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

Physcomitrella transcriptome atlas

ABSTRACT: ***This experiment was updated on 26-02-2016 to correct the accidental mis-labelling of some raw data files. For data downloaded before this date, please note that the file labelled as Caulonema_a.pair contains the raw data for Chloronema A and the file labelled as Chloronema_a.pair contains the data for Caulonema A. ***** We analyzed the transcriptional profile of all phases in the life cycle of P. patens, including all major tissues and 4 different sporophyte developmental stages. For this analysis we took advantage of a custom designed NimbleGene microarray based on genome version 1.6, and developed adequate protocols for the isolation and purification of mRNA directly from mechanically purified cells of chloronema, caulonema, rhizoids, gametophores, sporophytes, spores, archegonia and protoplasts.

INSTRUMENT(S): Agilent 2100 Bioanalyzer, Hybridization system 4 station, Roche Nimblegen MS200 scanner

ORGANISM(S): Physcomitrella patens

SUBMITTER: Jörg Becker

PROVIDER: E-MTAB-3069 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Physcomitrella patens reproductive organs from wt and Ppglr1/2 knock out samples

Project description:Physcomitrella patens reproductive organs (archegonia and antheridia) were mechanically isolated for transcriptome profiling. Comparison between wt and Ppglr1/2, a glutamate receptor double knock-out mutant, was done to identify deferentially expressed genes. A custom designed NimbleGene microarray based on genome version 1.6 was used for this study.

2017-05-17 | E-MTAB-5268 | biostudies-arrayexpress

EVOREPRO: Physcomitrella

Project description:RNA-seq expression atlas

2021-04-14 | E-MTAB-9466 | biostudies-arrayexpress

Transcription factor transcriptome during somatic embryogenesis (SE) in Arabidopsis thaliana

Project description:To identify transcription factor (TF) genes exhibiting preferential expression during SE, expression profiles of 1,880 TFs were compared in two genotypes with largely different capacities for SE induction in IZE culture on auxin medium, namely the highly embryonic Col-0 accession and the tanmei mutant unable to form somatic embryos. Our study revealed 729 TFs whose expression changes during the 10-day incubation period of SE; 141 TFs displayed distinct differences in expression patterns in embryogenic versus non-embryogenic cultures. This study provides comprehensive data focused on the expression of TF genes during SE and provides guidelines for further research on functional genomics of SE. The experiment was designed to monitor the expression of 1,880 TF genes at three distinctive stages of IZE-derived embryogenic culture, which refer to: (i) freshly isolated explants competent to undergo embryogenic transition (0 d), (ii) explant tissue subjected to SE induction (5 d), and (iii) the advanced phase of embryogenesis related to somatic embryo formation (10 d).

2013-07-31 | E-GEOD-45697 | biostudies-arrayexpress

Expression analysis of both total and polysomal mRNAs under drought, salt and cold stress conditions

Project description:Using 3′-tiling microarray covering the rice genes, we carried out genome-wide expression analyses of total and polysome-fractionated samples treated with drought, salt and cold at 2-week-old rice leaves. compared to non-treated negative control (NC) samples. Our study is the first report which elucidated the global alternation of polysome association in response to abiotic stress. A total of 24 chips were used for microarray. At 2h, total and polysomal RNAs were extracted from drought, salt and cold at 2-week-old rice leaves with three biological replicates.

2012-03-02 | E-GEOD-32065 | biostudies-arrayexpress

Medicago truncatula seed development under different growth conditions

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

2013-12-19 | E-GEOD-53526 | biostudies-arrayexpress

Medicago truncatula seed development at 20/18Â°C 16 h light/dark in osmotic stress conditions: -0.1 Mpa

Project description:Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 20/18Â°C 16 h light/dark, in osmotic stress conditions (-0.1 Mpa). Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation. Seeds of Medicago truncatula grown at 20/18Â°C 16 h light/dark in osmotic stress conditions of -0.1 Mpa, were collected at different developmental stages, 7 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment corresponding to the later developmental stage. For each repetition 4 hybridisation were made: 12DAP vs 15DAP, 20DAP vs 25DAP, 30DAP vs Abs, DS (Rep1 and Rep2) vs 12DAP (Rep3 and Rep4). For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.

2013-12-05 | E-GEOD-53003 | 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

Medicago truncatula seed development at 26/24Â°C 16 h light/dark

Project description:Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 26/24Â°C 16 h light/dark. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation. Seeds of Medicago truncatula grown at 26/24Â°C 16 h light/dark were collected at different developmental stages, 8 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment corresponding to the later developmental stage. For each repetition 4 hybridisation were made: 7DAP vs 9DAP, 11DAP vs 14DAP, 17DAP vs 20DAP, Abs vs DS. For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.

2013-12-05 | E-GEOD-52832 | biostudies-arrayexpress

Medicago truncatula seed development at 14/11Â°C 16 light/dark

Project description:Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 14/11Â°C, 16h light/dark. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation. Seeds of Medicago truncatula grown at 14/11Â°C, 16h light/dark were collected at different developmental stages, 10 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment, corresponding to the later developmental stage. For each repetition 5 hybridisation were made: 22DAP vs 28DAP, 34DAP vs 40DAP, 46DAP vs 52DAP, 58DAP vs 65DAP,Abs vs DS. For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.

2013-12-18 | E-GEOD-53002 | biostudies-arrayexpress

Analysis of PHOTOPERIOD SENSITIVITY5 Sheds Light on the Role of Phytochromes in Photoperiodic Flowering in Rice

Project description:A great majority of plants synchronize flowering with day length. In rice, the most important environmental cue that triggers flowering is the photoperiod. Here, we show that the s73 mutant, identified in a gamma irradiated Bahia collection, displays early flowering and photoperiodic insensitivity due to a null mutation in the SE5 gene, which encodes an enzyme implicated in phytochrome chromophore biosynthesis. s73 mutant plants showed a number of alterations in the characteristic diurnal expression patterns of master genes involved in photoperiodic control of flowering, resulting in up-regulation of Hd3a, the most important floral integrator. Ehd1, an additional rice floral activator, was also highly expressed in the s73 mutant, suggesting that SE5 represses Ehd1 in wild-type plants. Silencing of Ehd1 in both Bahia and s73 backgrounds implies that SE5 regulates Ehd1 expression. The data also indicate that SE5 confers photoperiodic sensitivity through regulation of Hd1. These results provide direct evidence that phytochromes inhibit flowering affecting both Hd1 and Ehd1 flowering pathways. Four biological replicates from each genotype (s73 mutant and Bahia wt) were labelled with Cy3 and Cy5 alternatively (2+2) following a dye-swap design. In total, 4 microarrays were hybridized. The supplementary file 'GSE16796_stat_analysis.txt' contains the final statistical analysis of study GSE16796.

2010-05-16 | E-GEOD-16796 | 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