Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiling of Hansenula polymorpha in response to sulfur starvation and cadmium stress

ABSTRACT: Transcriptome profiling analysis of the Hansenula polymorpha MET4 gene deletion strain have been carried out to obtain comprehensive information on the HpMet4p-mediated regulatory networks in association with the cadmium (Cd) detoxification and sulfur regulation in H. polymorpha. Total RNA samples were collected from H. polymorpha wild type, and HpMET4 deletion strain, under sulfur starvation or Cd (0.6 mM) stress conditions. The differential fluorescence intensities of each RNA sample were measured after labeling with Cy3 or Cy5. For all analyses, we performed dye swapping experiments to avoid dye bias. Thus, four intensity values were generated for each ORF and averaged for analysis.

ORGANISM(S): Ogataea angusta

SUBMITTER: Min Jeong Sohn

PROVIDER: E-GEOD-31197 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome profiling of H. polymorpha in response to hydrogen peroxide exposure

Project description:To gain insight into the basic mechanism of Hydrogen peroxide detoxification in the methylotrophic yeast, H. polymorpha, we analyzed changes in transcriptional profiles in response to hydrogen peroxide exposure. Total RNA samples were collected from H. polymorpha cells after 30 min incubation with 0.5mM hydrogen peroxide. Using the RNA sample obtained prior to hydrogen peroxide addition as a reference, the differential fluorescence intensities of each RNA sample prepared at the indicated time was measured after labeling with Cy3 or Cy5 fluorochromes. For all analyses, we performed dye swapping experiments to avoid dye bias.

2015-02-28 | E-GEOD-43048 | biostudies-arrayexpress

Transcriptome profiling of Hansenula polymorpha in response to sulfur starvation and cadmium stress

Project description:Transcriptome profiling analysis of the Hansenula polymorpha MET4 gene deletion strain have been carried out to obtain comprehensive information on the HpMet4p-mediated regulatory networks in association with the cadmium (Cd) detoxification and sulfur regulation in H. polymorpha.

2014-07-31 | GSE31197 | GEO

Transcriptome profiling of H. polymorpha in response to Cd exposure.

Project description:To gain insight into the basic mechanism of Cd detoxification in the methylotrophic yeast, H. polymorpha, we analyzed temporal changes in transcriptional profiles in response to Cd exposure. We used H. polymorpha whole-genome cDNA microarrays, which contain 98% of all H. polymorpha ORFs in duplicate or triplicate. Keywords: time course, cadmium

2007-08-30 | GSE6989 | GEO

A combinatorial code for pattern formation in Drosophila oogenesis

Project description:Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and Decapentaplegic (DPP) pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation. Keywords: EGFR, BMP, gain/loss-of-function RNA was isolated from hand dissected, stage 9-10 egg chambers. Five genetic backgrounds were profiled including: wild type, EGFR gain of function, EGFR loss of function, BMP gain of function, and BMP loss of function. Three biological replicates were hybridized for each pathway perturbation. The samples were split across two rounds of hybridization. Each round of hybridizations included three biological replicates for wild type: The first round included EGFR gof, EGFR lof, BMP gof, and wild type controls A1-A3 (GSM313514-16). For these 12 arrays the extraction, labeling, and hybridization steps were done in parallel. The second round included the BMP lof and wild type controls B1-B3 (GSM313517-19). For these 6 arrays, the extraction, labeling, and hybridization steps were done in parallel.

2008-11-11 | E-GEOD-12477 | biostudies-arrayexpress

Physiological and transcriptomic analyses reveal sulfur is essential for cadmium detoxification and accumulation in poplar leaves

Project description:Although poplars are good candidates for the phytoremediation of cadmium (Cd)-polluted soils and sulfur is a key player in modulating Cd detoxification and accumulation in plants, the physiological and molecular mechanisms underlying sulfur-mediated Cd accumulation remain largely unknown. To investigate physiological and transcriptomic regulation mechanisms of poplars in response to Cd exposure and different sulphate (S) supply levels, Populus deltoides saplings were exposed to either 0 or 50 µM Cd together with one of low, moderate and high S levels. Cd was accumulated in the leaves of Cd-exposed poplars under moderate S condition, and its accumulation is inhibited by low S but tended to increase by high S. Sulfur nutrition became deficient in Cd-treated leaves, and it was aggravated by low S but improved by high S. Concentrations of cysteine and glutathione were increased in Cd-treated leaves, and the Cd-induced increases were limited by low S but stimulated by high S. In line with the physiological changes, a number of mRNAs and microRNAs (miRNAs) involved in Cd accumulation and sulfur assimilation were identified and the miRNAs-mRNAs networks were dissected. In the networks, miR395 and miR399 members were identified as hub miRNAs and their targets were ATP sulfurylase 3 (ATPS3), and phosphate 2 (PHO2) and beta galactosidase 1 (BGAL1), respectively. These results suggest that Cd-induced changes in Cd accumulation and sulfur assimilation are exacerbated by low S but alleviated by high S supply, and that miRNAs-mRNAs regulatory networks play pivotal roles in sulfur-mediated Cd detoxification and accumulation in poplars.

