Project description:This experiment aims at analyzing genotype profiles of wild-type and apomictic BRS CIRAD-302 rice. Leaf samples from plants of the parental, F1, F2, T0, T1, and T2 were used for DNA purification and library preparation for Illumina sequencing (2x150 bp), performed by the Max Planck-Genome-centre Cologne, Germany (https://mpgc.mpipz.mpg.de/home/).
Project description:Background Brugada syndrome (BrS) is a rare inherited disease causing sudden cardiac death (SCD). Copy number variants (CNVs) can contribute to disease susceptibility, but their role in Brugada syndrome (BrS) is unknown. We aimed to identify a CNV associated with BrS and elucidated its clinical implications. Methods We enrolled 335 unrelated BrS patients from 2000 to 2018 in the Taiwanese population. Microarray and exome sequencing were used for discovery phase whereas Sanger sequencing was used for the validation phase. HEK cells and zebrafish were used to characterize the function of the CNV variant. Findings A copy number deletion of GSTM3 (chr1:109737011-109737301, hg38) containing the eighth exon and the transcription stop codon was observed in 23.9% of BrS patients versus 0.8% of 15,829 controls in Taiwan Biobank (P < 0.001), and 0% in gnomAD. Co-segregation analysis showed that the co-segregation rate was 20%. Patch clamp experiments showed that in an oxidative stress environment, GSTM3 down-regulation leads to a significant decrease of cardiac sodium channel current amplitude. Ventricular arrhythmia incidence was significantly greater in gstm3 knockout zebrafish at baseline and after flecainide, but was reduced after quinidine, consistent with clinical observations. BrS patients carrying the GSTM3 deletion had higher rates of sudden cardiac arrest and syncope compared to those without (OR: 3.18 (1.77–5.74), P<0.001; OR: 1.76 (1.02–3.05), P = 0.04, respectively). Interpretation This GSTM3 deletion is frequently observed in BrS patients and is associated with reduced INa, pointing to this as a novel potential genetic modifier/risk predictor for the development of the electrocardiographic and arrhythmic manifestations of BrS.
Project description:We have designed a method for direct measurement of in vitro noise. Using a synthetic STR sequencing library, we have measured the stutter patterns at various levels of PCR amplification during targeted amplification and library preparation processes
Project description:To know BRs was how to cause transgenic line L100 leaves changed, we took the sixth leaves of transgenic line L100 to RNA-seq sequence. Total RNA was extracted from the sixth leaves of six-leaf stage of transgenic line L100 and wild type Q319. cDNA library was builded in the BIOMARKER, 100.20M original reads were sequenced based on Illumina HiSeq2000, and through rRNA, low quality fragment DNA of filtering, ultimately, we obtained 69.01M high quality clean reads. Compared with reference gene sequence(AGPv3), according to genes function annotation, we found 201 different expression genes. We classified the different expression genes according to Cellular Component, Molecular Function and Biological Process. It showed that BRs could affect many genes expression involved in different biological process.
Project description:High-density gene expression profile of 20,000+ genes for synthetic miR-155 oligo-treated mouse CD4+ T-cells using RNA deep sequencing technology.
Project description:sgRNA whole genome library sequencing in OCI-AML5-Cas9 EKO library cells overexpressing HMGA-YFP or control YFP vectors. The goal of this experiment is to identify synthetic lethal and synthetic rescue sgRNAs with regard to HMGA2 overexpression in AML.
Project description:To identify possible novel targets for the treatment of plexiform neurofibroma formation through a synthetic lethal shRNA library screen in the tumorigenic cell of origin, Schwann cells.
