Transcriptome analysis of a N. punctiforme sigG mutant
Ontology highlight
ABSTRACT:
ORGANISM(S): Nostoc punctiforme
SUBMITTER: Michael Summers
PROVIDER: E-GEOD-61442 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Nostoc punctiforme is a filamentous cyanobacterium capable if differentiating normal vegetative cells into nitrogen fixing heterocysts and spore-like akinetes. Here the effects of a sigma factor (sigG) mutation on the transcriptome was analyzed under 1) normal vegetative growth, and 2) following akinete induction. A zwf strain grown with fructose differentiates into akinetes following transfer to darkness. A DNA microarray was used to compare gene expression from the zwf strain to a zwf sigG double mutant two days following akinte induction by darkness.
2015-09-01 | GSE61442 | GEO
Project description:For the filamentous cyanobacterium Anabaena variabilis to grow without combined nitrogen, certain cells differentiate into heterocysts that fix N2, while vegetative cells perform photosynthesis. Much remains unknown on how heterocysts differ from vegetative cells in terms of carbon and energy metabolisms. Microarrays were used to investigate gene transcription patterns in vegetative cells, heterocysts, and filaments of N2-fixing phototrophic, mixotrophic, and heterotrophic cultures. Hybridizations used NimbleGen expression array chips (Product no. A4385-00-01, platform accession no GPL15883) designed against the 5,657 ORFs encoded in the A. variabilis genome (GenBank accession no. CP000117). Each ORF was represented by seventeen 60-mer oligonucleotides. Each oligonucleotide was present in four internal replicates. The twenty-seven microarray data files were normalized against each other. Expression array data were analyzed using ArrayStar 3.0 (DNASTAR, Madison, WI).
2013-11-01 | E-GEOD-46076 | biostudies-arrayexpress
Project description:We performed a laboratory experiment with vegetative gametophytes of the kelp Saccharina latissima and exposed the gametophytes to three temperatures (4°C, 12°C and 20°C) by sex (female, male) for 14 days.
2019-09-25 | E-MTAB-8267 | biostudies-arrayexpress
Project description:Microarray analysis was used to compare different developmental stages of the filamentous fungus Aspergillus nidulans. Cells were grown for various times and comparisons made between: 1. Isolated conidia (0 hours) and isotropically expanding cells (3 hours). 2. Isotropically expanding cells (3 hours) and polarly extending cells (5 hours). 3. Undifferentiated vegetative hyphae (18 hours) and synchronously conidiating cultures (42 hours). A total of 4 hybridizations were performed for each microarray experiment described in the summary. The following replicates were carried out: 1. Two biological replicates were performed using cultures grown in parallel. 2. Two Technical ‘dye swap’ replicates were carried out for each biological replicate.
2008-05-01 | E-GEOD-7698 | biostudies-arrayexpress
Project description:Strand specific RNA sequencing of S. pombe revealed a highly structured programme of ncRNA expression at over 600 loci. Waves of antisense transcription accompanied sexual differentiation. A substantial proportion of ncRNA arose from mechanisms previously considered to be largely artefactual, including improper 3’ termination and bi-directional transcription. Constitutive induction of the entire spk1+, spo4+, dis1+ and spo6+ antisense transcripts from an integrated, ectopic, locus disrupted their respective meiotic functions. This ability of antisense transcripts to disrupt gene function when expressed in trans suggests that cis production at native loci during sexual differentiation may also control gene function. Consistently, insertion of a marker gene adjacent to the dis1+ antisense start site mimicked ectopic antisense expression in reducing the levels of this microtubule regulator and abolishing the microtubule-dependent “horsetail” stage of meiosis. Antisense production had no impact at any of these loci when the RNAi machinery was removed. Thus, far from being simply ‘genome chatter’, this extensive ncRNA landscape constitutes a fundamental component in the controls that drive the complex programme of sexual differentiation in S. pombe. Thorough interrogation of the Schizosaccharomyces pombe transcriptome during sexual differentiation using strand-specific total RNA sequencing (AB SOLiD 3.0 and 3.0+). A total of 19 samples were analysed by two separate machine runs (henceforth first and second runs, respectively). In the first machine run the following 5 samples were processed (on a single sequencing slide): Vegetative haploid (strain IH5974), pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following temperature shift from 25ºC to 32ºC to induce meiosis by Pat1 inactivation. In the second machine run the following 14 samples were processed (on two sequencing slides): Vegetative haploid (IH5974), pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following the temperature shift (a biological replicate of the first machine run). In addition, asynchronous IH3365 (wild type diploid) was also sequenced to enable a series of pair-wise haploid/diploid comparisons between itself, asynchronous haploid (IH5974) and pat1.114 diploid (IH2912) at vegetative growth. Finally, to find putative targets of the two bzip transcription factors atf21 and atf31, we sequenced RNA extracts from IH8832 (atf21.delta diploid) and IH8814 (atf31.delta diploid) before (0), and 3, 5, and 10 hours after the temperature shift, while the pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following the temperature shift were used as reference for this analysis.
