Filters
Organism
Technology
Platform
SRP139931
Homo sapiens
8 Downloadable Samples
Illumina HiSeq 2000
Description
Preterm birth (PTB), defined as the delivery of an infant before 37 weeks of completed gestation, results of the interaction of both, genetic and environmental components and constitutes a complex multifactorial syndrome. Transcriptome analysis of PTB has proved challenging because of the multiple causes of PTB and the numerous maternal and foetal gestational tissues that must interact to facilitate parturition. A common pathway of labour and PTB may be the activation of fetal membranes. In this work chorioamnion membranes from severe preterm and term fetus were analysed using RNA seq. The primary goal of this study was to identify differentially expressed transcripts and dilucidate molecular mechanisms distinguishing severe PTBs from term births. Overall design: Chorioamnion tissues were collected immediately after labor from women who had spontaneous severe preterm births between 24-33 weeks (n=4) and women with spontaneous term labor (>37 weeks)(n=4).
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Disease stage
View Samples- Homo sapiens
- 16 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
Defining the aging-cancer relationship is a challenging task. Mice deficient in Zmpste24, a metalloproteinase mutated in human progeria and involved in nuclear prelamin A maturation, recapitulate many features of aging. However, their short lifespan and cell-intrinsic and -extrinsic alterations restrict the application and interpretation of carcinogenesis protocols. To circumvent these limitations we have generated Zmpste24 mosaic mice. Interestingly, these mice develop normally - revealing cell-extrinsic mechanisms are preeminent in progeria- and display decreased incidence of infiltrating oral carcinomas. Moreover, ZMPSTE24 knock-down reduces human cancer cell invasiveness. Our results disclose the ZMPSTE24-prelamin A system as an example of antagonistic pleiotropy on cancer and aging, support the potential of cell-based and systemic therapies for progeria, and highlight ZMPSTE24 as a new anticancer target.
Publication Title
Prelamin A causes progeria through cell-extrinsic mechanisms and prevents cancer invasion.
Alternate Accession IDs
Sample Metadata Fields
Cell line
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
DELLA proteins interact with ARR1 and modulate its activity.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
We used microarrays to investigate gene expression changes in the pancreas of RasGrf1 KO mice. These animals have a reduction in the number and size of the pancreatic islets which lead to lower levels of insulin and glucagon in their blood.
Publication Title
Transcriptional profiling reveals functional links between RasGrf1 and Pttg1 in pancreatic beta cells.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Despite the importance of amino acids as basic components of proteins, amino acids also serve as substrates for multiple other metabolic pathways, such as the TCA cycle that regulates energy homeostasis. The response to deficiency in the biosynthesis of specific amino acids (also termed “amino acid starvation”) has been studied extensively in yeast (See for example Petti et. al., 2011 Survival of starving yeast is correlated with oxidative stress response and non-respiratory mitochondria function. Proc. Natl. Acad. Sci. USA 108: 1089-1098). In contrast, very little is known about the metabolic responses to deficiency in the biosynthesis of amino acids in plants. A number of recent reports have already shown that catabolism of amino acids can significantly contribute to cellular energy homeostasis particularly during the nighttime and particularly in response to stress. In the present manuscript we used a previously characterized Arabidopsis mutant with reduced expression of the Lys biosynthesis enzyme L,L-diaminopimelate aminotransferase (dapat) to investigate the physiological and metabolic impacts of deficient Lys biosynthesis. The results obtained demonstrate that not stomatal limitations but rather biochemical alterations are responsible for the decreased photosynthesis and growth of the dapat mutants which mimic stress conditions associated to Lys deficiency. Our findings suggest that manipulation of Lys biosynthesis in dapat mutant simulates a stress response culminating in a highly exquisite metabolic reprogramming such that alternative substrates support energy generation once carbohydrate metabolism is down-regulated.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
To gain insights into the mechanism responsible for the protumorigenic actions of NRG we performed gene expression analyses of MCF7 cells treated with soluble NRG for 3, 6, 12 and 24 hours.
Publication Title
Breast cancer dissemination promoted by a neuregulin-collagenase 3 signalling node.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Disease, Cell line, Treatment, Time
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
Plants with decreased SWC4 expression levels displayed several pleiotropic phenotypic alterations, suggesting that this gene participates in the regulation of different developmental processes. To evaluate genes whose expression was misregulated in SCW4 RNAi line, we performed RNA-seq differential expression analysis.
Publication Title
Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes.
