Expression profile analysis of C. elegans intermediate sized non-coding transcriptome
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ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
SUBMITTER: Yunfei Wang
PROVIDER: E-GEOD-24023 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We applied a middle-down proteomics strategy for large scale protein analysis during in vivo development of Caenorhabditis elegans. We characterized post-translational modifications (PTMs) on histone H3 N-terminal tails at eight time points during the C. elegans lifecycle, including embryo, larval stages (L1 to L4), dauer and L1/L4 post dauer. Histones were analyzed by our optimized middle-down protein sequencing platform using high mass accuracy tandem mass spectrometry. This allows quantification of intact histone tails and detailed characterization of distinct histone tails carrying co-occurring PTMs. We measured temporally distinct combinatorial PTM profiles during C. elegans development. We show that the doubly modified form H3K23me3K27me3, which is rare or non-existent in mammals, is the most abundant PTM in all stages of C. elegans lifecycle. The abundance of H3K23me3 increased during development and it was mutually exclusive of the active marks H3K18ac, R26me1 and R40me1, suggesting a role for H3K23me3 in to silent chromatin. We observed distinct PTM profiles for normal L1 larvae and for L1-post dauer larvae, or L4 and L4 post-dauer, suggesting that histone PTMs mediate an epigenetic memory that is transmitted during dauer formation. Collectively, our data describe the dynamics of histone H3 combinatorial code during C. elegans lifecycle and demonstrate the feasibility of using middle-down proteomics to study in vivo development of multicellular organisms.
2015-11-02 | PXD002525 | Pride
Project description:We acquied the RNA polymerase II binding profiles in ama-1 transgenic worms. The large subuint of POL II, AMA-1, was C-terminally tagged with GFP, the binding regions were determined using chromatin immunoprecipitation with anti-GFP and anti-polymerase II antibodies followed by illumina high-throughput sequencing (ChIP-seq). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf RNA polymerase II binding profiles at L4/young adult stage were acquied with anti-native protein antibody (8WG16) and anti-epitope (GFP) antibody
2009-04-11 | E-GEOD-15535 | biostudies-arrayexpress
Project description:We identified the DNA binding sites of DAF-16 in transgenic line TJ356 (daf-16::gfp) that carries high-copy number daf-16. The expression pattern was examined through fluorescent microscopy. The binding sites were determined using chromatin immunoprecipitation with anti-GFP antibody and anti-POL II antibody followed by illumina high-throughput sequencing (ChIP-seq). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Identification of DAF-16 binding sites at L4/Young adult stage when DAF-16 was highly overexpressed
2009-04-11 | E-GEOD-15567 | biostudies-arrayexpress
Project description:AMPK (AAK-2) and calcineurin (TAX-6) mediate longevity exclusively through post-translational modification of CRTC-1, the sole C. elegans CRTC (CREB regulated transcriptional coactivator). We performed microarrays to examine the transcriptional responses elicited by the pro-longevity: activation of AMPK, deactivation of calcineurin, and decrease of CREB (CRH-1) activity. Gene expression profiles for crh1 (nn3315) and tax-6 (ok2065) mutants, aak-2c (aa1-321) overexpressers and WT (N2) controls were obtained by measuring RNA levels in replicate pools of 3000 synchronized L4 worms. Three replicate pools of each strain were prepared on separate days.
2010-11-20 | E-GEOD-25513 | biostudies-arrayexpress
Project description:Analysis of tiling array data identified 358 genomic regions commonly enriched by the AS1 and T7 antibody datasets. AS1 antibody data set (AS1 antibody versus mock) and the T7 antibody data set (T7 antibody versus mock)
2013-03-06 | E-GEOD-44872 | biostudies-arrayexpress
Project description:The overall goal of this investigation was to investigate X-content of sex-biased genes in several nematode species. The following species of nematode were investigated: *C. elegans, *N2; *C. brenneri, *PB2801; *C. briggsae, *AF16; *C. remanei*, PB4641; *P. **pacificus, *PS312*.* Genomic DNA sequencing data was used to assign X and autosomal - linkage to unassembled sequencing contigs. Male and female RNA seq data was then generated and used to determine sex-biased expression. For both DNA and RNA experiments, 50bp paired-end (DNA) or single-end (RNA) reads were generated on the Illumina HiSeq 2500. Sequencing lanes were multiplexed. Genomic DNA was isolated from 50-100 hand-picked young adult worms. At least two replicates for each sex were prepared. DNA was sheared via sonication and 350-500 bp sequencing libraries were prepared following the Illumina protocol. Total RNA was isolated from at least 1000 hand-picked L4/young adult worms (*C. **elegans, *N2) or J4/young adult worms (*P. pacificus, *PS312*). *PolyA beads were used to enrich for mRNA. Stranded RNAseq libraries were prepared via incorporation of dUTPs during cDNA synthesis, following the protocol detailed in Parkhomchuk et al, 2009. DNAseq and RNAseq reads were aligned to the appropriate WS228 reference genomes. DNA sequencing data (2-3 replicates) from male and female YA worms are included along with RNAseq data from C.elegans YA hermaphrodites and P.pacificus YA males and hermaphrodites.
2014-04-17 | E-GEOD-53144 | 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:In Drosophila, two chromosome-wide compensatory systems have been characterized; the dosage compensation system acting on the male X-chromosome and the chromosome specific regulation of genes located on the heterochromatic 4th chromosome. Dosage compensation in Drosophila is accomplished by hypertranscription of the single male X-chromosome mediated by the MSL-complex. The mechanism for this compensation is suggested to be an MSL-complex mediated enhanced transcriptional elongation while the mechanism for the compensation mediated by Painting of fourth (POF) on the 4th chromosome has remained elusive. Here we show that POF binds to nascent RNA and this binding is associated with an increase in amount of chromosome 4 transcripts. Furthermore, genes located on the 4th chromosome are enriched in binding of the nucleoplasmic nucleporin component NUP98 and this enrichment correlates to increased POF binding. We also show that genes located in heterochromatic regions have a shorter transition time from site of transcription and to the nuclear envelope. Our current work broadens the understanding about how genes in heterochromatic regions can overcome the repressive influence of their hostile environment. Pof mutant vs. wild type, 3 replicates
2012-05-30 | E-GEOD-28513 | 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_655 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: NC1700 (engineered, target gene dat-1 tagged by 3xFlag::PAB-1); Tissue: Dopaminergic neurons (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119 (ed1); wdEx637 [unc-119 (+); dat-1::3XFLAG::PAB-1]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1700 (engineered, target gene dat-1 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue Dopaminergic neurons (L3-L4)
2010-08-04 | E-GEOD-23279 | biostudies-arrayexpress