Caenorhabditis elegans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA285045 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2040670.fastq.gz | Fastqsanger.gz | |||
| SRR2040680.fastq.gz | Fastqsanger.gz | |||
| SRR2040671.fastq.gz | Fastqsanger.gz | |||
| SRR2040681.fastq.gz | Fastqsanger.gz | |||
| SRR2040662.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptional profile of C. elegans following RNAi of elt-2 [L4 stage]
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Project description:Transcriptional profile of C. elegans following RNAi of elt-2 [L1 stage]
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Project description:L4, day 1, day 7 and day 10 old total RNA-Seq from Caenorhabditis elegans
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Project description:ELT-2 is the major transcription factor required for Caenorhabditis elegans intestinal development. It initiates in embryos to promote development then persists after hatching through larval and adult stages. Though the sites of ELT-2 binding are characterized and the transcriptional changes that result from ELT-2 depletion are described, a major missing piece has been the lack of an intestine-specific transcriptome profile over developmental time. We generated this dataset by Fluorescence Activated Cell Sorting (FACS) intestine cells at distinct developmental stages. We analyzed this dataset in conjunction with previously conducted ELT-2 studies to evaluate ELT-2’s role in directing the intestinal regulatory network through development. We found that only 33% of intestine-enriched genes in the embryo were direct targets of ELT-2 but that number increased to 75% by the L3 stage. This suggests additional transcription factors promote intestinal transcription especially in the embryo. Furthermore, only half of ELT-2’s direct target genes were dependent on ELT-2 for their proper expression levels, and an equal proportion of those responded to elt-2 depletion with over-expression as with under-expression. That is, ELT-2 can either activate or repress direct target genes. Indeed, we observed that ELT-2 repressed its own promoter, implicating new models for its autoregulation. Together, our results illustrate that ELT-2 impacts roughly 20 – 50% of intestine-specific genes, that ELT-2 both positively and negatively controls its direct targets, and that our current model of the intestinal regulatory network is incomplete as the factors responsible for directing the expression of many intestinal genes remain unknown.
2023-05-04 | GSE214581 | GEO
Project description:Comparison of gene expression profiles from C. elegans mutant strains (MIR73, MIR75 or MIR77) overexpressing genes involved in proline metabolism (B0513.5 or T22H6.2) with wildtype strain (N2) at 5 days after L4 larvae stage. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
2021-10-19 | GSE110842 | GEO
Project description:We used RNA-seq to assay gene expression changes over time in response to OP50 and PY79 To understand the molecular processes underlying aging, we screened modENCODE ChIP-seq data to identify transcription factors that bind to age-regulated genes in C. elegans. The most significant hit was the GATA transcription factor encoded by elt-2, which is responsible for inducing expression of intestinal genes during embryogenesis. Expression of ELT-2 decreases during aging, beginning in middle age. We identified genes regulated by ELT-2 in the intestine during embryogenesis, and then showed that these developmental genes markedly decrease in expression as worms grow old. Overexpression of elt-2 extends lifespan and slows the rate of gene expression changes that occur during normal aging. Thus, our results identify the developmental regulator ELT-2 as a major driver of normal aging in C. elegans. Whole-worm mRNA was sequenced from E. coli- and B.subtilis-fed worms. For each condidtion, one replicate was sequenced at Day 4 and Day 13
2016-03-22 | E-GEOD-79415 | biostudies-arrayexpress
Project description:Comparison of gene expression profiles from C. elegans mutant strain CF1038 treated with L4440 and K02A4.1 RNAi and C. elegans mutant strain TU3311 treated with L4440 and B0412.2 RNAi for 5 days after L4 larvae stage. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
2021-10-19 | GSE110840 | GEO
Project description:Transcriptional profiling of C. elegans aptf-1(gk7954) mutant in L4 sleep stage.
| PRJNA296527 | ENA
Project description:Purpose: The objective of this study was to identify genes whose expression changes significantly between the L4 larval stage (Day 0 of adulthood) and the sixth day of adulthood (Day 6) in C. elegans. Methods: Wild type N2 animals were synchronized by sodium hypochlorite treatment and dropped as L1 larvae to NGM RNAi plates containing 2mM IPTG, 100 mg/mL carbenicillin and seeded with E. coli strain HT115 harboring the L4440 plasmid (vector only control for feeding-based RNAi experiments). Animals were maintained on these plates at 20˚C until the L4 larval stage when half of the cohort was harvested for total RNA (brief description to follow). The other half of the cohort was transferred to new NGM RNAi plates containing 2mM IPTG, 100 mg/mL carbenicillin, 25ug/mL FUDR and seeded with E. coli strain HT115 harboring the L4440 plasmid. C. elegans were maintained on these plates at 20˚C until they reached the sixth day of adulthood when they were harvested for total RNA. To isolate RNA, worms were washed off of plates in M9 buffer, pelletted by centrifugation and resuspended in Trizol. Following a phenol/chloroform extraction, total RNA was precipitated in isopropanol, washed in 70% ethanol, and resuspended in RNase-free H2O. Total RNA was treated with DNase and reisolated using Qiagen RNeasy columns. RNA was isolated from two independent cohorts of L4 animals and three independent cohorts of Day 6 adults. rRNA was depleted from total RNA using Ribo-Zero and libraries were prepared by strand-specific cDNA synthesis for Illumina HiSeq sequencing. Following quality control steps to check for ribosomal depletion, contamination, and leftover adapter sequences, sequences were trimmed and alinged to the C. elegans genome using TopHat2. Alignments were then run with featureCounts then normalized using edgeR's calcNormFactors then transformmed using limma's voom. Changes in gene expression were identified by performing a differential expression analysis using DESeq2 on the Igenbio ERGO platform (Igenbio, Inc., Chicago, Il). Results: Results from DESeq2 were filtered for statistically significant changes in expression by accepting only those changes with a q-value of less than 0.05. As compared to expression at the L4 larval stage, at Day 6 of adulthood we found there to be 1441 genes that were upregulated by more than 5-fold and 2660 genes were downregulated by more than 5-fold. Conclusions: Aging is commensurate with significant and substantial changes in gene expression in C. elegans. By the time adults enter the post-reproductive phase of their life, we found that approximately 4000 genes are differentially expressed as compared to their expression levels in L4 larvae. While some of these changes in expression may drive the aging process, others may protect animals from age-associated damage.
2020-03-06 | GSE146443 | GEO
Project description:The nematode Caenorhabditis elegans (C. elegans) is often used as a model organism to study cell and developmental biology. Quantitative mass spectrometry has only recently been performed in C. elegans and, so far, most studies have been done on adult worm samples. Here we use quantitative mass spectrometry to characterise protein level changes across the four larval developmental stages (L1-L4) of C. elegans, in biological triplicate. In total, we identify 4,130 proteins and quantify 1,541 proteins that were identified across all four stages in all three biological repeats with at least 2 unique peptides per protein. Using hierarchical clustering and functional ontological analyses, we identify 21 protein groups containing proteins with similar protein profiles across the four stages, and highlight the most overrepresented biological functions in each of these protein clusters. In addition, we use the dataset to identify putative larval stage specific proteins in each individual developmental stage, as well as in the early and late developmental stages. In summary, this dataset provides a system-wide analysis of protein level changes across the four C. elegans larval developmental stages, which serves as a useful resource for the worm development research community.
2017-12-04 | PXD006676 | Pride