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Steady state +/- Gly

ABSTRACT: Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) with or without supplementation with 10 mM glycine and harvested. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen. Arrays compared expression of Gly- cells to the Gly+ controls. Strain BY4741 was the wild type and several deletion strains were also used. Keywords: parallel sample

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE1553 | GEO | 2004/07/17

SECONDARY ACCESSION(S): PRJNA89955

REPOSITORIES: GEO

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Steady state +/- Gly

Project description:Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) with or without supplementation with 10 mM glycine and harvested. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen. Arrays compared expression of Gly- cells to the Gly+ controls. Strain BY4741 was the wild type and several deletion strains were also used. Keywords: parallel sample

2004-07-17 | E-GEOD-1553 | biostudies-arrayexpress

Time course of glycine addition or withdrawal

Project description:+Gly 20, 40, 80: Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) and t=0 time point samples were harvested (250 ml). The remainder of the medium was supplemented with 10 mM glycine incubated at 30oC and samples (250 ml) harvested at 20, 40 and 80 minutes. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen. -Gly 20, 40, 80: Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) supplemented with 10 mM glycine and t=0 time point samples were harvested (250 ml). The remainder of the medium was filtered and the cells were rapidly resuspended in 750 ml of pre-warmed B minimal medium, incubated at 30oC and samples (250 ml) harvested at 20, 40 and 80 minutes. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen. Keywords: time-course

2004-07-17 | GSE1554 | GEO

Time course of glycine addition or withdrawal

2010-10-08 | E-GEOD-1554 | biostudies-arrayexpress

Expression data from HeLa cells treated with Casiopeina Cas-II-gly

Project description:Copper-based chemotherapeutic compounds Casiopeinas, have been presented as able to promote selective programmed cell death in cancer cells, thus being proper candidates for targeted cancer therapy. DNA fragmentation and apoptosis -in a process mediated by reactive oxygen species- for a number of tumor cells, have been argued to be the main mechanisms. However, a detailed functional mechanism (a model) is still to be defined and interrogated for a wide variety of cellular conditions; before establishing settings and parameters needed for their wide clinical application. Microarrays were used to determine the expression profile from HeLa cells in order to propose a model for the role played by intrinsic apoptosis triggered by the oxidative stress caused by Cas-II-gly. The cervix-uterine cell line HeLa was maintained at 37C in 5% CO2 under sterile conditions in Dulbecco's modified Eagle medium (DMEM, Sigma), supplemented with 10% fetal bovine serum (Sigma). Cells were treated with Cas II-gly in 96-well microplates by 6 h. HeLa cells whole genome gene expression experiments (triplicates for cases/controls) were performed in total mRNA extracted under the GPL570 protocol.

2012-10-31 | E-GEOD-41827 | biostudies-arrayexpress

Comparison of Candida albicans lab strain SC5314 grown at different temperatures

Project description:Candida albicans lab strain SC5314 was grown in YPD broth at 30C and 37C from OD600=0.1 till 1.0. Cells were harvested and flash frozen in liquid nitrogen. Then the transcriptome was compared.

2022-07-18 | E-MTAB-11924 | biostudies-arrayexpress

Expression data from HeLa cells treated with Casiopeina Cas-II-gly

2012-10-31 | GSE41827 | GEO

SLF1 overexpression versus control cells

Project description:Measure the relative changes of gene expression upon GIS2 overexpression; BY4741 cells bearing plasmid pBG1805-Slf1 or control plasmid pBG1805 were grown in SC ura- gal at 30 C for 6 or 24 hours. An overnight culture of cells was inoculated at an OD600 of 0.1 and further grown to an OD600 of 0.5- 0.7 in 60 ml SC Ura- Gal at 30 C. Cells were harvested by centrifugation, washed twice with 600 ul of ice-cold sterile water. 200 ul of cells were removed and RNA was isolated by hot phenol extraction for microarray analysis. 7.5 ug of total RNA derived from cells expressing the empty vector (pBG1805) or Slf1p (pBG1805_Slf1) were reverse transcribed in the presence of 5-(3-aminoallyl)-dUTP and natural dNTPs with a mixture of N9 and dT20V primers, and cDNAs were covalently linked to Cy3 and Cy5 NHS-monoesters (GE HealthSciences Cat# RPN5661), respectively, and competitively hybridized on yeast oligo arrays at 42 degrees celsius for 14 hours in formamide-based hybridization buffer. Microarrays were scanned with an Axonscanner 4200 (Molecular Devices) and analyzed with GenePix Pro 5.1 (Molecular devices).

2012-02-08 | GSE27311 | GEO

Comparison of the transcriptomes of one aneuploid strain and the parent lab strain SC5314

Project description:We did RNA-seq in Candida albicans of one chromosome 1 trisomy strain as well as the parent SC5314. Strains were grown in YPD broth from OD600 of 0.1 till 1.0. Then cells were harvested and flash frozen. The purpose was to see what genes were regulated by chromosome 1 trisomy and thereby causing tolerance to aureobasidin A.

2022-12-05 | E-MTAB-12403 | biostudies-arrayexpress

Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock

Project description:Glyphosate (GLY) is an effective antimetabolite that acts against the shikimate pathway 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, However, little is known about the genome-scale transcriptional responses of bacteria after glyphosate shock. To investigate further the mechanisms by which E. coli response to a glyphosate shock, a DNA-based microarray was used for transcriptional analysis of E. coli exposed to 200 mM glyphosate. RNA extracted from cells of E. coli K-12 JM109 cells after 4 h of growth to OD600 achieve 0.4, or cells after 200 mM glyphosate shock for 1 h when their OD600 achieved 0.4.

2011-07-21 | E-GEOD-30838 | biostudies-arrayexpress

Expression profile of S. pombe cells with ribosomal protein L32 paralogs

Project description:We cultured the cells of S. pmbe in EMM2, and harvested them in the OD600 of 0.5 and 10 respectively. We used microarrays to detail the the global program of gene expression of SP-Q01 and SP-Q01 carrying vevtor pESP3X to overexpress either ribosomal protein L32 paralog in the OD600 of 0.5 and 10 respectively.

2013-03-01 | GSE43827 | GEO

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