Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10851031_1.fastq.gz | Fastqsanger.gz | |||
| SRR10851031_2.fastq.gz | Fastqsanger.gz | |||
| SRR10851032_1.fastq.gz | Fastqsanger.gz | |||
| SRR10851032_2.fastq.gz | Fastqsanger.gz | |||
| SRR10851033_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Here we report a metatranscriptomic analysis of gene expression and regulation of “Candidatus Accumulibacter”-enriched lab-scale sludge during enhanced biological phosphorus removal (EBPR). Medium density oligonucleotide microarrays were generated with probes targeting most predicted genes hypothesized to be important for the EBPR phenotype. The objectives were to investigate which genes were expressed during EBPR and which genes were differentially expressed between the early stage of anaerobic and aerobic phases (defined as 15 min after acetate addition and 15 min after switching to aeration respectively).
2009-12-31 | GSE17857 | GEO
Project description:Eukaryotic RNA polymerase II (RNAPII) transcribes mRNA genes and non-protein coding RNAs (ncRNAs) including small nuclear and nucleolar RNAs (sn/snoRNAs). In metazoans, RNAPII transcription of sn/snoRNAs is facilitated by a number of specialized complexes, but no such complexes have been discovered in yeast. It has been proposed that yeast sn/snoRNA promoters use the same factors as mRNA promoters, but the extent to which regulators of mRNA genes function at yeast sn/snoRNA genes is unclear. Here, we investigated a potential role for the Mediator complex, essential for mRNA gene transcription, in the transcription of sn/snoRNA genes. We found that the Mediator maps to most sn/snoRNA gene regulatory regions and that rapid depletion of the essential structural subunit Med14 strongly reduces RNAPII and TFIIB occupancy as well as nascent transcription of sn/snoRNA genes. Deletion of Med3 and Med15, subunits of the activator-interacting Mediator tail module, does not affect Mediator recruitment to or RNAPII and TFIIB occupancy of sn/snoRNA genes. Our analyses suggest that Mediator promotes PIC formation and transcription at sn/snoRNA genes, expanding the role of this critical regulator beyond its known functions in mRNA gene transcription and demonstrating further mechanistic similarity between the transcription of mRNA and sn/snoRNA genes.
2018-10-08 | GSE112721 | GEO
Project description:In E. faecalis OG1RF, disruption of the ahrC gene encoding a predicted ArgR family transcription factor results in a severe defect in biofilm formation in vitro, as well as significant attenuation of virulence in multiple experimental infection models. Using RNA-seq, we observed ahrC-dependent changes in expression of over 20 genes. AhrC-repressed genes included predicted determinants of arginine catabolism and several other metabolic genes and predicted transporters, while AhrC-activated genes included determinants involved in production of surface protein adhesins. Most notably, the structural and regulatory genes of the ebp locus encoding adhesive pili were positively regulated, as well as the ace gene, encoding a collagen binding adhesin. Using lacZ transcription reporter fusions, we determined that ahrC and a second argR transcription factor gene, argR2, both function to activate expression of ebpR, which directly activates transcription of the pilus structural genes. Our data suggest that in wild-type E. faecalis, the low levels of EbpR limit expression of pili, and that biofilm biomass is also limited by the amount of pili expressed by the bacteria. Expression of ace is similarly activated by AhrC and ArgR2, but ace expression is not dependent on EbpR. Our results demonstrate the existence of novel regulatory cascades controlled by a pair of ArgR family transcription factors that may function as a heteromeric protein complex.
2018-07-12 | GSE112936 | GEO
Project description:During oocyte maturation, the transition from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) stage coincides with dramatic chromatin reconfiguration and transcriptional silencing and is crucial for developmental competence. To study the transcriptome and DNA methylation dynamics during the NSN to SN transition we used single cell (sc)M&T-seq to generate scRNA-seq and sc bisulphite-seq data from GV oocytes, classified as NSN or SN by Hoechst staining of their nuclei. Transcriptome analysis showed a lower number of detected transcripts in SN oocytes as well as downregulation of 576 genes, which were enriched for processes related to mRNA processing. We used the RNA-seq data to generate a classifier, which can infer chromatin stage in scRNA-seq data sets, based on their transcription profile. The classifier was successfully tested in multiple published datasets of mouse models with a known skew in NSN:SN ratios. DNA methylation analysis showed increased methylation in SN compared to NSN oocytes, which was most pronounced in regions with intermediate levels of DNA methylation. Overlap with ChIP-seq data for the histone modifications H3K36me3, H3K4me3 and H3K27me3 showed that regions gaining methylation in SN oocytes are enriched for overlapping H3K36me3 and H3K27me3, which is unusual as these marks do not typically coincide. We believe that these late-methylating SN regions are in regions with high chromatin plasticity and that the overlap of H3K36me3 and H3K27me3 may indicate a transient switch or heterogeneity on a single-cell level.
