Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide small RNAtranscriptome analysis during dehydration and recovery in gametophores of Physcomitrella patens

ABSTRACT: Small RNA transcript abundances were analyzed with samples taken from hydrated (HD), moderate dehydration (MDH), desiccated (SDH), partially recovered (PRE) and fully recovered (FRE) gametophores of P. patens by using next generation sequencing. Totally, 147 microRNAs were identified as differentially expressed miRNAs.The results provided insight for exploring the mechanisms of desiccation tolerance and their evolution.

ORGANISM(S): Physcomitrium patens

PROVIDER: GSE66589 | GEO | 2018/02/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide transcriptome analysis during dehydration and recovery in gametophores of Physcomitrella patens

Project description:Gene transcript abundances were analyzed with samples taken from hydrated (HD), moderate dehydration (MDH), desiccated (SDH), partially recovered (PRE) and fully recovered (FRE) gametophores of P. patens by using RNA-Seq. Totally, 14686 transcripts were identified as differentially expressed transcripts.The results provided insight for exploring the mechanisms of desiccation tolerance and their evolution.

2018-02-22 | GSE66467 | GEO

Genome-wide DNA methylation maps during rehydration in gametophores of Physcomitrella patens.

Project description:To examine the P. patens genome-wide methylation landscape and assess its functional significance during dehydration, we generated the first single-base resolution genome methylation maps for P. patens gametophores of hydrated (HD), moderate dehydrated (MDH), severe dehydrated (SDH), partially recovered (PRE) and fully recovered (FRE). The overall density of methyl-cytosine was not broadly altered by dehydration and recovery. There is, however, a small increase in intensity both for the whole genome and regionally during MDH and FRE. Only 225 differentially expressed genes were located in differentially methylated regions (DMRs) during the dehydration-recovery cycle. The finding may provide an important clue for exploring molecular mechanisms and the regulation of desiccation tolerance at the whole-genome level.

2018-02-22 | GSE66485 | GEO

Small RNAs from the moss Physcomitrella patens

Project description:High-throughput sequencing of endogenous small RNAs from the moss Physcomitrella patens. This dataset encompasses microRNAs and other small RNAs of ~20-24 nucleotides expressed in the moss P. patens. SAMPLES UPDATED JULY 9, 2007 TO INCLUDE DATA ON SEQUENCED SMALL RNAS THAT DO NOT MATCH THE P. PATENS GENOME Keywords: High throughput small RNA sequencing

2006-08-15 | GSE5103 | GEO

small RNA-seq of Physcomitrella patens rdr mutants

Project description:To investigate the effects of rdr2 and rdr6 mutations upon small RNAs in Physcomitrella patens , small RNA-seq was performed.

2015-06-30 | GSE51416 | GEO

Genome-wide transcriptome analysis during dehydration in leaf tissues of Boea hygrometrica

Project description:Gene transcript abundances were analyzed with samples taken from hydrated, moderate dehydration (70% RWC) and desiccated (10% RWC) leaf tissues of resurrection plant species B. hygrometrica by using RNA-Seq. Totally, 9888 genes were identified as differentially expressed genes.The results provided insight for exploring the mechanisms of desiccation tolerance.

2015-04-22 | GSE48671 | GEO

dsRNA-seq of Physcomitrella patens rdr mutants

Project description:To investigate the effects of rdr2 and rdr6 mutations upon the strucutred component of the Physcomitrella patens transcriptome, dsRNAseq performed. The accumulation of dsRNAseq reads within known small RNA (microRNA and siRNA) loci was quantified and compared between wild-type and the two mutants.

2015-06-30 | GSE51418 | GEO

The DNA damage response transcriptome of the moss Physcomitrella patens

Project description:The moss Physcomitrella patens is remarkable for the ease with which mutant alleles of any gene can be generated by highly efficient homologous recombination-mediated gene targeting. Targeted transgene integration is believed to be mediated through the capture of transforming DNA by the homologous recombination DNA repair pathway. To identify components of this pathway in P. patens we have undertaken a transcriptomic analysis of the response to the sublethal induction of bleomycin-induced DNA double-strand breaks using massively parallel (Illumina) cDNA sequencing. Transcripts significantly increased in bleomycin-treated tissue include a number encoding conserved DNA-DSB components in both the homology-dependent pathway (including Rad51, CTiP, DNA ligase 1, Replication protein A, ATR) and the non-homologous end-joining pathway (including Xrcc4, DNA ligase 4, Ku70, Ku80, PARP). Differentially regulated cell-cycle components include up-regulated Rad9 and Hus1 DNA-damage-related checkpoint proteins and down-regulated D-type cyclins and B-type CDKs, commensurate with the imposition of a checkpoint in the G2 stage of the cell cycle characteristic of homology-dependent DNA-DSB repair. Comparison of the DNA damage transcriptome of P. patens with that of A. thaliana reveals significant up-regulation of a number of P. patens genes encoding ATP-dependent chromatin remodelling helicases of the SNF-2 class. These represent candidates for investigation of their role in mediating efficient gene targeting in P. patens.

2010-11-10 | GSE25237 | GEO

small RNA-seq of Physcomitrella patens small RNA mutants

Project description:To investigate the effects of dcl3,dcl4,mDCL,rdr2,rdr6,nrpd1b, and nrpd1c mutations upon small RNAs in Physcomitrella patens , small RNA-seq was performed.

2015-06-30 | GSE51419 | GEO

Physcomitrella patens ABA response

Project description:Transcriptome profiling by Combimatrix array of Physcomitrella patens Gransden protonemata treated with ABA

2019-03-11 | E-MTAB-5492 | 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

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