Project description:We studied the lipidome (236 individual lipid species including sphingolipids, ceramides, cholesterol, gangliosides, phosphatidylethanolamines) in basal and LPS-stimulated human monocyte derived macrophages (MDMs) over a time-course by LC-MS (30min, 3h, 8h, 16h; n=12 human donors). In order to explore how transcriptomic changes induced by LPS stimulation can correlate with changes in the lipidome, we performed RNAsequencing on MDMs from 4 donors over a time-course (30min, 3h, 8h, 16h)
Project description:We used a comprehensive approach that combined proteome, lipidome, and metabolome data to investigate the segmentation atlas of hepatocellular carcinoma (HCC).
Project description:Genomicus (http://www.dyogen.ens.fr/genomicus/) is a database and an online tool that allows easy comparative genomic visualization in >150 eukaryote genomes. It provides a way to explore spatial information related to gene organization within and between genomes and temporal relationships related to gene and genome evolution. For the specific vertebrate phylum, it also provides access to ancestral gene order reconstructions and conserved non-coding elements information. We extended the Genomicus database originally dedicated to vertebrate to four new clades, including plants, non-vertebrate metazoa, protists and fungi. This visualization tool allows evolutionary phylogenomics analysis and exploration. Here, we describe the graphical modules of Genomicus and show how it is capable of revealing differential gene loss and gain, segmental or genome duplications and study the evolution of a locus through homology relationships.
Project description:We provide an atlas of gene and protein expression in Arabidopsis root hair cells, generated by paired-end RNA-seq and LC/MS-MS analysis from protoplasts that carry the root hair-specific pEXP7-GFP reporter construct. In total, transcripts from 23,234 genes were detected in root hairs; those related to cell wall biosynthesis and translation differed most dramatically in abundance when compared to non-GFP root protoplasts.