2011-12-20 | E-GEOD-28113 | biostudies-arrayexpress
Project description:To investigate the dynamics of the meiotic transcriptome and to ensure meiotic synchrony of our samples, we measured RNA abundance in vegetative cells, respiratory (pre-meiotic) cells and in synchronously sporulating cells at various times after transfer to sporulation media (SM). SK1 yeast strain SHy002 (MATa/MATα ho::LYS2/ho::LYS2 leu2::hisG/leu2::hisG lys2/lys2 ura3/ura3)<br> Meiotic Time Course with samples collected during vegetative growth (YPD), respiratory growth (pre-meiotic/YPA 8 hours) and 0 hr, 1.5hr, 3hr, 4.5hr, 6hr, 9hr and 12hr after transfer to sporulation media (SM).<br> 3 separate biological replicates were used for each condition/time-point.<br> Total RNA from each sample was hybridized competitively with a genomic DNA common reference.<br> The expression analysis was carried out from the same biological samples as the FAIRE analysis.<br>
2010-05-22 | E-GEOD-18181 | biostudies-arrayexpress
Project description:To investigate transcriptome dynamics during the transition from vegetative growth to meiosis, we measured RNA abundance in vegetative cells (YPD), respiratory cells (pre-meiotic/YPA 8 hours), and in cells undergoing synchronous meiosis/sporulation in the budding yeast Saccharomyces cerevisiae. There is growing recognition that the binding of a transcription factor near a gene does not always indicate regulatory function, and further that a single factor may function to either activate or repress its targets depending on the cellular context. We examined these issues through a series of experiments involving the S. cerevisiae transcription factor Rap1, and its function throughout critical metabolic and developmental transitions between vegetative growth, respiratory growth, meiosis and sporulation. We simultaneously monitored the expression of all genes and the genomic binding locations of Rap1 throughout the timecourse. Genes downstream of Rap1 binding were activated and repressed dynamically, but a change - or lack of change - in Rap1 binding status was not predictive of activation, repression, or no change in regulation. Despite this, we show that Rap1 is required, at a given point in time, for both activation and repression of different gene targets, within the same cell. Specification of the transcriptional consequences of Rap1 binding is thus highly promoter-specific. The presence of other transcription factor binding motifs, the subtype of Rap1 motif, and the underlying chromatin structure of the promoter cannot fully account for the observed transcriptional outcomes. There is a better accounting for the dynamic binding behavior of Rap1 including specification of an expanded meiotic target set through a Tup1- dependent nucleosome-loss mechanism. The variable and dynamic association between binding and transcription in this simple unicellular system portends a similarly volatile relationship in more complex eukaryotes. Biological interpretations of transcription factor occupancy should be made cautiously and in conjunction with supporting data obtained under the precise condition of interest. SK1 yeast strain SHy002 (MATa/MATα ho::LYS2/ho::LYS2 leu2::hisG/leu2::hisG lys2/lys2 ura3/ura3). Meiosis timecourse with samples collected during vegetative growth (YPD), respiratory growth (pre-meiotic/YPA 8 hours) and 0 hr, 1.5hr, 3hr, 4.5hr, 6hr, 9hr and 12hr after transfer to sporulation media (SM). 7 separate biological replicates were used for each condition/time-point. Labeled total RNA from each sample and a labeled genomic DNA common reference were competitively hybridized to yeast whole genome PCR based spotted arrays (resolution ~1kb). The Rap1 ChIP, RNA abundance/expression analysis, and FAIRE analysis were all carried out on the same biological samples.
