Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

78 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene transcription profiling of Physcomitrella patens Pp_A_Doko#069 (DOKO69; Koprivova et al., 2004) protonema grown in liquid cultures.

ABSTRACT: Protonema of Physcomitrella patens Pp_A_Doko#069 (DOKO69; Koprivova et al., 2004) grown in liquid cultures with Knop medium (Reski and Abel, 1985) were harvested 6 days after last subculture and setting density to 120 mg/L dry weight.

ORGANISM(S): Physcomitrella patens

SUBMITTER: Sebastian Hoernstein

PROVIDER: E-MTAB-5374 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Gene transcription profiling of Physcomitrella patens ΔPpcmt and ΔPpmet deletion mutants compared to wild type.

Project description:7 days old protonema of Physcomitrella patens Wildtype and two transgenic lines, ΔPpcmt line 281 (Noy-Malka et al. 2014; IMSC accession 40738) and ΔPpmet line 5 (Yaari et al. 2015; IMSC accession 40758) grown on BCDAT solid medium.

2015-05-09 | E-MTAB-3431 | biostudies-arrayexpress

Ppatens transcriptome

Project description:We studied peptide generation process in moss Physcomitrella patens. For this purpose, analysis of peptidome and transcriptome of two different life forms (gametophores and protonema) and also of protoplasts were made.

2014-04-22 | E-MTAB-1637 | biostudies-arrayexpress

Transcription profiling of Physcomitrella patens response to fungal exudates

Project description:Physcomitrella patens gametophores were treated with exudates from the arbuscular mycorrhiza fungi (AMF) Rhizophagus irregularis (formerly known as Glomus intraradices) and Gigaspora margerita for one hour and 24 hours.

2014-11-10 | E-MTAB-3081 | biostudies-arrayexpress

Physcomitrella patens Reute development

Project description:Transcriptome profiling by Nimblegen array of Physcomitrella patens Reute gametophores, gametophores with gametangia, green sporophytes and brown sporophytes.

2017-05-24 | E-MTAB-4630 | biostudies-arrayexpress

Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens

Project description:Gene expression was analyzed with digital gene expression tag profiling (DGEP) with samples taken from P. patens protonema at 3, 14 and 24 days, and also from or leafy shoot tissues l at 30 days after protoplastes isolated, and from 14-day-old caulonemal and chloronemal tissues. Totally, 4333 genes were identified as differentially displayed. Among them, 4129 were developmental-stage specific and 423 were preferentially expressed in either chloronemal or caulonemal tissues. Most of the differentially displayed genes could be assigned to functions in organic substance and energy metabolism or macromolecule biosynthetic and catabolic process based on gene ontology (GO) description. In addition, some regulatory genes were identified as candidates that might be involved in controlling the developmental stage transition and cell differentiation, namely: MYB-like, HB-8, AL3, zinc finger family proteins, bHLH superfamily, GATA superfamily, GATA and bZIP transcription factors, protein kinases, the genes related to protein/amino acid methylation, and auxin, ethylene, and cytokinin signaling pathways. Examination of 4 different sampling times and 2 different organelles.

2011-12-20 | E-GEOD-33279 | biostudies-arrayexpress

Transcriptional Profiling of Protonema Development in Physcomitrella patens

Project description:Transcriptional Profiling of Protonema Development in Physcomitrella patens

2014-05-07 | E-MTAB-976 | biostudies-arrayexpress

Transcriptomic and proteomic analysis of alternative splicing in Physcomitrella patens moss

Project description:Alternative splicing (AS) has a significant potential to impact on the eukaryotic cell transcriptome and proteome. However, the extent of this influence as well as mechanisms, providing the tissue-specific pattern of AS are poorly studied. Here, we analyzed the AS of two life forms, protonema and gametophores, as well as the protoplasts, of a model organism, the Physcomitrella patens moss, using the data of transcriptome and proteome profiling. Altogether, 12,043 genes subjected to alternative splicing were identified. The alternative splicing patterns of 302 genes involved in stress response, growth, and development are changed considerably in the process of the gametophore development, whereas AS of 276 genes involved in transcription regulation, development, cell interactions, and cell response to biotic and abiotic stresses altered upon protoplastitation. Using mass spectrometry analysis, we studied the extent to which AS contributes to proteome diversity and identified 117 isoform-specific peptides for 36 genes with AS events. Our results indicate that AS event have a little impact on the proteome diversity and mostly result in the addition of extra amino acids rather than editing of existing proteins sequences. Among differentially expressed and spliced genes we found serine/arginine-rich (SR) genes, which are known to regulate AS in cells. We identified new isoforms of these genes and data evidencing their translation were obtained at transcriptome and proteome level. We also found that treatment with abscisic and jasmonic acids led to the isoform-specific response in protonema. Besides, we revealed the potential lncRNAmRNA and lncRNApre-mRNA interactions that can influence both the expression and alternative splicing of genes. It can point at an additional level of gene expression and AS regulation by non-coding transcripts in the Physcomitrella patens moss.

2018-01-15 | PXD005223 | Pride

In vitro exposure of rat hepatocytes to a variety of toxicants, assayed by Affymetrix microarray

Project description:DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development. Complete Drug Matrix dataset for primary rat hepatocytes. Cells were exposed to toxicants in culture medium and harvested after 0.67 or 1 day.

2014-05-27 | E-GEOD-57805 | biostudies-arrayexpress

mRNA-seq of Physcomitrella protonema responding to 1 hr red light in wild type and the phytochrome-deficient mutant

Project description:The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. Datasets here provides the transcriptome profiling of Physcomitrella protonema grown in the dark and exposed to one hour red light. Wild type and the hy2 pubs double mutant were used to dissect the regulated genes of moss phytochromes. 4 samples, dark-grown wild-type and pubs hy2 protonema as time 0 control, followed by red light irradiation for one hour respectively

2012-05-08 | E-GEOD-36274 | biostudies-arrayexpress

Deep sequencing analysis of human red blood cells

Project description:Small RNAs isolated from RBCs were size fractionated by gel electrophoresis and used for the creation of 6 libraries. For the library from healthy children (library 1), RNA from 4 individuals was pooled. Libraries were multiplexed and analyzed on a 454 sequencing platform 26 yielding 569,621 sequence reads after demultiplexing into the 6 libraries Analysis of 6 small RNA libraries from human red blood cells

2012-06-30 | E-GEOD-27250 | 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