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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of yeast treated withNaCl + FK506, time series

ABSTRACT: Cells were grown in YPD medium (pH 5.0) at 30oC to a density of 0.6 X 107 cells/ml (A600=0.6). The culture was supplemented with FK506 (1.0 mg/ml) in ET at 30oC for 15 min. Cells were collected for the t=0 min sample. Next, an equal volume of YPD medium (pH 5.0) containing FK506 (1.0 mg/ml) and 1.6 M NaCl was added to the FK506-treated culture (final concentration 0.8 M NaCl). Samples were collected 15, 30, 45 and 60 minutes after Na+ addition.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Hiroyuki Yoshimoto

PROVIDER: E-SMDB-14 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.

Yoshimoto Hiroyuki H Saltsman Kirstie K Gasch Audrey P AP Li Hong Xia HX Ogawa Nobuo N Botstein David D Brown Patrick O PO Cyert Martha S MS

The Journal of biological chemistry 20020610 34

In Saccharomyces cerevisiae, the Ca(2+)/calmodulin-dependent protein phosphatase, calcineurin, is activated by specific environmental conditions, including exposure to Ca(2+) and Na(+), and induces gene expression by regulating the Crz1p/Tcn1p transcription factor. We used DNA microarrays to perform a comprehensive analysis of calcineurin/Crz1p-dependent gene expression following addition of Ca(2+) (200 mm) or Na(+) (0.8 m) to yeast. 163 genes exhibited increased expression that was reduced 50% ...[more]

PMID: 12058033

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Transcription profiling of yeast treated with calcium + FK506 time series

Project description:Cells were grown at 30oC in YPD medium (buffered to pH 5.0 with 7.5 mM succinate) containing ET solution to a density of 0.6 X 107 cells/ml (A600 0.6). The culture was supplemented with FK506 (1.0 mg/ml final concentration) in ET at 30oC for 15 min. Cells were collected for the t=0 min sample. Next, an equal volume of YPD medium (pH 5.0) containing FK506 (1.0 mg/ml) and 0.4 M CaCl2 was added to the FK506-treated culture (final concentration 0.2 M CaCl2). Cells were collected by centrifugation at 5, 15, 30 and 60 min, frozen at 80oC and processed for RNA extraction. For the publication this experiment was done twice, and corresponding time points were averaged. The first 4 and last 4 arrays in the set define each experiment.

2013-01-30 | E-SMDB-8 | biostudies-arrayexpress

Transcription profiling of yeast treated with NaCl time series

Project description:Cells were grown in YPD medium (pH 5.0) at 30oC to a density of 0.6 X 107 cells/ml (A600=0.6). The culture was supplemented with ET at 30 oC for 15 min. Cells were collected for the t=0 min sample. Next, an equal volume of YPD medium (pH 5.0) containing ET solution and 1.6 M NaCl was added to the ET-treated culture (final concentration 0.8 M NaCl). Samples were collected 15, 30, 45 and 60 minutes after Na+ addition.

2005-01-01 | E-SMDB-12 | biostudies-arrayexpress

Transcription profiling of yeast treated with calcium, time series

Project description:Cells were grown at 30oC in YPD medium (buffered to pH 5.0 with 7.5 mM succinate) containing ET solution to a density of 0.6 X 107 cells/ml (A600 0.6). The culture was supplemented with ET at 30oC for 15 min. Cells were collected for the t=0 min sample. Next, an equal volume of YPD medium (pH 5.0) containing ET and 0.4M CaCl2 was added to the ET-treated culture (final concentration 0.2 M CaCl2). Cells were collected by centrifugation at 5, 15, 30 and 60 min, frozen at 80oC and processed for RNA extraction. For the publication, the experiment was repeated twoce, and corresponding timepoints from each experiment were averaged. The first 4 and last 4 arrays in this set correspond to each experiment.

2005-09-23 | E-SMDB-1407 | biostudies-arrayexpress

Transcription profiling of yeast ET/Calcium Time Series

Project description:Cells were grown at 30oC in YPD medium (buffered to pH 5.0 with 7.5 mM succinate) containing ET solution to a density of 0.6 X 107 cells/ml (A600 0.6). The culture was supplemented with ET at 30oC for 15 min. Cells were collected for the t=0 min sample. Next, an equal volume of YPD medium (pH 5.0) containing ET and 0.4M CaCl2 was added to the ET-treated culture (final concentration 0.2 M CaCl2). Cells were collected by centrifugation at 5, 15, 30 and 60 min, frozen at 80oC and processed for RNA extraction. For the publication, the experiment was repeated twoce, and corresponding timepoints from each experiment were averaged. The first 4 and last 4 arrays in this set correspond to each experiment.

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Identification of E93 binding sites in Drosophila melanogaster

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2019-02-02 | E-MTAB-4083 | biostudies-arrayexpress

Plasma small RNASeq comparison with Illumina TruSeq and Biooscientific NextFlex

Project description:Comparison of small RNA sequencing for 5.0, 3.0, 2.0, 1.0, 0.5, and 0.2 ml starting volumes of plasma

2018-04-13 | GSE113044 | GEO

Transcription profiling of yeast treated with NaCl and FK506 vs NaCl

Project description:Cells were cultured with or without FK506 treatment and exposed to 0.8 M NaCl. Samples were collected from the drug-treated and control cultures at 30 and 45 min after Na+ addition. For the publication, the experiment was repeated twice, and the corresponding time points from each experiment were averaged. The first two arrays and the last two arrays of this set correspond to the two experiments.

2005-01-01 | E-SMDB-13 | biostudies-arrayexpress

rrp6 delta and rrp6 delta, trf4 delta vs WT

Project description:BMA64 rrp6 delta::HIS3 vs BMA64 WT (Mat a), grown at 30°C to OD 0.6 in YPD. BMA64 rrp6 delta::URA3, trf4 delta::KAN vs BMA64 WT, grown at 30°C to OD<0.6 in YPD. Keywords: other

2005-04-28 | GSE2579 | GEO

RNAseq analysis for lung resident cells from protease allergen and FK506 treated mice

Project description:There is evidence for the beneficial effect of FK506, an effective immunosuppressive agent, for the treatment of asthma; however, the mechanisms underlying these effects are unclear. Using a mouse model of airway inflammation induced by Papain, a protease allergen, and RNAseq analysis of lung innate cells, we found that FK506 inhibited the activation of ILC2s, which initiate airway inflammation, as well as the induction of TH2 cells, which cause chronic inflammation. Our findings further support the clinical value of FK506 for the treatment of allergen-induced airway inflammation and clarify its targets and mechanisms of action.

2021-12-07 | GSE189918 | GEO

Identification and characterization of C4 dicarboxylic acid transporters in Pichia kudriavzevii CY902 strain

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

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