Project description:The goal of this study is to identify and characterize sites in the C. elegans genome bound by the transcription factor TRA-1. TRA-1 ChIP-seq was performed in the following stages of animals in duplicate: 1) L2 stage of C. elegans wild-type N2 strain; 2) L3 stage of C. elegans wild-type N2 strain; 3) young adult stage of C. elegans glp-4(bn2) mutant; 4) young adult stage of C. elegans spe-11(hc77) mutant; 5) L3 stage of C. briggsae wild-type AF16 strain. As a negative control, TRA-1 ChIP-seq was also performed in C. elegans L3 stage with tra-1(e1834) homozygous and heterozygous mutation. Input DNA was also sequenced in each condition.
Project description:Transactive response DNA-binding protein of 43 kDa (TDP-43), a heterogeneous nuclear ribonucleoprotein (hnRNP) with diverse activities, is a common denominator in several neurodegenerative disorders including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Orthologs of TDP-43 exist from mammals to invertebrates, but their functions in lower organisms remain poorly understood. Here we systematically studied mutant Caenorhabditis elegans lacking the nematode TDP-43 ortholog, TDP-1. To understand the global gene expression regulation induced by the loss of tdp-1, the C. elegans transcriptomes were compared between the N2 WT animals and the tdp-1(ok803lf) mutant. Transcriptional profiling demonstrated that the loss of TDP-1 altered expression of genes functioning in RNA processing and protein folding. These results suggest that the C. elegans TDP-1 as an RNA-processing protein may have a role in the regulation of protein homeostasis and aging. Global gene expression profiling was performed to compare the transcriptome of wild-type (N2) Caenorabditis elegans and that of tdp-1(ok803) loss-of-function mutant. We analyzed mixed stages of Caenorabditis elegans, wild-type N2 versus tdp-1(ok803), using the Affymetrix C. elegans genome array. Three biological replicates were performed.
Project description:Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-15B(n744) mutants and N2 (wild type) at 26 degrees. One-condition experiment, mutant (lin-15B) vs. WT. Biological replicates 4 mutant, 4 wildtype harvested indepedently. One lin-35 replicate and one WT replicate per array.
Project description:Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-35(n745) mutants and N2 (wild type) at 26 degrees. One-condition experiment, mutant (lin-35) vs. WT. Biological replicates 4 mutant, 4 wildtype harvested indepedently. One lin-35 replicate and one WT replicate per array.
Project description:To investigate the effect of mutant E. coli on Caenorhabditis elegans, we performed gene expression profiling of RNA-seq data from Caenorhabditis elegans fed with different E. coli mutants.
Project description:Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-35(n745) mutants and lin-35(n745) treated with mes-4(RNAi) at 26 degrees. One-condition experiment, mutant (lin-35) vs. mutant plus RNAi (lin-35, mes-4RNAi). Biological replicates 4 mutant, 4 mutant plus RNAi harvested indepedently. One lin-35 replicate and one lin-35, mes-4(RNAi) replicate per array.
Project description:To investigate which genes are up- or down-regulated by aptf-1 transcription factor in C. elegans, aptf-1(gk794) mutants pretzel-stage embryos were used to performe whole genome microarray expression profiling using the C. elegans (V2) Gene Expression Microarray, 4x44K from Agilent Technologies. Approximately 3000 pretzel-stage embryos were used per sample. As a control we have used N2 C. elegans wild type strain. Mutant condition (aptf-1(gk794)) and control (N2) were done in four replicates.