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RNA seq to determine differential gene expression in pgph-2 oe C.elegans animals and the subset of HLH-30-dependent genes on normal growth and excess glucose conditions.

ABSTRACT: RNA seq to determine differential gene expression in pgph-2 oe C.elegans animals and the subset of HLH-30-dependent genes on normal growth and excess glucose conditions.

PROVIDER: PRJNA951630 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24046026_1.fastq.gz	Fastqsanger.gz
	SRR24046026_2.fastq.gz	Fastqsanger.gz
	SRR24046027_1.fastq.gz	Fastqsanger.gz
	SRR24046027_2.fastq.gz	Fastqsanger.gz
	SRR24046028_1.fastq.gz	Fastqsanger.gz

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RNA seq to determine differential gene expression in pgph-2 oe C.elegans animals and the subset of HLH-30-dependent genes on normal growth and excess glucose conditions.

Project description:Metabolic stress caused by excess nutrients accelerates aging. We recently demonstrated that the newly-discovered enzyme glycerol-3-phosphate phosphatase (G3PP; gene Pgp), which operates an evolutionarily conserved glycerol shunt that hydrolyzes glucose-derived glycerol-3-phosphate to glycerol, counters metabolic stress and promotes healthy aging in C. elegans. However, the mechanism whereby G3PP activation extends healthspan and lifespan, particularly under glucotoxicity, remained unknown. We demonstrated that G3PP (PGPH-2) overexpression activates three key longevity factors, AMPK, the TFEB homolog HLH-30, and autophagy, and is an attractive target for age-related metabolic disorders linked to excess nutrients. This transcriptomics analysis was designed to determine genes that are differentially regulated in pgph-2 oe animals in comparison to wild-type animals on normal and excess glucose conditions. To determine the role of HLH-30 in the regulation of gene expression, we also used pgph-2 oe; hlh-30 and hlh-30 mutant animals and found a signature mediated by pgph-2 oe and HLH-30-dependent.

2023-04-30 | GSE228784 | GEO

Identification of transcription factor HLH-8 binding sites in C.elegans

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mRNA-seq of wild-type(N2), hlh-11 knock-out(KO) and hlh-11 over-expression(OE) worms

Project description:Purpose: Comparing the transcriptome of wild-type(N2), hlh-11 knock-out and hlh-11 over-expression worms to identify genes with differential expression. Methods: For each condition, two replicates were examined. For each sample, approximately 2,000 synchronized young adult worms were collected and resuspended in TRIzon Reagent (CW0580, CWBIO). Total RNA was isolated by chloroform extraction, followed by isopropanol precipitation. Sequencing was performed using HiSeq2500. The clean reads were aligned to WBcel235 genomes with TopHat2. Gene differential expression was analyzed using DEseq2. A threshold of p < 0.05 was set to determine differentially expressed genes. Induction (KO_up or OE_up) or suppression (KO_down or OE_down) of genes were obtained through comparing gene expressions in hlh-11 KO or OE worms to wild-type N2. Results: >86% reads were uniquely mapped. 2637 genes were significantly up regulated and 2845 genes were significantly down regulated in hlh-11 knock-out worms compared to wild-type. 107 genes were significantly up regulated and 237 genes were significantly down regulated in hlh-11 over-expression worms compared to wild-type. Conclusions: This study revealed the genes transcriptionally regulated by hlh-11.

2019-11-23 | GSE140866 | GEO

Identification of transcription factor HLH-8 binding sites in C.elegans

Project description:We, being members of modENCODE consortium, have established an experimetal pipeline in C.elegans that allows global identification of the binding sites for transcription factors using chromatin immunoprecipitation followed by illumina high-throughput sequencing (ChIP-seq). In current study, we identified the binding sites for HLH-8 at L3 stage, which is required for normal muscle development and normal defecation and egg-laying. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf HLH-8 was tagged with a dual GFP:3xFLAG tag at the carboxy terminus, whose expression pattern was confirmed through both fluorescence imaging and immunoblot analysis. The binding sites were determined using ChIP-seq. Two biological replicates (one is early early L3) were used in this study and non-immunoprecipitated chromatin (input) from the same sample served as a control. The concordance between two replicates is just above 50% when p-value is 0.05

2009-07-31 | E-GEOD-17458 | biostudies-arrayexpress

mRNA-seq of wild-type(N2), hlh-11 knock-out(KO) and hlh-11 over-expression(OE) worms

Project description:mRNA-seq of wild-type(N2), hlh-11 knock-out(KO) and hlh-11 over-expression(OE) worms

| PRJNA591182 | ENA

C.elegans exposed to P. aeurigonsa: Colonized vs Non colonized animals

2012-07-20 | GSE39536 | GEO

C.elegans exposed to P. aeurigonsa: Colonized vs Non colonized animals

Project description:Transcriptional profiling of adult C.elegans exposed to E.coli or to GFP-expressing P. aeruginosa (strain PA14). For P. aeruginosa exposure, worms were separated into 2 groups - fully colonized (green) or non-colonized (dark). Three conditions (E.coli, P. aeurginosa colonized, and P. aeurginosa non-colonized). 2-color arrrays, each sample co-hybridized with the same reference RNA sample from mixed stage C.elegans cultures Each condition includes 3 biological replicates - 2 using the wormsorter (WS) to separate colonized from non-colonized and one hand picked (HP) under a fluorescent stereoscope

2012-07-19 | E-GEOD-39536 | biostudies-arrayexpress

Expression data from C. elegans wild type, hlh-25 mutant and hlh-29 mutant strains

Project description:In Caenorhabditis elegans, the six proteins that make up the REF-1 family are HES homologs that act in both Notch dependent and Notch-independent pathways to regulate embryonic events. To further our understanding of how the REF-1 family works to coordinate post-embryonic cellular events, we performed transcriptome analysis of HLH-25 and HLH-29 mutant strains. Gene expression microarray, including probe preparation, hybridization, fluidics run and chip scan, was performed by Georgia State University DNA/Protein Core Facility. Global gene expression in synchronized young adult populations of VC1220 (hlh-25 mutant) and tm284 (hlh-29 mutant) animals were compared to expression in N2 (wild-type) animals using GeneChip C. elegans Genome Array (Affymetrix). Data collection was carried out using GCOS 1.4 software (Affymetrix). Probe intensity values were normalized to a target value of 500 with normalization factor equal to 1. Data analysis was performed using GeneSpring GX 11 Software (Aglient, Palo Alto,CA).

2016-07-03 | E-GEOD-65417 | biostudies-arrayexpress

Expression data from C. elegans wild type, hlh-25 mutant and hlh-29 mutant strains

2016-01-01 | GSE65417 | GEO

Genome-wide maps of HLH-1 binding in muscle-enriched embryos.

Project description:To investigate the structure of the bodywall muscle differentiation network, we sought to both identify what role HLH-1 binding has in this regulation. We mapped the relationship between the regulatory targets and HLH-1 binding, as measured by ChIP-seq in animals enriched for bodywall muscle tissue through RNAi feeding. While regulatory targets are enriched for HLH-1 binding, the majority of HLH-1 binding actually occurs away from genes that are affected by hlh-1 loss of function. Nevertheless, HLH-1 binding is associated with both the expected E-box and, near genes belonging to specific regulatory subgroups, novel motifs that may serve as binding sites for cooperative transcription factors. HLH-1 binding genome-wide in the early embryo of C. elegans

2012-06-21 | E-GEOD-28561 | biostudies-arrayexpress

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