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SRX12276316: GSM5590182: DMSO2 0h rep2; Hydra vulgaris; RNA-Seq
2 ILLUMINA (Illumina HiSeq 2000) runs: 25.2M spots, 2.3G bases, 925.6Mb downloads

Submitted by: NCBI (GEO)
Study: Differential gene regulation in DAPT-treated Hydra reveals candidate direct Notch signalling targets
show Abstracthide Abstract
In Hydra, Notch inhibition causes defects in head patterning and prevents differentiation of proliferating nematocyte progenitor cells into mature nematocytes. To understand the molecular mechanisms by which the Notch pathway regulates these processes, we performed RNA-seq and identified genes that are differentially regulated in response to 48 h of treating the animals with the Notch inhibitor DAPT. To identify candidate direct regulators of Notch signalling, we profiled gene expression changes that occur during subsequent restoration of Notch activity and performed promoter analyses to identify RBPJ transcription factor-binding sites in the regulatory regions of Notch-responsive genes. Interrogating the available single-cell sequencing data set revealed the gene expression patterns of Notch-regulated Hydra genes. Through these analyses, a comprehensive picture of the molecular pathways regulated by Notch signalling in head patterning and in interstitial cell differentiation in Hydra emerged. As prime candidates for direct Notch target genes, in addition to Hydra (Hy)Hes, we suggest Sp5 and HyAlx. They rapidly recovered their expression levels after DAPT removal and possess Notch-responsive RBPJ transcription factorbinding sites in their regulatory regions Overall design: We aimed to identify the transcriptional target genes of Notch signalling by comparing DAPT-treated animals to control ones at three different time points. Six biological repeats were used.
Sample: DMSO2 0h rep2
SAMN21528782 • SRS10251410 • All experiments • All runs
Organism: Hydra vulgaris
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Selection: cDNA
Layout: SINGLE
Construction protocol: RNA-seq libraries were prepared for six biological replicates for each experimental condition. cDNA libraries were synthesized from total RNA using the strand specific SENSE mRNA-Seq Library Prep Kit V2 for Illumina (Lexogen) and the Purification Module with Magnetic Beads (Lexogen). The samples were multiplexed and sequenced on three lanes on Illumina Hiseq2000 with a 100 bpsequencing strategy.
Experiment attributes:
GEO Accession: GSM5590182
Runs: 2 runs, 25.2M spots, 2.3G bases, 925.6Mb
Run# of Spots# of BasesSizePublished


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