Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Profiling of bulk and ribosome associated mRNA of Arabidopsis roots upon lateral root induction upon TOR activity inhibition with AZD8055 [dataset2]

ABSTRACT: We performed targeted purification of polysomal mRNA (TRAP-Seq, Vragović et al, 2015 - http://dx.doi.org/10.1073/pnas.1417947112) using a transgenic line ubiquitously expressing a GFP-tagged RPL18 (Mustroph et al, 2009 - https://doi.org/10.1073/pnas.0906131106) 6h after the synchronous induction of lateral root formation by auxin treatment (IAA) upon inhibition of TOR activity (AZD8055 treatment, AZD). To correct for abundance of mRNA, bulk RNA-Seq was performed on the same samples and used to normalise the reads purified with the ribosomes.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE199203 | GEO | 2022/03/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Constitutive Piezo 1 knock out in mouse brain development

Project description:E10.5 whole brain were isolated from WT and Piezo1-KO mice (C57BL/6J strain backgound) described in Ranade et al 2014. https://doi.org/10.1073/pnas.1409233111

2022-08-20 | GSE193099 | GEO

RNAseq of Pdgfb' brain cells obtained by from young male mice

Project description:RiboTag mice B6N.129-Rpl22tm1.1Psam/J (# 011029, Jackson Laboratories), which carry a conditional Rpl22 allele (Sanz et al., 2009; doi: 10.1073/pnas.0907143106),were crossed with Pdgfb-iCreER mice that are tamoxifen-inducible form of Cre recombinase in vascular endothelial cells (Claxton et al., 2008; doi: 10.1002/dvg.20367),to generate Ribotag-Pdgf-β1 Cre mice

2023-09-20 | GSE223714 | GEO

Interactions of CDK19 with MED12 and cyclin-C assessed by chemical cross-linking mass spectrometry

Project description:Chemical cross-linking coupled to mass spectrometry was used to study binary and ternary complexes involving cyclin-dependent kinase 19 (CDK19), cyclin-C, and an N-terminal fragment of subunit 12 of the Mediator complex (MED12 1-100). Cross-linking was performed using disuccinimidyl suberate (DSS). These results were generated in the context of the study published as Klatt et al., A precisely positioned MED12 activation helix stimulates CDK8 kinase activity, Proc. Natl. Acad. Sci. USA 2020 (DOI: 10.1073/pnas.1917635117) with the associated data set PXD015394, but were not included in the article.

2020-05-18 | PXD019251 | Pride

Inter-chromosomal contacts of the 16p11.2 locus connect with gene expression changes of Pcdh genes in autism spectrum disorder

Project description:Differentiation experiment of mouse embryonic stem cells (ESCs) to neuronal precursor (NPC) and immature dopaminergic neurons (NEU) commited to ventral midbrain lineage. Controls and mutant cell lines harboring heterozygous deletion (del) or duplication-deletion (dupdel) of 7qF3 locus which is synteny conserved with human 16p11.2 locus. Mice harbouring CNVs in this locus display behavioural phenotypes and distinct changes in brain architecture resembling ASD-like traits. Mouse models are described in Guy Horev et al., 2011 (doi: 10.1073/pnas.1114042108). Samples with same numeric identifier were differentiated in parallel.

2024-03-21 | GSE147239 | GEO

Batrachochytrium dendrobatidis

Project description:DNAseq of Batrachochytrium dendrobatidis (Farrer et al PNAS 2011)

| PRJNA222638 | ENA

Transcriptome profiling of Arabidopsis roots upon lateral root induction in WT and TOR knock down [dataset1]

Project description:To get a genome wide picture of the effects of TOR knockdown during the early phase of lateral root formation, we compared by RNA-seq the transcriptomes of roots 6h after the synchronous induction of lateral formation by auxin treatment (Himanen et al, 2002 - http://dx.doi.org/10.1105/tpc.004960) in the inducible UB10pro>>amiR-TOR background.

2022-03-23 | GSE199202 | GEO

Evidence for Zoonotic Transmission of a Novel Adenovirus Associated with a Fulminant Pneumonia Outbreak in a Titi Monkey Colony

Project description:We used the Virochip microarray to detect and discover a novel adenovirus, TMAdV (titi monkey adenovirus). We used custom-commercial microarrays from Agilent Technologies. The microarray platform GPL11662 consists of 62,976 probes, of which 19,058 probes are 70-mer viral oligonucleotides (the union of the V3 and V4 platforms -- please see Wang, et al., PNAS, 2002; Chiu, et al., Clin Infect Dis, 2006; Chiu, et al., PNAS, 2008).

2011-02-05 | GSE26898 | GEO

Transcriptome profiling of EPB41L5 WT and KO podocytes

Project description:We generated EPB41L5 WT and KO podocytes to model human glomerular kidney disease in vitro. Immortalized human podocytes were genome edited applying the CRISPR/Cas9 technique. Two monoclonal cell lines were generated for WT and KO genotypes (WT-1, WT-2, KO-1 & KO-2). Transcriptome profiling (RNA-Sequencing) and differential gene expression analysis was performed in duplicate for each cell line. EPB41L5 KO podocytes exhibit transcriptional changes compared to WT cells. Analyzed cell were previously described: Schell C, Rogg M, Suhm M, et al. The FERM protein EPB41L5 regulates actomyosin contractility and focal adhesion formation to maintain the kidney filtration barrier. Proc Natl Acad Sci U S A. 2017;114(23):E4621-E4630. doi:10.1073/pnas.1617004114

2023-07-03 | GSE220299 | GEO

Arabidopsis thaliana:seedlings treated by cis-cinnamic acid derivatives versus control seedlings

Project description:Transcriptional profiling of Arabidopsis thaliana seedlings treated with cis-cinnamic acid derivatives constructed by Nishikawa et al. (2013) Phytochemistry (http://dx.doi.org/10.1016/j.phytochem.2013.08.013), evaluating the candidate of herbicide chemicals by observing early response of gene expressions in Arabidopsis seedlings.

2013-12-28 | GSE51400 | GEO

Gastric Cancer Study GC_126

Project description:126 gastric tissues (90 tumor, 14 lymphnode and 22 normal) assayed using 44K human arrays against common reference (CRG). Published by Leung et al, PNAS, 2002 (PubMed ID 12456890) and Chen et al, MBC, 2003. A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Series_overall_design: Using regression correlation Keywords: other

2005-05-25 | GSE2701 | 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