development, and their interaction (quality x development).
Project description:Microarray analysis was performed in ooplast samples to identify gene expression profiles associated with the embryo capacity to develop to blastocyst stage A fraction of the cytoplasm from in vitro matured oocytes was collected and snap frozen. The oocytes were chemically activated and presumptive zygotes were in vitro cultured in individual medium microdrops. The embryo development was recorded and oocytes classified according to the stage of embryo development. Oocyte was considered of good quality if the development proceeded to blastocyst stage, whereas it was considered of bad quality if there was a development block between 8-16 cells stage and morula formation.
Project description:This study compared 9 human islet preparations, extracted and prepared for clinical transplantation. Human islets were isolated as, and all were of transplant quality. Unamplified RNA was extracted and hybridized to Affymetrix HGU133+2 arrays. By using gene set enrichment analysis to investigate the variability of each probeset on the array, it was clear that isolated human islets undergo varying degrees of hypoxic stress. Further to this, key glycolytic genes, all of which are under the control of hypoxia inducing factor 1a (HIF-1a) were activated, indicating a switch towards anareobic glycolysis. Glycolysis severely impairs the ability of islets to sense glucose and secrete insulin in response to elevated blood sugar. We confirmed these findings in mouse rodents, demonstrated a dependance upon HIF-1a, and showed that even after 4 weeks, hypoxic islets retained their glycolytic molecular profile.
Project description:Transcriptional profiling of zebrafish embryo comparing wild type untreated embryos with embryos injected with morpholino of zf-bad. This assay is used for determination of expression profiling at 24 hpf and 48 hpf under Bad deficiency.
Project description:Transcriptional profiling of zebrafish embryo comparing wild type untreated embryos with embryos injected with morpholino of zf-bad. This assay is used for determination of expression profiling at 24 hpf and 48 hpf under Bad deficiency. Two-condition experiment, wild type vs. MO-Bad treated cells. Biological replicates: each group contains 200 embryos.