2025-01-02 | GSE274329 | GEO
Project description:Biofilms are ubiquitous in nature, forming diverse adherent microbial communities that perform a plethora of functions. Here, we operated two laboratory-scale sequence batch reactors enriched with Candidatus Accumulibacter phosphatis (Accumulibacter) performing enhanced biological phosphorus removal (EBPR). Reactors formed two distinct biofilms, a floccular biofilm, consisting of small, loose, microbial aggregates, and a granular biofilm, forming larger, dense, spherical aggregates. Using metaproteomic methods we investigated the proteomic differences between these two biofilm communities, identifying a total of 2022 unique proteins. Both biofilms contained proteins that were indicative of core EBPR metabolisms and cellular function. To understand the proteomic differences between floccular and granular biofilm communities, we compared protein abundances that were statistically enriched in both biofilm states (alpha level = 0.05). Floccular biofilms were enriched with pathogenic secretion systems suggesting a previously unrecognized, highly competitive, mixed microbial community. Comparatively, granular biofilms revealed a high stress environment with evidence of nutrient starvation, phage predation pressure, extracellular polymeric substance (EPS) synthesis, and increased cell lysis. Granular biofilms enriched outermembrane transport proteins to scavenge the extracellular milieu for amino acids and other metabolites, likely released through cell lysis, to supplement core EBPR metabolic pathways. This study provides the first detailed proteomic comparison between Accumulibacter–enriched floccular and granular biofilm communities, proposes a conceptual model for the granule biofilm, and offers novel insights into granule biofilm formation and stability.
2015-08-24 | PXD002404 | Pride
Project description:We selected NSN and SN GV oocytes based on FBL-GFP localization, and performed transcriptome profiling of single NSN and SN GV oocytes, and MII oocytes in vitro matured from NSN and SN GV oocytes.
2021-03-27 | GSE163935 | GEO
Project description:The molecular properties of benign melanocytic lesions are poorly understood. Only few studies have been performed on specific nevi subtypes, including common nevocellular nevi (NCN) or Spitz nevi (SN). Genomic alterations in melanoma-associated oncogenes are typically absent in SN. In the present study, mRNA expression of 25 SN and 15 NCN were analyzed. Molecular profiling was done using the RNA NanoString nCounter Gene Expression Platform (No. of genes = 770). Marker discovery was performed with a training set consisting of 7 SN and 7 NCN samples from the same patients, and validation was performed using a second set consisting of 18 SN and 8 NCN samples. Using the training set, 197 differentially expressed genes were identified in SN versus NCN. Of these, 74 genes validated in the validation set (FDR Q value ≤ 0.13). In addition, using Random Forest and LASSO feature selection a molecular signature of SN versus NCN was identified including 15 top-ranked genes. Gene set analysis showed upregulation of gene pathways with increased expression of transcripts related to immunomodulatory, inflammatory and extracellular matrix interactions as well as angiogenesis associated processes in SN. Although the molecular characteristics of malignant melanoma have been studied in detail, the molecular properties of benign melanocytic lesions such as common nevocellular nevi (NCN) and Spitz nevi (SN) remain poorly understood. This limited knowledge hinders a better understanding of atypical and malignant transformation of melanocytes. The present study identified a distinct molecular expression profile in SN compared to NCN, even when lesions were obtained from the same patients. These findings strongly indicate that SN represent a distinct group of melanocytic neoplasms and evolve differentially and not sequentially from NCN.
2018-02-15 | GSE110589 | GEO
Project description:Manufactured nanomaterials (MNMs) are increasingly incorporated into consumer products that are disposed into sewage. In wastewater treatment, MNMs adsorb to activated sludge biomass where they may impact biological wastewater treatment performance, including nutrient removal. Here, we studied MNM effects on bacterial polyhydroxyalkanoate (PHA), specifically polyhydroxybutyrate (PHB), biosynthesis because of its importance to enhanced biological phosphorus (P) removal (EBPR). Activated sludge was sampled from an anoxic selector of a municipal wastewater treatment plant (WWTP), and PHB-containing bacteria were concentrated by density gradient centrifugation. After starvation to decrease intracellular PHB stores, bacteria were nutritionally augmented to promote PHB biosynthesis while being exposed to either MNMs (TiO2 or Ag) or to Ag salts (each at a concentration of 5 mg L-1). Cellular PHB concentration and PhyloChip community composition were analyzed. The final bacterial community composition differed from activated sludge, demonstrating that laboratory enrichment was selective. Still, PHB was synthesized to near-activated sludge levels. Ag salts altered final bacterial communities, although MNMs did not. PHB biosynthesis was diminished with Ag (salt or MNMs), indicating the potential for Ag-MNMs to physiologically impact EBPR through the effects of dissolved Ag ions on PHB producers.
2014-12-03 | GSE63781 | GEO