Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SRNA sequencing from wild-type Arabidopsis (diverse tissue types)

ABSTRACT: This set consists of small RNAs sequenced from wild-type Arabidopsis samples from multiple tissue types (floral, leaf, seedling, silique). Samples were prepared in two different labs and presumably under different (unknown) growth conditions, hence type A (UEA) and type B (University of Cambridge) samples.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE31211 | GEO | 2012/01/10

SECONDARY ACCESSION(S): PRJNA145973

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

sRNA sequencing from wild-type Arabidopsis (diverse tissue types)

Project description:This set consists of small RNAs sequenced from wild-type Arabidopsis samples from multiple tissue types (floral, leaf, seedling, silique). Samples were prepared in two different labs and presumably under different (unknown) growth conditions, hence type A (UEA) and type B (University of Cambridge) samples. 4 biological replicates (7 technical replicates) of Floral A; 3 biological replicates of Floral B; 1 biological replicate of Leaf B; 2 biological replicates of Leaf A; 3 biological replicates of Seedling; 1 biological replicate of Silique. Note that GSM415783, GSM415784 and GSM415785 form part of the 'Floral A' category; GSM415783, GSM415784 are technical replicates.

2012-01-10 | E-GEOD-31211 | biostudies-arrayexpress

Brassica rapa subsp. chinensis Transcriptome

Project description:Deep RNA-Seq of two Brassica rapa genotypes—R500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)—using eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads.

2013-05-01 | E-MTAB-4192 | biostudies-arrayexpress

Understanding the nitrate responsive regulatory modules in Rice [ncRNA-seq]

Project description:To identify the differetially expressed sRNAs under nitrate stress, sRNA-seq was performed using total RNA extracted from root and seedling tissues from plants were grown in both low (0 mM) and high (100 mM) nitrate conditions. The analysis was performed in duplicates and the reads were processed and analysed using UEA sRNA workbench.

2022-04-01 | GSE166668 | GEO

Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids [RNA-seq]

Project description:We integrated data of transcriptome and histone modifications (H3K4me3 and H3K27me3) for HZ62 in three tissue types (seedling, flower bud and silique). Transcriptome analysis suggested that gene expression level altered in hybrids compared with parents.

2023-07-18 | GSE218591 | GEO

Transcript Profiling of Arabidopsis Plant Life Cycle

Project description:This series contain all stages Arabidopsis plant development. Stages of development includes unfertilized ovule, 24-Hr post-fertilization seed, globular stage seed, cotyledon stage seed, mature green seed, post-mature green seed, post-germination seedling, rosette leaf, root, stem, and floral bud. Keywords = Arabidopsis Keywords = Seed development Keywords = seedling Keywords = germination Keywords = leaf Keywords = root Keywords = stem Keywords = floral bud Keywords: ordered

2005-01-01 | GSE680 | GEO

Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids [ChIP-seq]

Project description:We integrated data of transcriptome and histone modifications (H3K4me3 and H3K27me3) for HZ62 in three tissue types (seedling, flower bud and silique).Histone modifications analysis suggested there was histone modifications reprogramming in the B. napus hybrids compeared with parents.

2023-07-18 | GSE218583 | GEO

Expression analysis of TRANSPOSABLE ELEMENT KILLER (TEK) knockdown lines

Project description:Investigation of the effect of the knockdown of AT-hook motif DNA binding nuclear matrix protein TRANSPOSABLE ELEMENT KILLER (TEK) in the Arabidopsis Landsberg erecta (Ler) background Transposable elements (TEs) are silenced by epigenetic mechanisms of DNA and histone methylation. The repressive histone modification H3 lysine 9 dimethylation (H3K9me2) is TE-associated epigenetic hallmark, and is necessary for DNA methylation. However the mechanism to direct the repressive epigenetic modification in TEs has remained elusive. Here we show that knockdown of the AT-hook motif DNA binding nuclear matrix protein TRANSPOSABLE ELEMENT KILLER (TEK) in the Arabidopsis Landsberg erecta (Ler) background results in robust activation of various TEs, the repeat-containing floral repressor gene FWA and the TE-containing floral repressor FLOWERING LOCUS C (FLC). A four chip study using two separate wild-type seedling mRNA samples and two separate TEKi seedling mRNA samples

2012-09-12 | E-GEOD-39158 | biostudies-arrayexpress

Gene expression ATLAS of Arabidopsis thaliana (accession Columbia) across its lifecycle

Project description:Arabidopsis thaliana (accession- Columbia) is an important model plant. RNA-Seq based study of 36 libraries was carried out to explore transcriptional programs operating in different plant parts (seedling, rosette, root, inflorescence, flower, fruit silique, and seed) and developmental stages (2-leaf stage, 6-leaf stage, 12-leaf stage, senescence stage, dry mature and imbibed seed stage). For each tissue type and developmental stage, three individual plants were used as biological replicates.

2022-05-04 | E-MTAB-6422 | biostudies-arrayexpress

The Histone Deacetylases HDA6 and HDA9 coordinately regulate valve cell elongation through depressing auxin signaling in Arabidopsis

Project description:Both of Histone Deacetylases HDA6 and HDA9 belong to RPD3/HDA1 class I subfamily, and they have similar protein structure. Loss of function of HDA9 display a blunt silique. Although there is not protein-protein interaction between HDA6 and HDA9, they simultaneously loss function led to “nock-shape” silique that more seriously silique phenotype than hda9. The silique valve cell of hda9 and hda6 hda9 were longer than wild type and hda6. The transcripts level of auxin signaling related genes were mis-regulated in hda9 and hda6 hda9 silique, and GFP signaling derived by auxin response promoter DR5 were weaker in hda9 and hda6 hda9 than wild type and hda6. Thus, our findings reveal that HDA6 and HDA9 coordinately control silique valve cell elongation through affecting auxin signaling related genes expression in silique.

2018-12-30 | GSE122047 | GEO

Genome annotation improvement of Brassica rapa

Project description:The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability of physically positioned, gene-based genetic markers and accurate genome annotation. In this study, deep transcriptome RNA sequencing (RNA-Seq) of Brassica rapa was undertaken with two objectives: SNP detection and improved transcriptome annotation. We performed SNP detection on two varieties that are parents of a mapping population to aid in development of a marker system for this population and subsequent development of high-resolution genetic map. An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation. Deep RNA-Seq of two Brassica rapa genotypesâR500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)âusing eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads. In this experiment, two pools were made, with one pool consisting of 66 samples collected from growth chamber and another pool consisting of 60 samples collected from greenhouse and field. Each pool was sequenced on eight lanes (total 16 lanes) of an Illumina Genome Analyzer (GAIIx) as 100-bp paired end reads.

2014-04-22 | E-MTAB-4276 | 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