Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Response of yeast to saponin treatment

ABSTRACT: Genome-wide expression profiling was used to identify genes that showed altered expression in response to treatment with the saponins tomatidine, tomatine and the sterol biosynthesis inhibitory compound fenpropimorph Growth inhibition by the compounds was monitored by measuring the OD600nm. Cells were pelleted and frozen in liquid nitrogen. Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA). Microarray hybridisation was performed using the Affymetrix GeneChip® Yeast genome S98 array using protocols described by Affymetrix, Inc. (Santa Clara, CA, USA) (as previously described (Zhu et al., 2001). Data were analyzed using the RMA algorithm using Expressionist Pro (GeneData Inc., Switzerland). Keywords: response to abiotic stress

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE4669 | GEO | 2006/07/28

SECONDARY ACCESSION(S): PRJNA96767

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Response of yeast to tomatidine treatment

Project description:Genome-wide expression profiling was used to identify genes that showed altered expression in response to treatment with the fungistatic saponin tomatidine. Overnight batch cultures of strain S288C were diluted to an optical density at 600nm of 0.1. After 1 hour of growth at 30°C, the compounds were added and the cultures were incubated for an additional 5 hours prior to harvesting. Control cultures were treated with the solvent dimethylformamide (DMF). Tomatidine treated cultures were grown in the presence of tomatidine (dissolved in DMF) at concentations of 7.5 uM and 15 uM. Growth inhibition by the compounds was monitored by measuring the OD600nm. Cells were pelleted and frozen in liquid nitrogen. Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA). Microarray hybridisation was performed using the Affymetrix GeneChip® Yeast genome S98 array using protocols described by Affymetrix, Inc. (Santa Clara, CA, USA) (as previously described (Zhu et al., 2001). Data were analyzed using Affymetrix® Microarray Suite version 5.0 software Keywords: dose response

2004-11-06 | GSE1927 | GEO

Transcription profiling of S. cerevisiae cultures treated with the saponins tomatidine, tomatine or the sterol biosynthesis inhibitory compound fenpropimorph

Project description:Genome-wide expression profiling was used to identify genes that showed altered expression in response to treatment with the saponins tomatidine, tomatine and the sterol biosynthesis inhibitory compound fenpropimorph; Growth inhibition by the compounds was monitored by measuring the OD600nm. Cells were pelleted and frozen in liquid nitrogen. Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA). Microarray hybridisation was performed using the Affymetrix GeneChipÂ® Yeast genome S98 array using protocols described by Affymetrix, Inc. (Santa Clara, CA, USA) (as previously described (Zhu et al., 2001). Data were analyzed using the RMA algorithm using Expressionist Pro (GeneData Inc., Switzerland). Experiment Overall Design: Overnight batch cultures of strain S288C were diluted to an optical density at 600nm of 0.1. After 1 hour of growth at 30Â°C, the compounds were added and the cultures were incubated for an additional 5 hours prior to harvesting. Control cultures were treated with the solvent dimethylformamide (DMF). Tomatidine treated cultures were grown in the presence of 0.625 ppm tomatidine, 13.9 ppm Tomatine and 0.313 ppm Fenpropimorph, all dissolved in DMF. Each of the three replicates of the cultures produced on 3 independent days.

2007-09-21 | E-GEOD-4669 | biostudies-arrayexpress

Transcription profiling of S. cerevisiae response to tomatidine treatment

Project description:Genome-wide expression profiling was used to identify genes that showed altered expression in response to treatment with the fungistatic saponin tomatidine. Overnight batch cultures of strain S288C were diluted to an optical density at 600nm of 0.1. After 1 hour of growth at 30Â°C, the compounds were added and the cultures were incubated for an additional 5 hours prior to harvesting. Control cultures were treated with the solvent dimethylformamide (DMF). Tomatidine treated cultures were grown in the presence of tomatidine (dissolved in DMF) at concentations of 7.5 uM and 15 uM. Growth inhibition by the compounds was monitored by measuring the OD600nm. Cells were pelleted and frozen in liquid nitrogen. Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA). Microarray hybridisation was performed using the Affymetrix GeneChipÂ® Yeast genome S98 array using protocols described by Affymetrix, Inc. (Santa Clara, CA, USA) (as previously described (Zhu et al., 2001). Data were analyzed using AffymetrixÂ® Microarray Suite version 5.0 software

2008-06-11 | E-GEOD-1927 | biostudies-arrayexpress

Maternal Stress and Genomic Variation

Project description:Custom Affymetrix SNP used to assay 24 mothers for desired variants. Data processed using the Affymetrix SNP Genotyping Console (Version 4.2, Affymetrix Inc., Santa Clara, CA, USA).

