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Unknown,Transcriptomics,Genomics,Proteomics

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Stickleback embryos use ABC transporters as a buffer against exposure to maternally derived cortisol

ABSTRACT: Purpose: Offspring from females that experience stressful conditions during reproduction often exhibit altered phenotypes and many of these effects are thought to arise due to increased exposure to maternal glucocorticoids. Here we used RNAseq to test whether the embryonic transcriptional response to increased levels of cortisol was similar to the transcriptional response to maternal stress in sticklebacks Methods: Eggs were treated by immersing eggs for 30 mins in water that contained 0, 5, or 10 ug/L, which represented baseline, predator induced, and super physiological levels of maternally derived cortisol. To isolated enough RNA for RNAseq, 10 embyros from each clutch/treatment were pooled prior to RNA extraction for a total of 18 pools (6 clutches x 3 treatments). Results: Analysis of genome-wide transcriptional profiles suggests that 17251 (genes which survived a cut-off of having cpm more than 1 in at least two samples; and had a significant likelihood ratio calculated in edgeR) genes out of the possible 22,456 genes in the stickleback genome were expressed in 72-hour embryos. However, we did not detect any differences in gene expression between embryos that were treated with cortisol compared to the control group. mRNA profiles of egg clutches treated with 0, 5, or 10 ug/L are compared, which represented baseline, predator induced, and super physiological levels of maternally derived cortisol.

ORGANISM(S): Gasterosteus aculeatus

SUBMITTER: Alison Bell

PROVIDER: E-GEOD-71649 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Stickleback embryos use ABC transporters as a buffer against exposure to maternally derived cortisol

Project description:Purpose: Offspring from females that experience stressful conditions during reproduction often exhibit altered phenotypes and many of these effects are thought to arise due to increased exposure to maternal glucocorticoids. Here we used RNAseq to test whether the embryonic transcriptional response to increased levels of cortisol was similar to the transcriptional response to maternal stress in sticklebacks Methods: Eggs were treated by immersing eggs for 30 mins in water that contained 0, 5, or 10 ug/L, which represented baseline, predator induced, and super physiological levels of maternally derived cortisol. To isolated enough RNA for RNAseq, 10 embyros from each clutch/treatment were pooled prior to RNA extraction for a total of 18 pools (6 clutches x 3 treatments). Results: Analysis of genome-wide transcriptional profiles suggests that 17251 (genes which survived a cut-off of having cpm more than 1 in at least two samples; and had a significant likelihood ratio calculated in edgeR) genes out of the possible 22,456 genes in the stickleback genome were expressed in 72-hour embryos. However, we did not detect any differences in gene expression between embryos that were treated with cortisol compared to the control group.

2015-08-03 | GSE71649 | GEO

Human gastric organoids (34 days)

Project description:Human embryonic stem cells (WA01) were differentiated in a step-wise manner into three-dimensional human gastric organoids (hGOs). At day 34 of differentiation, the hGOs were collected and analyzed by RNA-sequencing.

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2016-01-09 | E-GEOD-72172 | biostudies-arrayexpress

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Microarray analysis of transcripts in the liver of gilthead sea bream with high plasma cortisol levels induced by slow-release cortisol implants

Project description:The present work was designed to assess the effects of high plasma cortisol levels induced by slow-release cortisol implants in the mRNA transcription of the GR in the different organs of the Sparus aurata, including liver. For that purpose fish were intraperitoneally injected with the implants containing two different concentrations of cortisol (50 or 200 µg/g body weight) and blood and organs were sampled after 7 and 14 days of implantation. Only fish with 200 µg/g implants exhibited a significant rise in the plasma cortisol. For microarray analysis we used livers of gilthead sea bream (N=36 fish). Fish were injected with 200 µg/g body weight of cortisol and sampled after 7 and 14 days (n=6 for each condition). RNA samples were grouped into pools of 2 animals for each time point. The analysis were carried out considering the transcripts differentially expressed in the group of fish implanted during 7 days with cortisol comparing to control group. Additionally, the transcripts differentially expressed at day 14 were compared with day 7.

2011-07-19 | E-GEOD-30782 | biostudies-arrayexpress

RNA-Sequencing of Klf6 silenced oligodendrocytes

Project description:We examine the role of Klf6 in oligodendrocyte progenitor cells and determine that Klf6 acts as a gp130-sensitive transactivator of the nuclear import factor importin-Î±5 (ImpÎ±5), a key controller of nuclear trafficking in oligodendrocytes. Examination of expression profiles of 2 different cell stages exposed to siRNA vs. control

2016-04-01 | E-GEOD-79244 | biostudies-arrayexpress

Cortisol binding sites on SARS-CoV-2 S1 identified by limited proteolysis-coupled mass spectrometry

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2022-06-10 | PXD032937 | Pride

RNA-seq of mouse pancreatic pericytes from wild-type and Tcf7l2-mutated mice

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The PIAS-like coactivator Zmiz1 directly and selectively coregulates Notch1 in T-cell development and leukemia [RNA-Seq]

Project description:The most recurrently mutated oncogene in T-cell acute lymphoblastic leukemia (T-ALL) is NOTCH1. The core Notch complex consists of an ICN protein, a Maml cofactor, and the DNA binding factor Rbpj. The known direct cofactors of Notch appear to act nonselectively, homogeneously driving Notch gene expression functions. It is unclear whether there are direct cofactors of Notch that act selectively and heterogeneously regulate ICN. We discovered that Zmiz1, a Protein Inhibitor of Activated STAT (PIAS)-like coactivator, directly bound ICN1. ChIP-Seq showed that Zmiz1 selectively co-bound only a subset of Notch-regulated enhancers. This led to hypothesize that Zmiz1 regulates only a subset of Notch1 target genes. To investigate this, we performed RNA-Seq on four 8946 cell linesin which L1601P (activated Notch1) or Zmiz1 were expressed alone or in combination. Zmiz1 induced ~10% of Notch target genes. The Notch target gene that was most strongly induced by Zmiz1 was Myc. Our data suggest that Zmiz1 selectively amplifies a subset of Notch target genes with strong amplification of Myc. RNA-Seq in a murine T-ALL cell line

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