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 23 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Plant cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes involved in Cys biosynthesis and located in different subcellular compartments. These enzymes are made up of a complex variety of isoforms resulting in different subcellular Cys pools. To unravel the contribution of cytosolic Cys to plant metabolism, we characterized the knockout oas-a1.1 and osa-a1.2 mutants, deficient in the most abundant cytosolic OASTL isoform in Arabidposis thaliana. Total intracellular Cys and glutathione concentrations were reduced, and the glutathione redox state was shifted in favour of its oxidized form. Interestingly, the capability of the mutants to chelate heavy metals did not differ from that of the wild type, but the mutants have an enhanced sensitivity to Cd. With the aim of establishing the metabolic network most influenced by the cytosolic Cys pool, we used the ATH1 GeneChip for evaluation of differentially expressed genes in the oas-a1.1 mutant grown under non-stress conditions. The transcriptomic footprints of mutant plants had predicted functions associated with various physiological responses that are dependent on reactive oxygen species and suggested that the mutant was oxidatively stressed. To further elucidate the specific function(s) of the OAS-A1 isoform in the adaptation response to cadmium we extended the trasncriptome experiment to the wild type and oas-a1.1 mutant plants exposed to Cd. The comparison of transcriptomic profiles showed a higher proportion of genes with altered expression in the mutant than in the wild type, highlighting up-regulated genes identified as of the general oxidative stress response rather than metal-responsive genes.
Publication Title
Knocking out cytosolic cysteine synthesis compromises the antioxidant capacity of the cytosol to maintain discrete concentrations of hydrogen peroxide in Arabidopsis.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis thaliana cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of cysteine. Recently, we have deeply investigated about one of the minor OASTL-like protein located in the cytosol, named DES1, highlighting some important clues about its metabolic function. We have demonstrated that DES1 catalyzes the desulfuration of L-cysteine to sulfide plus ammonia and pyruvate, instead of the biosynthesis of Cys, and thus, is a novel L-cysteine desulfhydrase (EC 4.4.1.1). The functionality of DES1 is being revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. We have performed a comparative transcriptomic analysis on leaves of the des1-1 and Col-0 wild type plants grown for 30 days under long-day conditions. The normalized data from the replicates showed differential expression of 1614 genes in the des1-1 mutant, with 701 genes down-regulated and 913 genes up-regulated by more than twofold, with a False Discovery Rate (FDR) of < 0.05 and an intensity signal restriction of lgSignal >7. This des1-1 transcriptional profile show a strong alteration when compared to a previous comparative transcriptomic analysis performed on leaves of the des1-1 and Col-0 wild type plants grown for 20 days under identical long-day conditions (GSE 19244). We have also performed a comparative transcriptomic analysis on leaves of the des1-1 and Col-0 wild type plants grown for 20 days and treated with sodium sulfide for 10 additional days. The comparison of the transcriptional profile of des1-1+Na2S versus Col-0+Na2S clearly shows that exogenous sulfide reversed the transcriptional level differences between the mutant and the wild type to reach similar transcriptional patterns as the array GSE19244. Our results suggest a role of sulfide as transcriptional regulator in the des1-1 mutant background.
Publication Title
Cysteine-generated sulfide in the cytosol negatively regulates autophagy and modulates the transcriptional profile in Arabidopsis.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cyanide is stoichiometrically produced as a co-product of the ethylene biosynthesis pathway, and it is detoxified by the b-cyanoalanine synthase enzyme. The molecular and phenotypical analysis of T-DNA insertional mutants of the mitochondrial b-cyanoalanine synthase CYS-C1 suggests that discrete accumulation of cyanide is not toxic for the plant and does not alter mitochondrial respiration rates, but does act as a strong inhibitor of root hair development. The cys-c1 null allele is defective in root hair formation and accumulates cyanide in root tissues. The root hair defect is phenocopied in wild type plants by the exogenous addition of cyanide to the growth medium and is reversed by the addition of hydroxocobalamin. Hydroxocobalamin not only recovers the root phenotype of the mutant, but also the formation of ROS at the initial step of the root hair tip. Transcriptional profile analysis of the cys-c1 mutant reveals that cyanide accumulation acts as a repressor signal for several genes encoding enzymes involved in cell wall rebuilding and the formation of the root hair tip, as well as genes involved in ethylene signaling and metabolism. Our results demonstrate that mitochondrial b-cyanoalanine synthase activity is essential to maintain a low level of cyanide for proper root hair development.
Publication Title
Mitochondrial beta-cyanoalanine synthase is essential for root hair formation in Arabidopsis thaliana.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples