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:Small endogenous C. elegans RNAs from L4 and young adult worms were prepared for sequencing using a protocol derived from Batista et al., (2008) and Lau et al. (2001). The small-RNA libraries were constructed using a method that does not require a 5M-bM-^@M-^Y monophosphate (called 5M-bM-^@M-^Y monophosphate-independent method, Ambros et al., 2003) to profile secondary siRNAs that have 5M-bM-^@M-^Y triphosphorylated G. All preprocessed small-RNA reads were mapped to genome (ce6), allowing no mismatches. After excluding miRNAs, 21U RNAs, rRNAs, and other structural ncRNAs, the remaining reads were classified as 22G RNAs, 26G RNAs, and other siRNAs, based on their length and 5M-bM-^@M-2 terminal nucleotide. Small-RNA libraries were sequenced in L4 and young adult stages in C.elegans.
Project description:To investigate which genes are up- or down-regulated during L4 sleep in C. elegans mutant aptf-1(gk794) we performed whole genome microarray expression profiling using the C. elegans (V2) Gene Expression Microarray, 4x44K from Agilent Technologies. Approximately 200 sleeping L4 worms 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.
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:Small endogenous C. elegans RNAs from L4 and young adult worms were prepared for sequencing using a protocol derived from Batista et al., (2008) and Lau et al. (2001). The small-RNA libraries were constructed using a method that does not require a 5’ monophosphate (called 5’ monophosphate-independent method, Ambros et al., 2003) to profile secondary siRNAs that have 5’ triphosphorylated G. All preprocessed small-RNA reads were mapped to genome (ce6), allowing no mismatches. After excluding miRNAs, 21U RNAs, rRNAs, and other structural ncRNAs, the remaining reads were classified as 22G RNAs, 26G RNAs, and other siRNAs, based on their length and 5′ terminal nucleotide.
Project description:Comparison of gene expression profiles from C. elegans wildtype strain (N2) treated with L4440 and T25B9.1 RNAi for 5 days after L4 larvae stage. Jena Centre for Systems Biology of Ageing - JenAge (ww.jenage.de)
Project description:Comparison of gene expression profiles from C. elegans wildtype strain (N2) treated with L4440 and T25B9.1 RNAi for 2 days after L4 larvae stage. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
Project description:To check cdk-12 and DAF-16 dependent gene expression change in different genetic backgrounds. We have collected the synchronized late L4 worms and isolated the total RNA and did the mRNA sequencing.