Delayed phosphate starvation response in cells with abundant high-affinity transporters
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE32067 | GEO | 2011/09/15
SECONDARY ACCESSION(S): PRJNA147607
REPOSITORIES: GEO
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Project description:Wild-type cells and cells with abundant high-affinity transporters (PHO84C) were transferred from rich medium (SD) to medium containing 0.5mM phosphate Cells were grown to logarithmic phase in SC medium (OD=0.5), washed and then incubated in SC medium with intermediate phosphate level (0.5mM, initial OD=0.05). During the experiment (0, 1, 5, 8 and 23 hours) cells were harvested, pelleted and frozen for further analysis. Total RNA was extracted using MasterPure™fication Kit (Epicentre). The samples were amplified, labeled, hybridized to yeast dual color expression microarrays and scanned, all using standard Agilent protocols, reagents, and instruments. The scanned images were analyzed using SpotReader software (Niles Scientific).
2011-09-14 | E-GEOD-32067 | biostudies-arrayexpress
Project description:Rooted sugarcane plantlets, originated from in vitro meristem culture (genotype SP80-3280, CTC, Brazil), were greenhouse acclimatized by initial cultivation on 1/20th strength Hoagland and Arnon (1950) nutrient solution. Nutrient solutions were aired from an oil-less compressor and replaced every 7 days, increasing nutrient concentration to ¼ strength in 3 weeks. Plants were then individually transferred to 2.8 L pots filled with fresh ¼ strength nutrient solution. After one week, half of the plants were transferred to fresh solution containing 250 µM Pi, while the other half was transferred to nutrient solution deprived of phosphate (Pi), with H2PO4 being replaced by H2SO4 (Muchhal et al., 1996). Roots from six plants from each treatment (0 and 250 µM Pi) were harvested 6, 12, 24 and 48 h after exposure to phosphate starvation and immediately frozen in liquid nitrogen. For each time point and each treatment, root samples were aggregated in three pools of two samples each. Extraction of total RNA was performed separately on each sample pool. Keywords: time course of stress response
2007-05-20 | GSE4966 | GEO
Project description:RNA-seq libraries were constructed for three samples, including (I) ΔURA3 strain grown in SD medium containing 2% w/v glucose(pH=5.0);(II)ΔURA3 strain grown in SD medium containing 2%w/v glucose and 2% w/v succinic acid(pH=5.0);(III)ΔURA3 strain grown in SD medium containing 2% w/v succinic acid(pH=5.0). For preparation of RNA samples, ΔURA3 cells grown overnight were inoculated into 50 ml liquid Synthetic Dextrose (SD) medium with the initial inoculation amount of OD600= 0.1, and cultured for 24 hours to the logarithmic growth phase (OD600= 2-3). The cells were collected by centrifugation at 6000g for 5 minutes. After washing twice with phosphate buffer saline (PBS), they were inoculated into new 50 mL SD medium containing carbon sources of different combinations of glucose and succinic acid .The pH of the culture sample is adjusted to 5.0 with NaOH. After flask culturing at 30°C and 250 rpm for an additional three hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction. Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The 150-nt paired-end RNA-seq libraries were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s Hiseq X Ten platform (Illumina, San Diego, USA). Each sample contains two biological replicates.
2021-05-05 | GSE159457 | GEO
Project description:Hyperphosphatemia is an independent risk factor for cardiovascular mortality in chronic kidney disease. High inorganic phosphorus can induce endothelial cell apoptosis, but the exact mechanism is not fully understood. This study addresses this knowledge gap.Microarray analysis was used to identify differentially expressed gene profiles in human umbilical vein endothelial cells (HUVECs) in high phosphate (3.0 mM) normal phosphate (1.0 mM) medium and low phosphate( 0.5mM).
