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SRP071333
Mus musculus
24 Downloadable Samples
Illumina HiSeq 2500
Description
Despite decades of interest, the mechanisms that control Hox gene expression are not yet fully understood. It was recently proposed that Hotair, a lncRNA transcribed from the HoxC cluster, regulates HoxD gene expression via Polycomb targeting and thus is important for correct skeletal development. However, genetic manipulations of the locus led to conflicting results regarding the roles of Hotair. Here, we analyze the molecular and phenotypic consequences of deleting the Hotair locus in vivo. In contradiction with previous findings, we show that deleting Hotair has no detectable effect on HoxD gene expression in vivo. We could not observe any morphological alteration in mice lacking the Hotair locus. However, we find a significant impact of deleting Hotair on the expression of neighboring genes Hoxc11 and Hoxc12. Our results do not support an RNA-dependent role for Hotair in vivo, but argue in favor of a DNA-dependent effect of Hotair deletion on the transcriptional landscape in cis. Overall design: We micro-dissected wild type and Del(Hotair)-/- E12.5 embryos into 6 segments: forelimbs (FL), hindlimbs (HL), genital tubercle (GT), trunk section corresponding to the lumbar/sacral region (T1); trunk section corresponding to the sacral/caudal region (T2) and trunk section corresponding to the caudal region (T3). We generated strand-specific RNA-seq data for each segment, in two biological replicates and we performed differential expression analyses for each tissue. Furthermore, we analyzed the impact of deleting the Hotair locus on the local transcriptional landscape, in the HoxC cluster.
Publication Title
Hotair Is Dispensible for Mouse Development.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Vitis vinifera
- 4 Downloadable Samples
Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Oxidative stress can arise when in vitro propagated plants developed under low light conditions are exposed to high light during transfer to ex vitro conditions. In such a situation, among the many potential stresses to which the transferred plant can be exposed, oxidative stress is commonly experienced, most likely brought about by absorption of light energy in excess of that required for very low levels of photosynthetic metabolism. In vitro propagated grapevine when transferred to ex vitro conditions with a 4 fold increase in PPFD shows an initial inhibition of PET accompanied by an accumulation of H2O2, suggesting a signal for the upregulation in gene expression and antioxidant enzyme activity, which peaked at 48h after transfer of in vitro grapevine to ex vitro growing conditions.
Publication Title
Comparative transcriptomic profiling of Vitis vinifera under high light using a custom-made array and the Affymetrix GeneChip.
Sample Metadata Fields
Specimen part, Treatment
View Samples