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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomic regulation during meiosis (Clb5Delta-Clb6Delta mutant)

ABSTRACT: We studied the meiotic regulation of transcription in the mutant Clb5Delta-Clb6Delta (deficient for the meiotic replication), by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h. Keywords: yeast meiotic time course, transcriptome For each time point, we measured the level of mRNA extracted at the time point to a mRNA meiotic mix composed of mRNA extracted at each time point. We normalize this ratio to the ratio measured at time t=0h and transform into log2ratios.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Nicolas Robine

PROVIDER: E-GEOD-10948 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptomic regulation during meiosis

Project description:We studied the meiotic regulation of transcription, by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h. Keywords: yeast meiotic time course, transcriptome For each time point, we measured the level of mRNA extracted at the time point to a mRNA meiotic mix composed of mRNA extracted at each time point. We normalize this ratio to the ratio measured at time t=0h and transform into log2ratios. The experiment is carried out in triplicates, from three independant cultures.

2008-10-31 | E-GEOD-10944 | biostudies-arrayexpress

Transcriptomic regulation during meiosis (Spo11Y135F mutant)

Project description:We studied the meiotic regulation of transcription in the mutant Spo11Y135F (deficient for the formation of meiotic double-strand breaks), by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h. Keywords: yeast meiotic time course, transcriptome For each time point, we measured the level of mRNA extracted at the time point to a mRNA meiotic mix composed of mRNA extracted at each time point. We normalize this ratio to the ratio measured at time t=0h and transform into log2ratios. The experiment is carried out in duplicates, from two independant cultures.

2008-10-31 | E-GEOD-10947 | biostudies-arrayexpress

Transcriptomic regulation during meiosis

2008-11-01 | GSE10944 | GEO

Transcriptomic regulation during meiosis (Clb5Delta-Clb6Delta mutant)

Project description:We studied the meiotic regulation of transcription in the mutant Clb5Delta-Clb6Delta (deficient for the meiotic replication), by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h. Keywords: yeast meiotic time course, transcriptome

2008-11-01 | GSE10948 | GEO

Transcriptomic regulation during meiosis (Spo11Y135F mutant)

2008-11-01 | GSE10947 | GEO

Transcriptomic regulation and methylation of the Lysine4 of Histone H3 during meiosis

Project description:This SuperSeries is composed of the following subset Series: GSE10836: Meiotic time course of Histone H3 occupancy GSE10837: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) in a mutant Spo11F GSE10838: Meiotic time course of Histone H3 occupancy in a mutant Spo11F GSE10839: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) in a mutant clb5Delta-clb6Delta GSE10840: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) GSE10944: Transcriptomic regulation during meiosis GSE10947: Transcriptomic regulation during meiosis (Spo11Y135F mutant) GSE10948: Transcriptomic regulation during meiosis (Clb5Delta-Clb6Delta mutant) GSE12879: Meiotic DNA double strand breaks in wild-type and set1 cells Keywords: SuperSeries Refer to individual Series

2008-10-31 | E-GEOD-11004 | biostudies-arrayexpress

T. Brucei, Nup-1 Depletion

Project description:Organization of the genome into compacted chromatin is a eukaryotic innovation facilitating increased sophistication in transcriptional regulation. In metazoa coiled-coil lamin proteins are major components of the chromatin organizer at the nuclear periphery and maintain nuclear integrity. While identifiable lamin homologues are restricted to metazoans, morphologically analogous structures maintaining nuclear organization in other eukaryotic lineages are known, but the molecular constituents remain undefined. Trypanosoma brucei NUP-1 is a large coiled-coil protein associated with fibrils at the inner face of the nuclear envelope. Using transcriptome analysis in combination with RNA interference and various imaging techniques, we demonstrate that NUP-1 forms a stable immobile cage around the nucleus, is required for viability and nuclear structural integrity, directs the positional organization of nuclear pore complexes, and serves to organize chromatin and specifically repress genes located at the nuclear periphery involved in immune evasion. Based on architectural similarity and functionality, we propose that NUP-1 is a novel, highly divergent lamin The effect of Nup-1 depletion on the transcriptome was examined in three independent experiments (A, B, & C). T. brucei cultures were either treated with RNAi (plus) or left untreated (minus) and RNA was extracted from each sample at the indicated time point (0h, 6h, 12h, 24h, or 48h). Two color microarrays were performed comparing treated and untreated samples at each time point. Dye swaps were performed and are indicated. Replicates of t=12h and t=24h for sample B were also included.

2011-12-15 | E-GEOD-26256 | biostudies-arrayexpress

A shotgun proteomics reference map for the alkali-sensitive covalently-linked proteins of the cell wall of A. fumigatus during specific stages of early fungal development (dormant conidia, isotropically expanding conidia, early germ tube emergence and young hyphae).

Project description:Four different developmental time points representing the Afu development from dormant conidia into young hyphae (0h, 4h, 6h, 8h) were chosen. Cell walls of the Afu samples were extracted using denaturing methods followed by isolation of solubilized proteins. Samples were processed using filter aided sample preparation (FASP) / trypsin digestion. The peptides were analyzed by one-dimensional LC (capillary C18 nano-Eflow mode) on-line with a nano-ESI source and tandem MS (LTQ ion trap).

2016-12-20 | PRD000567 | Pride

Gene expression time-course in the human skin during elicitation of allergic contact dermatitis

Project description:Genes involved in the inflammatory response resulting in allergic contact dermatitis (ACD) are only partly known. In this study, we introduce the use of high density oligonucleotide arrays for gene expression profiling in human skin during the elicitation of ACD. Skin biopsies from normal and nickel-exposed skin were obtained from 7 nickel-allergic patients and 5 non-allergic controls at four different time points during elicitation of eczema: 0h, 7h, 48h and 96h. Each gene expression profile was analysed by hybridization to high density oligonucletide arrays. Cluster analysis of 74 genes found to be differentially expressed in the patients over time revealed that the patient samples may be categorised into two groups: An early time point group (0h and 7h) and a late time point group (48h and 96h). Compared to the early time points, late time point skin samples were characterised by the up-regulation of inflammatory molecules including genes involved in the class I antigen presenting pathway and genes involved in lymphocyte adhesion and motility Correspondence analysis including both patients and controls revealed three distinct groups: i) the control group, ii) the early time point patient group (0h and 7h) and iii) the late time point patient group (48h and 96h). Keywords: time course, allergic response

2007-04-03 | GSE6281 | GEO

mer1D_SK1, mer2D_SK1, mer3D_SK1, spo22D_SK1, and spo70D_SK1 on expression/splicing microarrays

Project description:mer1D_SK1, mer2D_SK1, mer3D_SK1, spo22D_SK1, spo70D_SK1 late 9h meiotic time point. mer1D, mer2D, mer3D, spo22D diploid, and spo70D diploid was generated in the SK1 strain background (ATCC: MYA-2089) by PCR-mediated cassette-based gene replacement where the MER1, MER2, MER3, SPO22, or SPO70 ORF respectively was replaced with HIS3 from S. kluyveri then the transformants were sporulated and the homozygous deletion was verified by PCR. Meiotic time point =9h; Dye swap; Reference WT_SK1 9h

2011-04-05 | E-GEOD-24678 | biostudies-arrayexpress

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