2014-08-30 | GSE60937 | GEO
Project description:Hyperphosphatemia is an independent risk factor for cardiovascular mortality in chronic kidney disease. High inorganic phosphorus can induce endothelial cell apoptosis, but the exact mechanism is not fully understood. This study addresses this knowledge gap.Microarray analysis was used to identify differentially expressed gene profiles in human umbilical vein endothelial cells (HUVECs) in high phosphate (3.0 mM) normal phosphate (1.0 mM) medium and low phosphate( 0.5mM). Differential gene expression in HUVECs seeded in high phosphate (3.0 mM ) medium ,normal phosphate ( 1.0 mM ) medium and simulated hypophosphatemia (0.5mM) were identified using Affymetrix GeneChip Human Gene 1.0 ST arrays ( Affymetrix ). Three chips were used to minimize the random error in each group.
2014-08-30 | E-GEOD-60937 | biostudies-arrayexpress
Project description:Phosphorus (P) is an essential nutrient that is limiting in many environments. When P is scarce organisms employ strategies for conservation of internal stores, and to efficiently scavenge P from their external surroundings. In this study we investigated the acclimation response of Chlamydomonas reinhardtii to P deficiency, comparing the transcriptional profiles of P starved wild-type cells to the P replete condition. RNA was prepared from P-containing or P-deprived logarithmic growth phase cells and subjected to RNA-Seq analysis. During the 24 hours after the imposition of P starvation we observed that from the 407 significantly changing genes (> 2 fold change, corrected p-value < 0.05) in the wild-type 317 genes were up-regulated, in average 8.36-fold, and 90 genes were down-regulated by 3.43-fold, in average. Many of the upregulated genes encoded enzymes involved in specific responses to P starvation, including PHOX, encoding the major secreted alkaline phosphatase, and multiple putative, high-efficiency phosphate transporter genes. More general responses included the up-regulation of genes involved in photoprotective processes (LHCSR3, LHCSR1, LHCBM9, PTOX1) and genes involved in protein modification and degradation. Down-regulated mRNAs indicated an early stage of the reduction of chloroplast ribosomal proteins, which are considered to be a reservoir for P in the cell. Chlamydomonas reinhardtii strain 21 gr (CC1690, wild-type) grown in TAP medium (Harris 1989) in a rotary incubator (200 rpm) at 25 M-BM-0C in continuous light (70 M-BM-5mol m-2 s-1). For 24 hours, either 1.1 mM phosphate or 0 mM were provided with the growth media. P deprivation was achieved by washing cells twice in midlogarithmic growth phase with liquid TAP medium without P (TAP-P) and cells were resuspended at a density of 2.5 mg/ml Chlorophyll in TAP or TAP-P. Cell aliquots were collected for mRNA isolation 24 h after being transferred either to TAP or TAP-P medium.
2014-04-05 | E-GEOD-56505 | biostudies-arrayexpress
Project description:Wild type cells were grown in SC medium and then transferred to no phosphate medium
2013-09-07 | GSE50656 | GEO
Project description:Diploid wild type cells in a chemostat, in different times after changing the feeding medium from low to high Pi.
2013-09-07 | GSE50654 | GEO
Project description:The objective of this project is to identify genes that are expressed in the Arabidopsis thaliana root tip and that are early induced (or repressed) by phoshate deficiency. Seedlings were germinated and grown (for 6 days) on phosphate rich medium and transfered to either a phosphate poor medium (Pi- = 20uM Pi treatment) or a phosphate rich medium (Pi+ = 500uM, Pi = control). Fifteen and 60 minutes after transfer, the tip (~800um) of the primary root was cut under a dissecting microscope. About 100 root tips per condition were harvested and there mRNA was analysed with the use of microarrays.
2011-09-09 | GSE31135 | GEO
Project description:We performed a transcriptomic analysis of Pi-starvation and recovery after resupplying Pi in Arabidopsis thaliana (Columbia-0) wild type plants and double mutant spx1,spx2. Results show that SPX1 is a Pi-dependent inhibitor of the transcription factor PHR1, a central regulatory protein in the control of transcriptional responses to Pi starvation. The analysis was performed in wild-type and double spx1,spx2 double mutant plants grown for seven days in complete (+Pi) and Pi-lacking (-Pi) Johnson solid media. Then, plants were transferred to complete medium for 4 hours to analyze the effect of resupplying plants with Pi.
2014-09-30 | E-GEOD-52046 | biostudies-arrayexpress