2021-05-31 | GSE142565 | GEO

Two Forkhead transcription factors regulate the division of cardiac progenitor cells by a Polo-dependent pathway

Project description:The development of a complex organ requires the specification of appropriate numbers of each of its constituent cell types, as well as their proper differentiation and correct positioning relative to each other. During Drosophila cardiogenesis, all three of these processes are controlled by jumeau (jumu) and Checkpoint suppressor homologue (CHES-1-like), two genes encoding forkhead transcription factors that we discovered utilizing an integrated genetic, genomic and computational strategy for identifying novel genes expressed in the developing Drosophila heart. Both jumu and CHES-1-like are required during asymmetric cell division for the derivation of two distinct cardiac cell types from their mutual precursor, and in symmetric cell divisions that produce yet a third type of heart cell. jumu and CHES-1-like control the division of cardiac progenitors by regulating the activity of Polo, a kinase involved in multiple steps of mitosis. This pathway demonstrates how transcription factors integrate diverse developmental processes during organogenesis. GFP-positive and GFP-negative cells were profiled from Stage 11 TinD-GFP Drosophila embryos

2011-06-06 | E-GEOD-29573 | biostudies-arrayexpress

Proteomic analysis provides insights into the molecular bases of hydrogen gas-induced cadmium resistance in Medicago sativa

Project description:Recently, molecular hydrogen (H2) has emerged as a bio-regulator both in animals and plants. Normally, functions of endogenous generated H2 could be mimicked by exogenously applied hydrogen-rich water (HRW) or hydrogen-rich saline (particularly in animals). Although alfalfa seedlings showed more cadmium (Cd) resistance after the administration with HRW, corresponding molecular mechanism is still elusive. To address this gap, iTRAQ-based quantitative proteomics was used. In our experimental conditions, out of 238 significant differential proteins identified in the Cd- and HRW/Cd-treated samples, 60 were unique to Cd-stressed alone samples, 107 were unique to HRW plus Cd treatment samples, and 71 were shared between two groups. Furthermore, 58 proteins from the 238 proteins significantly responded in Cd- and HRW/Cd-treatment samples were selected for further bioinformatics analysis. Interestingly, results indicated that they were classified into six categories: oxidation-reduction process, carbon metabolism, citrate cycle, cysteine and methionine metabolism, metal ion homeostasis, and sulfur compound metabolic process. In addition, the protein expression patterns were consistent with the results of increased non-protein thiols abundant, as well as iron and zinc content, in seedling roots. These suggest that HRW alleviates Cd toxicity mainly by decreasing oxidative damage, enhancing sulfur compound metabolic process, and maintaining nutrient element homeostasis.

2016-12-24 | PXD004820 | Pride

SPR509: Lung metastasis

Project description:Determine gene expression differences between normal, metastatic and non-metastatic mouse lung tissue. Priming of the organ-specific premetastatic sites is thought to be an important yet incompletely understood step during metastasis. In this study, we show that the metastatic tumors we examined overexpress granulocyte-colony stimulating factor (G-CSF), which expands and mobilizes Ly6G+Ly6C+ granulocytes and facilitates their subsequent homing at distant organs even before the arrival of tumor cells. Moreover, G-CSF-mobilized Ly6G+Ly6C+ cells produce the Bv8 protein, which has been implicated in angiogenesis and mobilization of myeloid cells. Anti-G-CSF or anti-Bv8 antibodies significantly reduced lung metastasis. Transplantation of Bv8 null fetal liver cells into lethally irradiated hosts also reduced metastasis. We identified an unexpected role for Bv8: the ability to stimulate tumor cell migration through activation of one of the Bv8 receptors, prokineticin receptor (PKR)-1. Finally, we show that administration of recombinant G-CSF is sufficient to increase the numbers of Ly6G+Ly6C+ cells in organ-specific metastatic sites and results in enhanced metastatic ability of several tumors. 67NR and 4T1mouse breast carcinoma cell lines were injected into fourth mammary fat pad; lung tissue was collected when tumor reached volume of 50mm3. RNA was extracted using Qiagen kit.

2014-11-06 | E-GEOD-62817 | biostudies-arrayexpress

The Regulatory Specificity of a Homeodomain Protein is Determined by Unique DNA-Binding Sequences

Project description:Homeodomain (HD) proteins comprise a large family of evolutionarily conserved transcription factors (TFs) having diverse developmental functions, yet they paradoxically recognize very similar DNA sequences. To investigate how HDs control cell-specific gene expression patterns, we determined the DNA binding specificities of a broad range of HDs critical for Drosophila embryonic mesoderm development. These studies revealed particular sequences that are bound by one HD and not by others. Such HD-preferred binding sites are overrepresented in the noncoding regions of genes that are regulated by the corresponding HD. Moreover, we show at single-cell resolution in intact embryos that the HD Slouch (Slou) controls myoblast gene expression through unique DNA sequences that are preferentially bound by Slou. These findings demonstrate that the sequence of a HD-binding site dictates which HD family member binds to and regulates a particular enhancer. This represents a novel mechanism for how cell type-specific TFs induce the distinct genetic programs of individual embryonic cells. Mesodermal cells were profiled from wild type, slou gain-of-function and msh gain-of-function backgrounds.

2012-02-08 | E-GEOD-27163 | biostudies-arrayexpress

Gene expression profiling of caffeic acid phenethyl ester -treated human umbilical vein endothelial cells

Project description:This SuperSeries is composed of the following subset Series: GSE10413: Gene expression profiling of caffeic acid phenethyl ester-treated human umbilical vein endothelial cells-1 GSE10429: Gene expression profiling of caffeic acid phenethyl ester -treated human umbilical vein endothelial cells-2 Keywords: SuperSeries Refer to individual Series

2010-05-26 | E-GEOD-10465 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data