Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis thaliana

ABSTRACT: ldl3 mutant vs wild-type in Arabidopsis de novo shoot regeneration_RNA-seq and ChIP-seq

PROVIDER: PRJNA522929 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8643560.fastq.gz	Fastqsanger.gz
	SRR8643561.fastq.gz	Fastqsanger.gz
	SRR8643562.fastq.gz	Fastqsanger.gz
	SRR8643563.fastq.gz	Fastqsanger.gz
	SRR8643564.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Arabidopsis thaliana

Project description:ldl3 mutant vs wild-type in Arabidopsis de novo shoot regeneration_RNA-seq and ChIP-seq

| PRJDB7911 | ENA

AtPRMT5 regulates shoot regeneration through modulating multiple genes expression analyzed by RNA-seq

Project description:Protein arginine methylation plays essential roles in diverse biological processes, but its role in regulating shoot regeneration remains elusive. In this study, we analyzed the function of the protein arginine methyltransferase AtPRMT5 during de novo shoot regeneration in Arabidopsis. AtPRMT5 encodes a type II PRMT that methylates proteins, including histones and RNA splicing factors. Mutation of AtPMRT5 decreased the frequency of shoot regeneration and number of shoots per callus in the atprmt5 mutant compared with those of the wild type. To understand the mechanism of AtPRMT5 regulation of shoot regeneration, we analyzed the transcript levels of wild type and the mutant atprmt5 calli during shoot regeneration by RNA-seq. Three biological repeats of wild type and the mutant atprmt5-1 calli were used for RNA sequencing. Total RNAs were isolated from the calli of wild type Col and the mutant atprmt5-1 cultured on cultured on shoot-induction medium. The RNA-seq llibraries were constructed with TruSeq Stranded mRNA Library Prep Kit and sequenced using the Illumina Hiseq 2500. The raw reads were aligned to the genome sequences of TAIR10 using Tophat software. The gene expression levels were measured in RPKM, and many critical genes regulated by AtPRMT5 were identified to be involved in shoot regeneration.

2017-06-18 | E-MTAB-5044 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Arabidopsis thaliana Wild-type vs. mutant sdg2

| PRJNA172003 | ENA

Arabidopsis thaliana

Project description:Arabidopsis thaliana Wild-type vs. mutant (PcG)

| PRJNA373881 | ENA

Arabidopsis thaliana

Project description:Arabidopsis thaliana: wild type vs. scl15 mutant

| PRJNA279808 | ENA

Arabidopsis thaliana vegetative part: Col-0 vs. shr scl23 scr triple mutant

Project description:Transcriptional profiling of the vegetative part of Arabidopsis comparing wild type with the shr scl23 scr triple mutant. The latter is produced by crossing the strong null alleles of shr (shr-2), scl23 (scl23-1) and scr (scr-5). The goal was to determine the effects of the GRAS transcription factors SHR, SCL23 and SCR on growth and development of the Arabidopsis shoot system by global transcriptome analysis. Two-condition experiment: Col-0 vs. shr scl23 scr triple mutant. Biological replicates: 2 WT vs. triple mutant replicates, 2 WT vs. triple mutant replicates dye-swap replicates.

2012-10-11 | E-GEOD-41478 | biostudies-arrayexpress

Arabidopsis thaliana embryos: wild type vs cuc1 cuc2 double mutant

Project description:Transcriptional profiling of Arabidopsis embryos comparing cuc1-1 cuc2-1 mutant (test) and wild type Ler (reference). Goal was to screen genes regulated by CUC1 and CUC2 transcription factors, which are required for shoot meristem formation and cotyledon separation.

2020-03-19 | GSE147149 | GEO

PtWOX11 Promote de novo Shoot Regeneration by Involving a Two- Step Mechanism in Poplar

Project description:De novo shoot regeneration is an essential step for massive propagation and genetic engineering of elite germplasm in forestry. Poplar that is a fast growth tree species have a very important ecologically and economically role around the world, especially in China. In this study, we found that PtWOX11 that is a homologue of AtWOX11 not only involved de novo root formation but also promote de novo shoot regeneration in poplar. We demonstrated that PtWOX11 can enhance callus regeneration competence and shoot regeneration during two-step de novo shoot regeneration. Furthermore, by using RNA-seq and qPCR, we uncovered that during callus induction stage PtWOX11 activates PtPLTs expression to promote callus formation and regeneration competence, and promote PtCUC2/3, PtWUSa and PtSTM transcription to fulfil shoot organogenesis during shoot regeneration stage. Overall, our data indicated that PtWOX11 play a new function and transcriptional regulation mechanism on de novo shoot regeneration in poplar.

2018-03-26 | GSE101922 | GEO

Arabidopsis thaliana 6-day-old dark-grown hypocotyls; Col-0 and shr (LOF)

Project description:Transcriptional profiling of hypocotyl comparing wild type with shr mutant. We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SHORT-ROOT on growth and development of Arabidopsis shoot system (hypocotyl) by global transcriptome analysis and to identify the key players in the regulatory pathway.

2021-12-28 | GSE97670 | GEO

CPL4 is a suppressor of de novo shoot organogenesis from roots of Arabidopsis thaliana

Project description:De novo shoot organogenesis (DNSO) is a commonly used pathway for plant biotechnology, and is a hormonally regulated process, where auxin and cytokinin coordinates suites of genes encoding transcription factors, general transcription factors, and RNA metabolism machinery genes. Here we report that silencing Arabidopsis thaliana CTD phosphatase-like 4 (CPL4RNAi), which increases phosphorylation level of RNA polymerase II (pol II) CTD, altered lateral root development and DNSO efficiency of the host plants, suggesting an importance of precise control of pol II activities during DNSO. Under standard condition, roots of CPL4RNAi lines produced no or few lateral roots. When induced by high concentration of auxin, CPL4RNAi lines failed to produce focused auxin maxima at the meristem of lateral root primordia, and produced fasciated lateral roots. By contrast, root explants of CPL4RNAi lines were highly competent for DNSO. Efficient DNSO of CPL4RNAi lines were observed even under 10 times less cytokinin required for wild type explants. Transcriptome analysis showed CPL4RNAi but not wild type explants expressed high levels of shoot meristem related genes during priming by high auxin/cytokinin ratio, and subsequent shoot induction with cytokinin. These results indicate that CPL4 functions as a repressor of the early stage of DNSO, during acquisition of competency by high auxin/cytokinin ratio, perhaps via regulation of pol II activities.

2020-09-19 | GSE104083 | 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