Project description:Purpose: The goal of this study is to identify similarities and differences in the induction of the central nervous system and the sensory placodes in chick. Method: mRNA profiles for central and anterior pre-steak epiblast, neural plate, anterior and posterior pre-placodal region, non-neural epiblast, gastrula stage area opaca exposed to Hensen's node for 5 hours and control area of opaca from the same stage. Deep sequencing was carried with Illumina HiSeq 2000. After filtering low quality reads, alignment was carried using TopHat2, differential expression analysis was done using R-package (easyRNA-seq and DSEq). Results: Despite the differences in inducing tissues (i.e. node and lateral head mesoderm) and in the final outcome (neural plate and pre-placodal region), the initial set of genes induced by both tissues is largely identical. We define this transcriptional signature as 'pre-neural state', and demonstrate its functional significance for both inductive processes. An unbiased approach using GENEI3 and community clustering reveals the gene regulatory modules characterising the transcirptional states of pre-neural, neural and placodal cells. Conclusion: Induction of the neural plate and the pre-placodal region initially share common features, and diverge later. The pre-neural state is similar to the neural plate border and pre-streak epiblast state.
Project description:Single cell Methylome and Transcriptome Sequencing (scM&T-Seq) was performed on index-sorted single CD48- CD135- Lin- Sca-1+ c-Kit+ cells from Scl-tTA; H2B-GFP mouse bone marrow after 100 days of chase. Methylation data is uploaded here.
Project description:C8orf33-proficient and deficient DIvA cells were treated with 4-hydroxy tamoxifen (4OHT) to induce DNA double strand breaks (DSB) at several loci within the human genome. following 4OHT treatment cells were subject to ChIP-seq analysis for KAT8 acetyltransferase to map its enrichment at DSB sites in C8orf33 proficient deficient cells.
Project description:We performed deep targeted somatic mutation analysis to identify cases of clonal hematopoiesis (CH) associated with pre-leukemic mutations. For the healthy cohort, we used our CH panel V3, containing 705 probes, covering leukemia-related Single Nucleotide Variants (SNVs) and Indels in 47 genes, complemented by two amplicon sequencing reactions to cover GC-rich regions in SRSF2 and ASXL1. For the cytopenic cohort, we used our CH panel V4 (described in detail in Biezuner, T. et al., NAR Genom Bioinform, 2022). Both panels were designed to ensure capture uniformity and specificity. Each DNA sample was sequenced twice with a minimum depth of 1,000,000 paired-end reads on an Illumina Novaseq 6000 machine.
Project description:Obesity is well recognized as a risk factor for coronary heart disease and mortality. The relationship between abdominal obesity and ischemic stroke remains less clear. Previous publication showed the obesity is an independent, potent risk factor for ischemic stroke in all race-ethnic groups. It is a stronger risk factor than BMI and has a greater effect among younger persons. The goal of this experiment was to compare genome wide enrichment of H3K9ac histone mark profile of white blood cells of healthy controls, patients with obesity and/or stroke in order to understand the histone modifications differences behind the different phenotypes. There were 3 subjects in each group.
Project description:In a phenotypic screening approach of novel molecules composed of a synergistic combination of phthalimide, benzimidazole, and triazole scaffolds we discovered compounds with potent anti-leishmanial activity. The resulting early-lead compound PHT-39, which contains a trifluoromethyl substitution, demonstrated the highest efficacy in a Leishmania infantum intramacrophage assay, with an EC50 of 1.2+/- 3.2 μM.Cytotoxicity testing of PHT-39 in Hep-G2 cells indicated high selectivity of over 90-fold. To investigate the mechanism of action we carried out experiments in Trypanosoma brucei, which is also sensitive to PHT-39. Here we used a genome-wide RNAi library approach (PMID: 22278056; PMID: 21363968) to detect sensitivity determinants. This high-throughput phenotyping approach identified sensitivity determinants for PHT-39, which included a P-type ATPase that is crucial for the uptake of miltefosine and amphotericin, strongly indicating a shared route for cellular entry.