Project description:To identify genes differentially expressed during the molt, we collected RNA 30-40 minutes after feeding cessation at the start of the fourth larval stage (L4) lethargus. Additional time points for RNA collection were in the mid-L4 stage, approximately four hours prior to lethargus, and in the young adult stage, four hours after lethargus. These samples were interrogated with the Affymetrix C. elegans Genome Array. A total of 1,804 gene transcripts were up regulated, and 1,088 gene transcripts were down regulated, during the L4 lethargus period compared to the L4 and Adult stages (false discovery rate (FDR) < 0.05).
Project description:To adapt RNA polymerase DamID (RAPID) for FLP-mediated spatial control in Caenorhabditis elegans, we inserted a Dam::rpb-6 fusion gene downstream of a FRT-flanked mCh::his-58 cassette and under control of the hsp-16.41 promoter. We introduced a single copy of this construct into the C. elegans genome and crossed the resulting line with a dpy-7p::FLP driver to enable basal Dam::rpb-6 expression in the hypodermis. Nematodes were cultured at 20 degrees Celcius to ensure low levels of Dam::RPB-6 expression in the hypodermis and total genomic DNA was purified from L4 larvae. DNA from animals expressing GFP::Dam was used to control for unspecific methylation. The genome-wide association profile of Dam::RPB-6 was determined by deep sequencing, which revealed a list of 2331 protein coding genes with FDR < 0.05. Original RAPID reference: Gomez-Saldivar et al (2020) Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics 216, 931–945. doi:10.1534/genetics.120.303774
Project description:During development C. elegans GABAergic dorsal D-class (DD) motor neurons reverse polarity such that the axonal and dendritic compartments are switched. We found that the gene DVE-1 is important for this process. To elucidate potential targets of dve-1 transcriptional regulation we conducted bulk RNA sequencing of total RNA from L4 stage wild type and dve-1 mutant animals
Project description:To identify genes differentially expressed during the molt, we collected RNA 30-40 minutes after feeding cessation at the start of the fourth larval stage (L4) lethargus. Additional time points for RNA collection were in the mid-L4 stage, approximately four hours prior to lethargus, and in the young adult stage, four hours after lethargus. These samples were interrogated with the Affymetrix C. elegans Genome Array. A total of 1,804 gene transcripts were up regulated, and 1,088 gene transcripts were down regulated, during the L4 lethargus period compared to the L4 and Adult stages (false discovery rate (FDR) < 0.05). There were a total of 3 groups and 5x replication for each group, for 15 total samples that were analyzed. The groups were (1) L4, (2) L4-lethargus, (3) Adult. We generated the following pairwise comparisons using R/maanova: L4-lethargus vs L4, L4-lethargus vs Adult. The permutation based p-values for each test were multiplied by 2 and transcripts with an FDRM-bM-^IM-$5% were selected.
Project description:We analyzed RNA-seq data from C. elegans on six bacterial diets, 3 E. coli diets (OP50, HT115, HB101) found in the laboratory setting and 3 found in C. elegans natural environment (Methylobacterium, Xanthomonas, Sphingomonas). We compared gene expression between L4 worms on the OP50 diet to the other 5 bacterial diets. We found that diet influences many gene expression changes, leading to genes being both up regulated and down regulated in a diet-dependent manner.