Project description:small RNA libraries from total RNA isolated from young adult animals Wild-type and rem-1 mutant animals were used for RNA isolation. Regular libraries were made using adaptor ligations at both ends. In addition, librraies were made from oxidised and TAP treated RNA.
Project description:Synchronised animals were grown to young adult stage at 20C on HB101 seeded NGM plates. Animals were harvested and washed 3X in M9 buffer. Settled animals were mixed with Trisure reagent, bead beaten using zirconia beads, and the RNA is extracted using chloroform. For total RNA sequencing, Illumina Ribozero kit is used to remove ribosomal RNA from 1ug of total RNA prior to library preparation. RNA sequencing libraries are prepared using NEB Next Ultra library preparation kit. Small RNA sequencing is performed by treating 5ug of total RNA with Epicentre 5 polyphosphatase to remove the 5 triphosphate. After treatment, RNA is purified by phenol/chloroform extraction and 1ug of RNA is used to prepare small RNA libraries using Illumina TruSeq small RNA library preparation kit. Ribosomal depleted RNA and small RNA libraries are sequenced using Illumina HiSeq 1500 platform.
Project description:RNA was isolated from L4 stage animals for the following genotypes: N2, hif-1(ia4), egl-9(sa307), hif-1(ia4);egl-9(sa307) grown at 20C. Total RNA was isolated and used to prepare libraries using the Illumina Truseq with polyA selection. Libraries were sequenced across two lanes on an Illumina HiSeq2000 (GeneWiz) or an Illumina HiSeq 2500 in Rapid Run Mode (RUCDR).
Project description:To investigate the contribution of small non-coding RNAs, including microRNAs, to stress response in C. elegans, we examined their expression changes using Illumina deep-sequencing technology. Stress conditions we examined include heat shock, Pseudomonas aeruginosa (PA-14) and L1 arrest. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Total RNAs were purified from wild-type young adult animals that were exposed to each stress condition, and used for cDNA library preparation for small RNAs. As for the L1 arrest sample, first wild-type embryos were collected and cultured without a food source in M9 buffer for 48 hrs with rotation, and then RNAs purified from L1 animals in a developmentally arrested state were used for the library preparation. These cDNA libraries established were sequenced with Illumina Genome Analyzer II.
Project description:Small RNA libraries from total RNA isolated from adult animals Small RNA libraries were derived from genetically identical strains carrying a 21Usensor transgene in single copy. In one strain the transgene has become permanently silent and is not reactivated by RNAi against prg-1 (RNAe). In the other the transgene reactivates upon RNAi against prg-1.
Project description:To understand how microRNAs are involved in stress response, we examined their expression changes in C. elegans animals that were exposed to stress conditions, including heat shock, oxidation, hypoxia and starvation. Total RNAs were purified from young adult animals that were exposed to each stress, and used for cDNA library preparation for small RNAs. In this experiment, spe-9(hc88), a temperature sensitive sterile mutant, that were cultured at 23dC, was used in order to avoid the effect from developing embryos. Stress conditions we examined include: Heat shock (32M-BM-0C, 6 hrs), Recovery from heat shock (6 hrs recovery at 23M-BM-0C after heat shock treatment at 32M-BM-0C for 6 hrs), Hypoxia (0.01%, 6 hrs), Oxidation (Juglone 750 M-NM-<M, 6 hrs), Starvation (complete food deprivation, 12 hrs). In addition to these stress conditions, RNAs were prepared from normally cultured, untreated animals at three time points, 0 hr (baseline), 6 hrs (as controls for heat shock, hypoxia and oxidation) and 12 hrs (as controls for heat shock recovery and starvation) after starting stress exposure. These cDNA libraries established were sequenced with Illumina Genome Analyzer II.
Project description:Eggs were isolated by hypochlorite treatment and allowed to hatch in the absence of food as L1 stage arrested worms in S-buffer. Worms were then transferred to large plates containing NGM alone or NGM+ resveratrol and allowed to grow till young adult stage (ca 40 hours). Worms were harvested and total RNA extracted using trizol reagent. Poly-A+ RNA was isolated using Qiagen midi-prep kit and used for microarray hybridization. A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed. Compound Based Treatment: Resveratrol Keywords: compound_treatment_design