Changes in expression of small non-coding RNAs, including microRNAs, in response to stress in C. elegans
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
SUBMITTER: Frank Slack
PROVIDER: E-GEOD-25739 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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.
2012-02-04 | E-GEOD-35529 | biostudies-arrayexpress
Project description:We report a significant number of miRNAs and other non-coding small RNAs show dramatic changes in expression during aging in C. elegans. RNAs were prepared from four diffrent timepoints during adulthood of C. elegans hermaphrodites, Day 0, 5, 8 and 12 post-L4 molt, and used for making cDNA libraries for small RNAs. Each library was sequenced using recent advances in high-throughput sequencing technology, Solexa. This study should lead to a better understanding of the aging process and age-related diseases. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of small RNA expression in four timepoints during adulthood of C. elegans hermaphrodites (spe-9 (hc88), cultured at 23dC), Day 0, 5, 8 and 12 post L4-molt.
2009-12-31 | E-GEOD-18634 | biostudies-arrayexpress
Project description:modENCODE_submission_656 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Tissue: reference (YA); Developmental Stage: Young Adult 20dC 72hr post-L1; Genotype: wild type; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain N2; temperature 20; Developmental Stage Young Adult 20dC 72hr post-L1; Tissue reference (YA)
2010-08-04 | E-GEOD-23280 | biostudies-arrayexpress
Project description:modENCODE_submission_461 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Tissue: reference (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: wild type; Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain N2; temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue reference (L2)
2010-08-04 | E-GEOD-23251 | biostudies-arrayexpress
Project description:modENCODE_submission_659 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Tissue: reference (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: wild type; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain N2; temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue reference (L3-L4)
2010-08-04 | E-GEOD-23283 | biostudies-arrayexpress
Project description:modENCODE_submission_462 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: SD1241 (engineered, target gene F25B3.3 tagged by 3xFlag::PAB-1); Tissue: Pan-neural (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: gaIs153 [(F25B3.3::FLAG::PAB-1) + (sur-5::GFP)]; Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain SD1241 (engineered, target gene F25B3.3 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue Pan-neural (L2)
2010-08-04 | E-GEOD-23252 | biostudies-arrayexpress
Project description:modENCODE_submission_465 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: SD1075 (engineered, target gene myo-3 tagged by 3xFlag::PAB-1); Tissue: body wall muscle; Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: gaIs146 [(myo-3p::FLAG::PAB-1) + (sur-5::GFP)]; Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain SD1075 (engineered, target gene myo-3 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue body wall muscle
2010-08-04 | E-GEOD-23255 | biostudies-arrayexpress
Project description:modENCODE_submission_2454 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1); Tissue: hypodermis (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119(ed1); wdEx626[unc-119+; dpy-7::3xFLAG::PAB-1]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue hypodermis (L3-L4)
2010-08-04 | E-GEOD-23287 | biostudies-arrayexpress
Project description:modENCODE_submission_469 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC694 (engineered, target gene unc-119 tagged by 3xFlag::PAB-1); Tissue: L2-A-class; Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: unc-119(ed1) III; wdEx257. Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC694 (engineered, target gene unc-119 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue L2-A-class
2010-08-04 | E-GEOD-23259 | biostudies-arrayexpress
Project description:modENCODE_submission_657 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC1668 (engineered, target gene unc-122 tagged by 3xFlag::PAB-1); Tissue: Coelomocytes (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: unc-119(ed1); wdEx638 [unc-119(+); unc-122::3XFLAG::PAB-1]; Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1668 (engineered, target gene unc-122 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue Coelomocytes (L2)
2010-08-04 | E-GEOD-23281 | biostudies-arrayexpress