2017-11-30 | GSE107512 | GEO

CircRNA sequencing in peripheral blood mononuclear cells from Ankylosing Spondylitis patients and healthy controls

Project description:To identify the expression profiles of circRNAs in peripheral blood mononuclear cells (PBMCs) from Ankylosing Spondylitis (AS) patients and healthy controls, we used circRNA sequencing to detect circRNA in 3 samples of PBMCs from AS patients and 3 samples of PBMCs from healthy controls. In brief, total RNA was extracted and purified using Magen Hipure Total RNA Mini Kit (Magen, Guangzhou, China), followed by constructing RNA sequencing libraries with KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems, Inc., MA, USA). After the construction of RNA sequencing libraries, Qubit 3.0 fluorometer (Invitrogen, CA, USA) and the Agilent 2100 bioanalyzer (Applied Biosystems, CA, USA) were used for quality control. Then, the PE150 mode of HiSeq X10 (Illumina Inc., CA, USA) was used for sequencing. Differentially expressed circRNAs were screened with criteria of fold-change>1.5 and p<0.05.

2022-01-05 | GSE178408 | GEO

Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors (Illumina)

Project description:Gene expression profiling of 17 fresh frozen chondrosarcoma biopsies using the Human-6 v2 Expression BeadChip (Illumina Inc., San Diego, CA, USA). DNA copy number analyses was also performed in these tumors. Keywords: chondrosarcoma, gene expression profiling, Illumina

2009-04-01 | GSE12475 | GEO

Transcription profiling of human fibrotic liver samples

Project description:Human liver samples were obtained from Analytical Biological Services Inc.(Wilmington, DE, USA) via autopsy 4-10 hours post-mortem with appropriate consent. The specimens were quickly frozen and stored at -80C. Following pulverization of the liver specimens total RNA was isolated by QIAzol extraction and RNeasy Mini Kit(QIAGEN, Valencia, CA, USA) purification. The RNA was then amplified via Ambion<br>5X MessageAmp II aRNA Amplification Kit (Austin, TX, USA) and profiled using Agilent Human Whole Genome Microarray Kit (Agilent Technologies, Santa Clara, CA, USA).

2010-04-01 | E-MEXP-2589 | biostudies-arrayexpress

Transcriptomic analysis of Wild type M.tb H37Rv, HigB KO M.tb H37Rv and complemented Hig B KO M.tb H37Rv

Project description:Gene expression microarray was performed using early log phase culture at 37 degree and 200 rpm followed by RNA extraction from M.tb H37Rv, HigB KO M.tb H37Rv and complemented Hig B KO M.tb H37Rv For gene expression profiling, total RNA was isolated from wild type H37Rv, higB KO mutant strain and complemented strains. The bacterial pellets for M.tb H37Rv wild type, M.tb H37Rv HigB KO mutant strain and complemented strain were resuspended in 1.0 ml TRIzol (Invitrogen Corporation, Carlsbad, CA); mRNA was extracted as per standard protocols and cleaned using RNAeasy columns (Qiagen GmbH, Hilden, Germany). Extracted mRNA (1 μg) was treated with DNase I using the Ambion DNA-free kit (Invitrogen Corporation, Carlsbad, CA) to remove genomic DNA contamination and quantified using Nanodrop 2000c spectrophotometer (Thermo Scientific, USA). The purity and integrity of RNA samples were assessed Agilent 2100 Bio analyzer (Agilent TechnologiesInc., USA). Further, 25ng of RNA was amplified and labeled using Low input Quick Amp WT Labeling kit (Agilent Technologies, USA). The labeled cRNA was purified using RNAeasy columns (Qiagen, USA) and total yields were quantified using Nanodrop 2000c spectrophotometer.

2021-11-30 | GSE179403 | GEO

Combination of ABT-869 with SAHA on AML with FLT3-ITD

Project description:For the microarray experiments, MV4-11 and MOLM-14 cells were treated with DMSO control, ABT-869 3 nM, SAHA 6 uM and combination therapy for 24 hours. Cells were then washed in PBS and high-quality total RNA was extracted RNeasy Midi Kit, according to the manufacturer’s instruction (Qiagen, Valencia, USA). RNA quantity, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA, USA). Gene expression profiling was performed using Affymetric U133plus2.0 gene chip (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol.

2011-05-31 | GSE26114 | GEO

The effect of signal inhibitors on human induced pluripotent stem cells in suspension culture conditions

Project description:To examine the effect of the effects of PKCbeta and Wnt inhibitors on global gene expression of iPSCs in suspension conditions, RNA-seq experiments were performed. Total RNA was extracted with a FastGene RNA premium kit (Nippon Genetics, Co., Ltd, Tokyo, Japan) and strand-specific library preparation was performed. The prepared library was sequenced by a NovaSeq6000 (Illumina, Inc, CA, USA). Sequencing was performed in a 150 bp x2 paired-end configuration with a data output of about 6 Gb per sample (equivalent to about 20 million paired reads). Library preparation and its sequencing were performed in GENEWIZ (Azenta, MA, USA). The sequencing data were analyzed with a CLC Genomics Workbench (QIAGEN, Hulsterweg, the Neterlands) and the R package edgeR (v3.30.3) to identify differentially regulated genes.

2023-01-17 | GSE222833 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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