2016-09-01 | E-GEOD-75257 | biostudies-arrayexpress
Project description:The Solexa/Illuminaâs digital gene expression (DGE) system was used to gain insight into the broad range of transcriptional responses during the vegetative growth, sclerotial development, myceliogenic germination, carpogenic germination, apothecium formation (stipe) and infection of Sclerotinia sclerotiorum. We obtained a sequencing depth of approximately 3.3 million clean tags per cDNA library. Tag mapping indicated that these six cDNA libraries in total represented more than 66.7% of all of the genes presented in the predicted transcript databases of the Broad Institute. Thouthands of differentially expressed genes were indentified during the various developmental stages compared to the vegetative growth stage. Our results could increase and deepen the understanding of the vegetative and reproductive development as well as the infection of S. sclerotiorum The S. sclerotiorum strain Ep-1PNA367 was grown or treated under different conditions, and samples were collected for RNA extraction for DGE analysis during the following stages: (i) Vegetative stage: activating hyphal agar discs of the Ep-1PNA367 stain were placed on a cellophane membrane overlaid onto PDA medium at 20°C; subsequently, the mycelia were collected at 12, 24, 36, 48 and 60 h; (ii) Sclerotial formation stage: the colonies growing on the cellophane membrane overlaid onto PDA medium were further incubated under the same conditions and then the cultures were collected at 84, 96, 108, 120 and 132 h; (iii) Early stages of infection: fresh hyphal fragments of the Ep-1PNA367 strain were overlaid onto sterilized cheese cloth, which was overlaid onto the leaves of the A. thaliana ecotype Columbia-0, followed by inoculation at 20°C with 100% relative humility; the cheese cloth with hyphae was then rolled up from the leaves at 9 h and 12 h; (iv) Sclerotial myceliogenic germination stage: sclerotia were surface sterilized with sodium hypochlorite and were sowed on a PDA plate at 20°C to induce myceliogenic germination, and when approximately 50% of sclerotia had germinated, the sclerotia were harvested; (v) Sclerotial carpogenic germination stage: sclerotia were dried at room temperature and were pretreated in a freezer (4-6°C) for up to one month and then were surface sterilized and sowed on wet sterilized sands in a plate at 15°C to induce carpogenic germination; when approximately 50% of the sclerotia germinated (stipes having only emerged from sclerotia), the sclerotia were harvested; and (vi) Early apothecial formation stage: sclerotia were allowed to grow in the same incubator, and the stipes were cut and collected immediately before apothecium formation for RNA extraction. Finally, different time-point samples from the vegetative stage, sclerotial formation stage and infection stage were pooled together respectively according to equal quantities for RNA extraction.
2016-05-19 | E-GEOD-65301 | biostudies-arrayexpress
Project description:ume6D_BY4741 vegetative RNA compared to WT_BY4741 vegetative RNA. ume6D haploid was generated in the BY4741 strain background (ATCC: 201388) by PCR-mediated cassette-based gene replacement where the UME6 ORF was replaced with KANMX6, the deletion was verified by PCR. Vegetatively grown; Dye swap; Reference vegetative WT_BY4741
2011-04-05 | E-GEOD-24680 | biostudies-arrayexpress
Project description:To investigate chromatin organization dynamics during the transition from vegetative growth to meiosis, we used Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in vegetative cells (YPD) and in cells undergoing synchronous meiosis/sporulation in the budding yeast Saccharomyces cerevisiae. There is growing recognition that the binding of a transcription factor near a gene does not always indicate regulatory function, and further that a single factor may function to either activate or repress its targets depending on the cellular context. We examined these issues through a series of experiments involving the S. cerevisiae transcription factor Rap1, and its function throughout critical metabolic and developmental transitions between vegetative growth, respiratory growth, meiosis and sporulation. We simultaneously monitored the expression of all genes and the genomic binding locations of Rap1 throughout the timecourse. Genes downstream of Rap1 binding were activated and repressed dynamically, but a change - or lack of change - in Rap1 binding status was not predictive of activation, repression, or no change in regulation. Despite this, we show that Rap1 is required, at a given point in time, for both activation and repression of different gene targets, within the same cell. Specification of the transcriptional consequences of Rap1 binding is thus highly promoter-specific. The presence of other transcription factor binding motifs, the subtype of Rap1 motif, and the underlying chromatin structure of the promoter cannot fully account for the observed transcriptional outcomes. There is a better accounting for the dynamic binding behavior of Rap1 including specification of an expanded meiotic target set through a Tup1- dependent nucleosome-loss mechanism. The variable and dynamic association between binding and transcription in this simple unicellular system portends a similarly volatile relationship in more complex eukaryotes. Biological interpretations of transcription factor occupancy should be made cautiously and in conjunction with supporting data obtained under the precise condition of interest. SK1 yeast strain SHy002 (MATa/MATα ho::LYS2/ho::LYS2 leu2::hisG/leu2::hisG lys2/lys2 ura3/ura3). Meiosis timecourse with samples collected during vegetative growth (YPD), and 0 hr, 1.5hr, and 3hr after transfer to sporulation media (SM). 3 separate biological replicates were used for each condition/time-point. Labeled FAIRE enriched DNA from each sample and a labeled genomic DNA common reference were competitively hybridized to Agilent yeast whole genome 4 x 44k tiling microarrays (resolution ~270bp). The Rap1 ChIP, RNA abundance/expression analysis, and FAIRE analysis were all carried out on the same biological samples. The three FAIRE timecourse replicates correspond to timecourse replicates 1, 4, and 6.
2016-09-01 | E-GEOD-75258 | biostudies-arrayexpress