Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiling of Botrytis cinerea conidial germination reveals upregulation of infection-related genes during the pre-penetration stage

ABSTRACT: Investigation of whole genome gene expression level changes in Botrytis cinerea wild type conidia during germination in comparison to the bmp1 MAP kinase deletion mutant. A 18 chip study using total RNA recovered from four different time points for the wild-type and one time point for the bmp1 deletion mutant. Each time point was analyzed with three biological replicates. Expression level of 20,885 genes from Botrytis cinerea strain B05.10 and T4 with three 60mer probes per gene was analysed.

ORGANISM(S): Botryotinia fuckeliana

SUBMITTER: Michaela Leroch

PROVIDER: E-GEOD-43569 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The VELVET complex in the gray mold fungus Botrytis cinerea: impact of BcLAE1 on differentiation, secondary metabolism and virulence

Project description:Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and the null-mutants deltaBcVEL1 and deltaBcLAE1, cultured onto solid grape juice medium with cellophane overlays , were compared to identify BcVEL1 or/and BcLAE1-dependent genes. The Botrytis cinerea wild-type strain and the null-mutants deltaBcVEL1 and BcLAE1 were cultured for 48h onto solid grape juice medium with cellophane overlays. 4 replicates were performed. The 12 total-RNA samples (3 strains* 4 replicates) were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

2015-02-01 | E-GEOD-63021 | biostudies-arrayexpress

Light and BcLTF2-dependent gene expression profiles in the phytopathogenic fungus Botrytis cinerea

Project description:Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and the null-mutant deltaBcLTF2, cultured in continuous darkness or submitted to a light stimulation, were compared to identify light- or/and BcLTF2-dependent genes. The Botrytis cinerea wild-type strain and the null-mutant deltaBcLTF2 were cultured for 54h in continuous darkness ; then, cultures were exposed for 60 min to light before harvest (L) or were harvested after additional 60 min darkness (D). 4 replicates were performed. The 12 total-RNA samples (4 conditions* 3 replicates) were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

2016-06-01 | E-GEOD-79679 | biostudies-arrayexpress

Light and BcLTF1-dependent gene expression profiles in the phytopathogenic fungus Botrytis cinerea

Project description:Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and the null-mutant deltaBcLTF1, cultured in continuous darkness or submitted to a light stimulation, were compared to identify light- or/and BcLTF1-dependent genes. The Botrytis cinerea wild-type strain and the null-mutant deltaBcLTF1 were cultured for 52h in continuous darkness ; then, cultures were exposed for 60 min to light before harvest (L) or were harvested after additional 60 min darkness (D). 4 replicates were performed. The 16 total-RNA samples (4 conditions* 4 replicates) were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

2013-09-27 | E-GEOD-51192 | biostudies-arrayexpress

Transcriptome profiling of Botrytis cinerea conidial germination reveals upregulation of infection-related genes during the pre-penetration stage

Project description:Investigation of whole genome gene expression level changes in Botrytis cinerea wild type conidia during germination in comparison to the bmp1 MAP kinase deletion mutant.

2013-01-18 | GSE43569 | GEO

Expression analysis of prostate tissue on locus 8q24 part 2

Project description:Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24. The region chr8:127640000-129120000 is tiled with isothermal probes (hg17) 7 chip study, using 7 independent samples.

2013-04-11 | E-GEOD-45922 | biostudies-arrayexpress

Expression analysis of prostate tissue on locus 8q24 part 3

Project description:Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24. 3 chips with 3 arrays each study, using 3 pairs of normal vs. tumor tissue and 3 replicates of the same sample. Each chip contained one pair of normal vs. tumor and one copy of the repeated sample.

2013-04-11 | E-GEOD-45925 | biostudies-arrayexpress

Expression analysis of prostate tissue on locus 8q24 part 1

Project description:Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24. The region chr8:127640000-129120000 is tiled with 60 nt probes at 10 nt interval (hg18) 7 chip study, using 7 independent samples.

2013-04-11 | E-GEOD-45920 | biostudies-arrayexpress

Expression analysis of prostate tissue on locus 8q24

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-11 | E-GEOD-45934 | biostudies-arrayexpress

Nucleosome occupancy changes in mammalian cell differentiation and reprogramming (microarray)

Project description:Embryonic stem cells (ESCs) and induced-pluripotent stem cells (iPSCs) self-renew and differentiate into an array of cell types in vitro and in vivo. A complex network of genetic and epigenetic pathways regulates the self-renewal and differentiation of these pluripotent cells, and the structure and covalent modifications of chromatin play a prominent role in this process. We examine nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach that enabled the identification of regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. The majority of changes in nucleosomal signatures that occur in differentiation are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of pluripotency and likely identify key regulatory regions that play a role in determining cell identity. A six chip study using total RNA recovered from three cell types with 2 replicates each

2014-07-31 | E-GEOD-59061 | biostudies-arrayexpress

The gene expression profiling array of LncRNA between tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma

Project description:Investigation of whole genome gene expression level changes of LncRNAs in tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma. The different expression genes were further analysised. The human LncRNA microarray analysis of the 10 samples (5 non-tumor tissues and 5 paired tumor tissues) were completed. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Agilent Scanner G2505C. Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and mRNA level (*_RMA.calls) files were generated after normalization. All mRNAs level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.mRNAs that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable mRNAs expression pattern among samples.

2013-08-10 | E-GEOD-49713 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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