Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The lncRNA APOLO and the methylcytosine-binding protein VIM1 are thermomorphogenesis regulators

ABSTRACT: We compared the change of transcriptome induced by the over expression of the lncRNA APOLO, the downregulation of the methylcytosine-binding protein VIM1 and the increased temperature of growth. A correlation of up- and down-regulated genes in WT in response to 29°C is observed for OE APOLO-1 and vim1-3 at 23°C.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE167879 | GEO | 2021/03/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The lncRNA APOLO and the methylcytosine-binding protein VIM1 are thermomorphogenesis regulators

Project description:The lncRNA APOLO and the methylcytosine-binding protein VIM1 are thermomorphogenesis regulators

| PRJNA705455 | ENA

Protein response of lncRNA-DRC to HU treatment

Project description:protein response of lncRNA-DRC overexpression (mec1Δ sml1Δ-lncRNA-DRC-OE) to HU treatment

2024-10-10 | PXD056715 |

Powerdress Mediated Histone Deacetylation Is Essential For Thermomorphogenesis In Arabidopsis Thaliana

Project description:We report POWERDRESS (PWR), a SANT domain containing protein known to facilitate the deacetylation of lysine rich residues of histone H3 by HISTONE DEACETYLASE 9 (HDA9), to play key role in temperature induced growth in Arabidopsis thaliana. Mutations in PWR showed severe attenuation in high temperature associated phenotypes viz., temperature-induced hypocotyl elongation, petiole elongation and early flowering. The study involved analysing the impact of the loss of PWR on the transcriptome in response to changes in ambient temperature. About one hundred 6 day old seedlings of wild type (Col-0) and pwr-2 mutant (in Col-0 background) were grown at 23 °C in short days (SD) photoperiod in growth chambers (GR-36, Percival Scientific, Canada). Half of the samples were then shifted to 27°C under short day photoperiod. Total RNA was extracted from whole seedlings grown at 23 °C and 27°C after two hours. Two biological replicates were used for Col-0 and pwr-2 samples. RNA was extracted using Isolate II RNA plant kit (Bioline Pty Ltd, Australia). RNA-Seq libraries were generated on Illumina HiSeqTM 2000 platform using paired-end sequencing of 90 bp in length at BGI-Shenzen (Beijing Genomics Institute). Gene expression analysis was performed using DESeq2 (v1.14.1) differential expression analysis pipeline.

2017-12-01 | GSE101782 | GEO

Highly integrated epigenome maps in Arabidopsis - methylcytosine immunoprecipitation

Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: methylcytosine ChIP-chip on tiling array Identification of cytosine DNA methylation by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays for wildtype Columbia-0.

2008-04-20 | E-GEOD-10969 | biostudies-arrayexpress

5-methylcytosine promotes mRNA export

Project description:5-methylcytosine promotes mRNA export

| PRJNA362296 | ENA

DNA 5-methylcytosine in Paramecium

Project description:DNA 5-methylcytosine in Paramecium

| PRJNA437583 | ENA

A multiomics framework for high-throughput lncRNA characterization uncovers major immune regulators

Project description:Long noncoding RNAs (lncRNAs) play crucial roles in eukaryotic biology, yet their functions in the immune system are not fully understood. This study presents a comprehensive resource on the regulation, pathway dependencies, subcellular localizations, and protein interactomes of lncRNAs in immune cells exposed to pathogens. We developed GRADR, a methodology combining gradient profiling and RNA-bound proteome analysis, to map interactomes for all expressed RNAs in a single experiment. Using GRADR and targeted CRISPR multiomics, we identified a network of lncRNAs, including LINC01215, AC022816, and LINC01268 (ROCKI), that influence immunity, mainly through interactions with splicing factors. Our data are compiled into SMyLR, a web interface providing access to our lncRNA regulation and interactome atlas. This resource is expected to significantly advance research into RNA regulation in immunity.

2025-05-01 | PXD061457 | Pride

RNA-seq of the primary patient-derived GBM cell line G797 following siRNA-mediated knockdown and pcDNA3.1-Neomycin-mediated overexpression of the lncRNA HOXA10-AS

Project description:We used a machine-learning framework to systematically discover prognostic long non-coding RNAs (lncRNAs) in 9,446 patient tumors of 30 types. We identified 166 prognostic lncRNAs whose transcript abundance correlated with patient risk and improved the performance of common clinical variables and molecular tumor subtypes. In lower-grade gliomas, discrete activation of HOXA10-AS indicated poor patient prognosis, neurodevelopmental pathway activation and a transcriptomic similarity to glioblastomas. To understand the role of HOXA10-AS in the hallmark pathways of glioma, we used RNA-seq to profile the patient-derived G797 glioma cells with siRNA-mediated HOXA10-AS knockdown (KD) and pcDNA3.1-Neomycin-mediated overexpression (OE) phenotypes. Both KD and OE were validated using RT-PCR. We found a pronounced transcriptional response to HOXA10-AS deregulation with 1,715 and 408 differentially expressed protein-coding genes detected in KD and OE cells, respectively (FDR < 0.05, absolute FC > 1.2), including 23 genes detected in both experiments, as well as known genes involved in glioma biology and Hippo signaling. Our study underscores the pan-cancer potential of the non-coding transcriptome for developing molecular biomarkers and innovative therapeutic strategies.

2021-10-02 | E-MTAB-10944 | biostudies-arrayexpress

Prediction of the Chronicization of Radiation-induced Acute Intestinal Injury Based on the Expression Level of lncRNA

Project description:Our team has constructed a prediction model based on the expression level of lncRNA (lncRNA-UCID、NEAT1、ciRS-7) to predict the chronicization of radiation-induced acute intestinal injury (RAII) and verified the predictive efficacy of the system in retrospective studies. This clinical study intends to further prospectively verify the accuracy of this prediction model in rectal cancer patients. In this study, we plan to enroll 200 patients diagnosed with locally advanced rectal cancer by pathology and MRI, who undergo neoadjuvant chemoradiotherapy (NCRT) and total mesorectal excision (TME) and develop RAII during NCRT or within 1 month. We will follow up the occurrence and progression of radiation-induced intestinal injury within 1 year after TME. Expression levels of lncRNA will be detected in pathological tissue after TME and applied to the prediction model to predict the chronicization of RAII. Based on the clinical diagnosis of chronic radiation-induced intestinal injury, the area under curve (AUC), accuracy, precision, specificity, and sensitivity of this prediction model in predicting the chronicization of RAII will be evaluated. The main outcome hypothesis is that the AUC of chronicization of RAII predicted by the prediction model based on the expression level of lncRNA is more than 0.8.

| 9986 | ecrin-mdr-crc

sin-lncRNA interactors in senescent fibroblasts MS

Project description:sin-lncRNA is a noncoding RNA molecule with a role in cellular senescence. In vitro RNA pulldown of biotynilated sin-lncRNA was performed to identify sin-lncRNA specific protein partners

2025-04-29 | PXD044718 | Pride

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