Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

5 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq of Mucor strains cultured on potato dextrose agar (PDA)

ABSTRACT: Mucor species belongs to the Mucorales order within the phylum Mucoromycota, an early diverging fungal lineage. The purpose of this study was to investigate at the transcriptome scale the similarities and differences that could be linked to different lifestyles. Five strains pertaining to five species were studied: M. fuscus and M. lanceolatus, two species used in cheese ripening, M. racemosus, a recurrent cheese spoiler sometimes described as an opportunistic pathogen, M. circinelloides, often described as an opportunistic pathogen and M. endophyticus, a plant endophyte species.

INSTRUMENT(S): Illumina HiSeq 1500, Illumina HiSeq 2000

ORGANISM(S): Mucor lanceolatus

SUBMITTER: Erwan Corre

PROVIDER: E-MTAB-6453 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The heme-responsive PrrH sRNA regulates Pseudomonas aeruginosa pyochelin gene expression

Project description:Pseudomonas aeruginosa is an opportunistic pathogen that requires iron for growth and virulence, yet this nutrient is sequestered by the innate immune system during infection. When iron is limiting, P. aeruginosa expresses the PrrF1 and PrrF2 small regulatory RNAs (sRNAs), which post-transcriptionally repress expression of non-essential iron-containing proteins thus sparing this nutrient for more critical processes.The genes for the PrrF1 and PrrF2 sRNAs are arranged in tandem on the chromosome, allowing for the transcription of a longer heme-responsive sRNA, termed PrrH. While the functions of PrrF1 and PrrF2 have been studied extensively, the role of PrrH in P. aeruginosa physiology and virulence is not well understood. In this study, we performed transcriptomic and proteomic studies to identify the PrrH regulon.

2023-08-11 | PXD040948 | Pride

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

2019-11-12 | PXD010845 | Pride

Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors

Project description:We performed mRNA-seq of a PRKACA-mutant adrenal tumor and demonstrated that the mutation is expressed at the mRNA level. Total RNA obtained from a cortisol-producing adrenal tumor with a PRKACA p.Leu206Arg mutation.

2014-04-15 | E-GEOD-56016 | biostudies-arrayexpress

Rpd3L HDAC links H3K4me3 to transcriptional repression memory

Project description:Transcriptional memory is critical for the faster reactivation of necessary genes upon environmental changes and requires that the genes were previously in an active state. However, whether transcriptional repression also displays “memory” of the prior transcriptionally inactive state remains unknown. In this study, we show that transcriptional repression of approximately 540 genes in yeast occurs much more rapidly if the genes have been previously repressed during carbon source shifts. This novel transcriptional response has been termed transcriptional repression memory(TREM). Interestingly, Rpd3L histone deacetylase (HDAC), targeted to active promoters induces TREM. Mutants for Rpd3L exhibit increased acetylation at active promoters and delay TREM and RNA PolII dissociation significantly. Surprisingly, the interaction between H3K4me3 and Rpd3L via the Pho23 PHD finger is sufficient to induce histone deacetylation and TREM by Rpd3L. Therefore, we propose that an active mark, H3K4me3 enriched at promoters, instructs Rpd3L HDAC to induce histone deacetylation and TREM.

2018-10-23 | E-MTAB-6551 | biostudies-arrayexpress

RNA-seq analysis of Helicobacter cinaedi ATCC BAA-847 under microaerobic and aerobic culture conditions

Project description:Helicobacter cinaedi is an emerging bacterial pathogen of immunosuppressed individuals. The species is traditionally thought to require an H2-enhanced microaerobic atmosphere for growth, although it can proliferate under aerobic conditions when co-cultured with epithelial monolayers or supplemented with certain metabolites (notably, L-lactate). The goal of this experiment was to assess the global transcription changes that occur in the H. cinaedi type strain (ATCC BAA-847) under various media and atmospheric conditions. These include bacterial monoculture, as well as co-culture with Caco-2 intestinal epithelial cells. In total, Illumina mRNA-seq (stranded, paired-end) was performed on H. cinaedi grown under 9 in vitro culture conditions (4-5 biologic replicates per condition).

2016-09-19 | E-MTAB-5062 | biostudies-arrayexpress

Sequence database choice significantly affects taxonomic and functional metaproteomic results in gut microbiota studies

Project description:Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics (the study of the whole protein complement of a microbial community) can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Here we present a systematic investigation of variables concerning database construction and annotation, and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. Taxonomic and functional results were revealed to be strongly database-dependent, especially when dealing with mouse samples. As a striking example, in mouse the Firmicutes/Bacteroidetes ratio varied up to 10-fold depending on the database used. Finally, we provide recommendations regarding metagenomic sequence processing aimed at maximizing gut metaproteome characterization, and contribute to identify an optimized pipeline for metaproteomic data analysis.

2016-10-10 | PXD004039 | Pride

RNA-seq data from 74 patients with chronic lymphocytic leukemia

Project description:The RNA-seq data provided here were collected in order to examine the effect of identified coding and non-coding genomic aberrations on gene expression, as part of the publication ‘Whole-genome sequencing of chronic lymphocytic leukemia (CLL) identifies subgroups with distinct biological and clinical features’ by Robbe et al, Nat Gen, 2022.

2022-10-31 | E-MTAB-12124 | biostudies-arrayexpress

RNA-seq of 12-weeks-old male murine heart ventricles.

Project description:RNA-Seq analysis of mouse cardiac transcriptome. RNA was isolated from the ventricles of 12-weeks-old male mice. Sequencing libraries were prepared using TrueSeq Stranded RNA LT Kit Ribo-Zero Gold (Illumina, 15032619). Libraries were pair-end sequenced on a MiSeq sequencer (Illumina) and mapped to the Mus musculus reference genome GRCm38 (https://support.illumina.com/sequencing/sequencing_software/igenome.html) using TopHat2 (Kim et al., 2013). Differential gene-expression analysis between controls and the EphB4 flox mice was performed using DESeq2 (Love et al., 2014). Read counts were obtained with HTSeq (Anders et al., 2015). Genes were considered as differentially expressed when the FDR-adjusted p-value was Ôëñ0.05.

2020-01-15 | E-MTAB-7686 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes for Wild Type and Mutants including opaque2, PbfRNAi and PbfRNAi;o2 in Zea mays

Project description:The goals of this study are to study the regulatory network of the two maize endosperm-specific transcription factors O2 and PBF by 16-DAP endosperm transcriptome profiling (RNA-seq) of their mutants and wild type. The results utilize the expression pattern of global genes regulated by PBF and O2 to elucidate their control for storage compounds synthesis in maize kernels. The 16-DAP endosperm transcriptome of wild type (WT) and mutants including opaque2, PbfRNAi and PbfRNAi;o2 were generated by RNA-seq with three biological replicates per genotype on Illumina HiSeqTM2500.

2016-03-24 | E-GEOD-79513 | biostudies-arrayexpress

RNA-seq in 4 tissues of 10 mammals

Project description:To study the tissue-specific evolution of regulatory elements and gene expression in the mammalian lineage, we created a comprehensive map of promoters and enhancers in 4 tissues of 10 mammalian species. To assay tissue-specific gene expression we performed RNA-seq experiments in adult liver, muscle, brain and testis of all 10 species. The species included in the study are: macaque, marmoset, mouse, rat, rabbit, pig, dog, cat, horse and opossum. To map in-vivo promoters and enhancers, we performed ChIP-seq experiments for H3K4me3, H3K27ac and H3K4me1 in all tissues and species and submitted these separately to ArrayExpress.

2019-09-01 | E-MTAB-8122 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data