Transcriptional decay profiling of Neurospora crassa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA997929 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25396915.fastq.gz | Fastqsanger.gz | |||
| SRR25396916.fastq.gz | Fastqsanger.gz | |||
| SRR25396917.fastq.gz | Fastqsanger.gz | |||
| SRR25396918.fastq.gz | Fastqsanger.gz | |||
| SRR25396919.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Codon optimality mediated decay(COMD) is a conserved phenomenon from yeast to human. Our data suggests that COMD alson exist in neurospora crass. We resort thiolutin(inhibitor for transcription) to treat cells in different time point and transcriptionally profiled them to get the landscape of transpcriptional decay profiling.
2023-12-31 | GSE238077 | GEO
Project description:Transcriptional profiling with next-generation sequencing methods demonstrated that a Neurospora crassa mutant with the three most highly expressed beta-glucosidase genes deleted had a transcriptional response to cellobiose similair to that of wild type N. crassa exposed to cellulose.
2012-04-05 | GSE36719 | GEO
Project description:Transcriptional profiling with next-generation sequencing methods demonstrated that a Neurospora crassa mutant with the three most highly expressed beta-glucosidase genes deleted had a transcriptional response to cellobiose similair to that of wild type N. crassa exposed to cellulose. N. crassa was pregrown in Sucrose and transferred to Avicel (cellulose), Cellobiose, Sucrose or media with no carbon added. Biological triplicates used to identify differentially expressed genes in WT on Avicel. Single libraries for mutant strains identify which genes show similair expression on cellobiose as in the WT on cellulose.
2012-04-04 | E-GEOD-36719 | biostudies-arrayexpress
Project description:RNA-seq from Neurospora crassa at 5 time points of light induction, with 2 replicates for each, totalling 10 samples RNA-seq from Neurospora crassa at 5 time points of light induction, with 2 replicates for each, totalling 10 samples
2014-08-01 | E-GEOD-53534 | biostudies-arrayexpress
Project description:Purpose: Evaluate the transcriptional profile of Neurospora crassa cells treated with a group of novel antifungal compounds Methods: Conidial suspensions were obtained and 1 x 106 cells/ml incubated in minimal medium for 6 hours (26ºC, 140 rpm, constant light) followed by the addition of the indicated compound (or DMSO) and growth for 1 more hour. Cells were harvested using 0.45 μm filters and immediately frozen in liquid nitrogen. Total RNA was isolated by the Trizol-Phenol-Chloroform method. After digestion of 25 μg RNA with TURBO DNAse (Life Technologies), mRNA was purified using Dynabeads oligo(dT) magnetic beads (Life Technologies). The mRNA was chemically fragmented using the Ambion RNA fragmentation kit (Life Technologies). First and second strand cDNA synthesis was achieved using appropriate kits (Life Technologies). The illumina TruSeq kit was employed to generate the cDNA libraries with indexing adapters essentially following the manufacturerâs protocol. After purification of the libraries with AMPure XP beads (Roche), the quality of the libraries was analysed in a Agilent 2100 Bioanalyzer. The cDNA libraries were sequenced in a illumina HiSeq2000 and single reads of 50 bp were obtained. Sequencing data was handled essentially with Tophat, Cufflinks and Cuffdiff. Expression levels are presented as Fragments Per Kilobase of transcript per Million mapped reads (FPKM). Results: XP13 promoted a particularly active transcriptional response. Functional enrichment analysis of the genes with altered expression revealed novel pathways that are affected by these compounds. Conclusions: These compounds are active in Neurospora crassa and we anticipate that this and future studies will ascertain their potential as antifungal agents. The transcriptional profile of Neurospora crassa wild type cells exposed with a group of novel compounds with antifungal activity was analysed using illumina HiSeq2000 and single reads of 50 bp.
2015-11-25 | E-GEOD-53040 | biostudies-arrayexpress
Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Neurospora crassa mat A FGSC#2489 2 developmental stages and oligo(dT) primers.
2010-07-17 | E-GEOD-22972 | biostudies-arrayexpress
Project description:To determine the genes directly and indirectly under the control of the Grainy-head homolog (GHH) transcription factor in Neurospora crassa Three different sample types (Aerial Hyphae & Conidia; Mycelia; or Whole Colonies) of both wild-type (FGSC #2489) and grainy-head homolog (FGSC #13563) strains of Neurospora crassa were subjected to transcriptome analyses to determine the genes differentially expressed in the ghh background compared to wild type.
2012-03-01 | E-GEOD-35017 | biostudies-arrayexpress
Project description:Transcriptional profiling of Neurospora crassa ∆mak-2 strain grown under phosphate-shortage were compared the transcription profile of the control strain grown in both low- and high-Pi cultures. The filamentous fungus Neurospora crassa provides an excellent model system for the study of molecular responses to ambient signaling in eukaryotic microorganisms. Inorganic phosphate is an essential growth-limiting nutrient in nature and is crucial in genetic information. Numerous ambient signals activate the recruitment of mitogen-activated protein kinase (MAPK) cascades. Thus, in an attempt to identify genes involved in metabolic responses to exogenous phosphate sensing and in the functioning of a mitogen-activated protein kinase coding gene (mak-2) in N. crassa, we performed microarray experiments with the strain carrying the mak-2 gene knockout (Δmak-2) grown under phosphate-shortage by comparing the transcription profile to that of the control strain grown in both low- and high-phosphate cultures. Here we provide evidence that the mak-2 gene is an element of the adaptive response to extracellular Pi changes revealing novel aspects of phosphorus-sensing network in N. crassa.
2013-07-31 | GSE41806 | GEO
Project description:A colony of fungus is comprised of long, branching filamentous cells called hyphae. Genetic mechanisms underlying the development of hyphae are poorly understood. We sectioned hyphae of a model fungus, Neurospora crassa (pink bread mold), into six parts depending on the age of the cells; 1 hour, 3 hour, 9 hour, 15 hour, 21 hour and 27 hour old, respectively. This data submission reflects an RNAseq analysis of mRNA extracted from the 1 hour time-point. 1 mycelial mRNA profile of 1 hour growth (hyphal tip) from Neurospora crassa strain FGSC 2489, Data was generated using Illumina GAIIx.
2013-08-28 | E-GEOD-50205 | biostudies-arrayexpress
Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Neurospora crassa mat A FGSC#2489 Three developmental stages and two different primers used for reverse transcription: mycelium oligo(dT) M1 protoperithecia oligo(dT) PP1 perithecia oligo(dT) PT1 mycelium oligo(dT)+ Multi-Targeted Primer [MTP] (M2) protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2)
2010-07-03 | E-GEOD-22658 | biostudies-arrayexpress