Project description:We show there is minimal genome-wide chromatin rearrangements (as measured by DNA accessibility) during tissue differentiation in C. elegans transgenic expression of E. coli DAM (DNA Adenine Methyltransferase) from tissue-specific promoters followed by mapping of methylated sites using a procedure that captures 20bp sequences flanking methylated sites for Illumina sequencing PD3994 = transgenic line expressing DAM from myo-3 promoter PD3995 = transgenic line expressing DAM from rol-6 promoter PD3997 = transgenic line expressing DAM from vit-2 promoter N2dam = wildtype (N2) line; its genomic DNA was in vitro DAM-methylated parsed = Solexa reads in which linker sequences were successfully parsed out by the authors WS170DAMtags_ALL.txt = the set of all in_silico-generated DAM tags from C. elegans genome version WS170
Project description:Yilmaz2016 - Genome scale metabolic model -
Caenorhabditis elegans (iCEL1273)
This model is described in the article:
A Caenorhabditis elegans
Genome-Scale Metabolic Network Model.
Yilmaz LS, Walhout AJ.
Cell Syst 2016 May; 2(5): 297-311
Caenorhabditis elegans is a powerful model to study
metabolism and how it relates to nutrition, gene expression,
and life history traits. However, while numerous experimental
techniques that enable perturbation of its diet and gene
function are available, a high-quality metabolic network model
has been lacking. Here, we reconstruct an initial version of
the C. elegans metabolic network. This network model
contains 1,273 genes, 623 enzymes, and 1,985 metabolic
reactions and is referred to as iCEL1273. Using flux balance
analysis, we show that iCEL1273 is capable of representing the
conversion of bacterial biomass into C. elegans biomass
during growth and enables the predictions of gene essentiality
and other phenotypes. In addition, we demonstrate that gene
expression data can be integrated with the model by comparing
metabolic rewiring in dauer animals versus growing larvae.
iCEL1273 is available at a dedicated website
(wormflux.umassmed.edu) and will enable the unraveling of the
mechanisms by which different macro- and micronutrients
contribute to the animal's physiology.
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Project description:High throughput sequencing to derive function of cde-1 in endogenous RNAi in C. elegans Overall design: Small RNAs were cloned from C. elegans adults, following removal of tri-phosphate groups from 5' end. Sequencing was performed using the Illumina 1G platform.
Project description:High throughput sequencing to derive function of cde-1 in endogenous RNAi in C. elegans Small RNAs were cloned from C. elegans adults, following removal of tri-phosphate groups from 5' end. Sequencing was performed using the Illumina 1G platform.