Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genes affected by auxin and decapitation in moss gametophores

ABSTRACT: Genes affected by auxin and decapitation in moss gametophores

PROVIDER: PRJNA780504 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16948910_1.fastq.gz	Fastqsanger.gz
	SRR16948910_2.fastq.gz	Fastqsanger.gz
	SRR16948911_1.fastq.gz	Fastqsanger.gz
	SRR16948911_2.fastq.gz	Fastqsanger.gz
	SRR16948912_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 42

Similar Datasets

Genes affected by auxin and decapitation in moss gametophores

Project description:The goal of this study is to identify genes whose expression is affected by decapitation and auxin in moss gametophores Project ngs2017_09_moss1-auxin in CATdb What genes are misregulated in response to decapitation or auxin response?

2022-06-21 | GSE188843 | GEO

Analysis of the peptidome of the moss Physcomitrella patens

Project description:We performed the analysis of native peptides pool of gametophores, protonema and protoplast cells of the moss. To reduce endogenous proteolytic activity we used an acid extraction buffer with a mixture of plant protease inhibitors. All the actions were performed on ice. After the proper sample preparation, the extracted peptides were identified with use of tandem mass spectrometry on the basis of protein database uniref100, taxon Physcomitrella patens.

2016-05-18 | PXD000227 | Pride

Moss endogenous peptides, LC-MS/MS

Project description:Short (<100 codons) open reading frames (sORFs) are common features of all genomes. Proof of translation of sORFs is an important step towards finding of functional sORF-encoded peptides (SEPs). We verified translation of our predicted sORFs using mass-spectrometry (MS) analysis which is often considered as the gold standard in detection of proteins or peptides in cell. Taking into account the shortage of proteomic methods in identifying small proteins or peptides, in our study we used “peptidomic” dataset - endogenous peptides, extracted from three types of moss cells – gametophores, protonemata and protoplasts

2019-08-08 | PXD007922 | Pride

Moss Physcomitrella paten endogenous peptides, LC-MS/MS, part 2

2019-08-08 | PXD007923 | Pride

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

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

HUR affected genes in human skin cells

Project description:HUR affected genes in human skin cells

| PRJNA679558 | ENA

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

Discovery of novel auxin-responsive genes of Arabidopsis using auxin inhibitors

Project description:To obtain more information on auxin-regulated gene expression, we treated Arabidopsis seedlings with auxin biosynthesis or signaling inhibitors, then performed DNA microarray analyses.

2020-03-01 | GSE58028 | GEO

STEMIN transcription factor drives selective chromatin remodelling for gene activation within a relaxed chromatin during reprogramming in the moss Physcomitrium patens

Project description:Land plants exhibit remarkable cellular plasticity, readily reprogramming differentiated cells into stem cells in response to internal and external stimuli. While chromatin remodelling is crucial for cellular reprogramming, its interplay with gene expression during reprogramming into stem cells remains elusive. In the moss Physcomitrium patens, wounding induces reprogramming of leaf cells facing wounded cells to change into chloronema apical stem cells through the activation of the AP2/ERF transcription factor STEMIN. In this study, we employed combined single-nuclei RNA and ATAC-sequencing to explore the interplay between gene expression and chromatin dynamics during STEMIN-mediated reprogramming. Profiling 20,883 single-nuclei from gametophores, protonemata, and cut leaves, we identified eleven distinct cell types including reprogramming leaf cells. Our analysis revealed that reprogramming leaf cells exhibit a partly relaxed chromatin landscape and STEMIN transcription factors selectively enhance accessibility at specific genomic loci essential for stem cell formation. Thus, our results indicate that wounding initiates a broad chromatin relaxation, creating a permissive environment and specific transcription factors act to refine this permissive state by specifically relaxing chromatin regions critical for reprogramming.

2025-07-16 | GSE293939 | GEO

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