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Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonising the epidermal stem cell fate

ABSTRACT: Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonising the epidermal stem cell fate

PROVIDER: PRJNA685417 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13255750.fastq.gz	Fastqsanger.gz
	SRR13255751.fastq.gz	Fastqsanger.gz
	SRR13255752.fastq.gz	Fastqsanger.gz
	SRR13255753.fastq.gz	Fastqsanger.gz
	SRR13255754.fastq.gz	Fastqsanger.gz

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Similar Datasets

Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonising the epidermal stem cell fate

Project description:In this study we adapt targeted DamID (TaDa) for use in C.elegans and employ it to identify targets within the epidermis for the transcription factors LIN-22 and NHR-25 that are key epidermal development regulators.

2021-10-05 | GSE163243 | GEO

Targeted DamID in <i>C. elegans</i> reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate.

Project description:Transcription factors are key players in gene networks controlling cell fate specification during development. In multicellular organisms, they display complex patterns of expression and binding to their targets, hence, tissue specificity is required in the characterization of transcription factor-target interactions. We introduce here targeted DamID (TaDa) as a method for tissue-specific transcription factor target identification in intact Caenorhabditis elegans animals. We use TaDa to recover targets in the epidermis for two factors, the HES1 homolog LIN-22, and the NR5A1/2 nuclear hormone receptor NHR-25. We demonstrate a direct link between LIN-22 and the Wnt signaling pathway through repression of the Frizzled receptor lin-17. We report a direct role for NHR-25 in promoting cell differentiation via repressing the expression of stem cell-promoting GATA factors. Our results expand our understanding of the epidermal gene network and highlight the potential of TaDa to dissect the architecture of tissue-specific gene regulatory networks.

| S-EPMC8816332 | biostudies-literature

C. elegans: wildtype vs nhr-49-/-; wildtype vs nhr-66-/-; wildtype vs nhr-80-/-

Project description:Transcriptional profiling of C. elegans NHR-49, NHR-66 and NHR-80

2012-03-15 | GSE34856 | GEO

C. elegans: wildtype vs nhr-49-/-; wildtype vs nhr-66-/-; wildtype vs nhr-80-/-

Project description:Transcriptional profiling of C. elegans NHR-49, NHR-66 and NHR-80 Independent data sets were generated for each mutant vs wildtpe comparison: NHR-49 (N=2), NHR-66 (N=3), NHR-80 (N=4)

2012-03-15 | E-GEOD-34856 | biostudies-arrayexpress

Identification of Transcription Factor NHR-25::GFP Binding Regions in L2

Project description:modENCODE_submission_3835 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP33(official name : OP33 genotype : unc119(ed3);wgIs33(nhr-25::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs33(nhr-25::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene nhr-25; Strain OP33(official name : OP33 genotype : unc119(ed3);wgIs33(nhr-25::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

2013-07-11 | E-GEOD-48707 | biostudies-arrayexpress

Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID

Project description:Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID

| PRJNA691926 | ENA

Transcriptomic analysis of wild-type and lin-22 mutants in C.elegans

Project description:We used RNA-seq to identify gene expression changes associated with lin-22 mutations affecting seam cell pattering in C. elegans

2017-07-20 | GSE101645 | GEO

LMN-1-DamID in N2 and set-25(n5021) met-2(n4256) mutant early C. elegans embryos

2012-09-04 | GSE37226 | GEO

RNA-seq analysis of NHR-23-depleted, SPE-44-depleted, and NHR-23+SPE-44-depleted C. elegans

Project description:We performed RNA-seq analysis of control, NHR-23-depleted, SPE-44-depleted and NHR-23+SPE-44 depleted adult male animals, to identify genes regulated by NHR-23 and SPE-44.

2022-06-22 | GSE206676 | GEO

LMN-1-DamID in N2 and set-25(n5021) met-2(n4256) mutant early C. elegans embryos

Project description:We asked if the perinuclear position of chromosome arms in C. elegans depends on the histone methyltransferases MET-2 and SET-25. To this end, we performed LMN-1-DamID in wild-type (N2) and mutant (set-25 met-2) strains. LMN-1-DamID signal on chromosome arms was significantly reduced in the mutant. Three biological replicas were performed for each genotype. For one replica dyes were swapped. For each replica methylated DNA amplified from a strain expressing LMN-1-Dam was competitively hybridized against DNA amplified from a strain expressing GFP-Dam.

2012-09-04 | E-GEOD-37226 | biostudies-arrayexpress

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