Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential gene expression between wild type (Col 0) and mutants (Atplh1, Atplh2, Atplh3)

ABSTRACT: RNA sequencing of Arabidopsis 10 day old wild type and mutant seedlings (grown on MS media with and without ABA, NaCl for 5 days) using Illumina platform. Differential gene expression between wild type and mutants along with the effect of ABA and NaCl on gene expression was studied.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE272436 | GEO | 2025/09/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

STOP1 overexpressor vs. Col-0 and stop1 knockout vs Col-0 under control and NaCl

Project description:Transcriptional profiling of Arabidopsis thaliana seedlings comparing overexpressor with wild type, and knockout with wild type separately under control and NaCl stress.

2018-03-01 | GSE102948 | GEO

treatment g-butyrobetaine wt col.0-Effect of carnitine on the transcriptome of A. thaliana

Project description:rs07-01_carnitine - treatment g-butyrobetaine wt col.0 - Effect of carnitine on the transcriptome of A. thaliana - Seedlings WT are growing in a independent way on media MS. After seven days of culture, seedling are harvested and a pull is formed from the three prelevements. Extractions of RNA will be realised on this pull. We proceed in a identical way for the test sample. Seedlings are cultivated on media MS containing butyrobétaïne 1 mM. After seven days, seedlings are harvested and extractions of RNA will be realised on this second pull. All this experiment is repeated one more time independently. Keywords: treated vs untreated comparison

2009-02-18 | GSE10677 | GEO

Comparison of low water potential (drought)-regulated gene expression in wild type (Col-0) and the hai1-2 (At5g59220) mutant

Project description:The Clade A PP2C Highly ABA-Induced1 (HAI1, At5g59220) is strongly up-regulated by low water potential in an ABA-dependent manner. Using knockout mutants of hai1, we found that HAI1 functions as a negative regulator of low water potential-induced proline and osmoregulatory solute accumulation. We also found a relatively weak and limited interaction of HAI1 with the RCAR/PYL family of ABA receptors. This, plus its induced expression, suggest that HAI1 remains active during stress and attenuates specific aspects of drought response. Microarray experiments were used to identify genes differentially expressed in hai1-2 (SALK_108282) versus wild type under both unstress control conditions and after low water potential (i.e., drought, water deficit). A relatively long term (96 h) low water potential treatment was used as phenotypes of hai1-2 were most apparent after this longer term low water potential treatment. Seven-day-old seedlings of wild type (Col-0) or hai1-2 were transferred from agar plates of control media to low water potential stress (PEG-infused agar plates at -1.2 MPa) or to fresh control media (-0.25 Mpa). Samples (whole seedlings) were collected 96 h after transfer. Three independent experiments were conducted with one sample of each treatment (wild type stress and control, hai1-2 stress and control) collected from each experiment.

2012-02-03 | E-GEOD-35258 | biostudies-arrayexpress

RNA-seq of two-week-old seedlings of wild type (Col-0), dph1 and dph2 mutants (in Col-0 background) growing on 0.5x MS media with 0.5% (w/v) sucrose under normal growth conditions (16 h light/8 h dark).

Project description:This is comparative transcriptomics by using the wild type, dph1 and dph2 mutants to see the change of dph1 and dph2 mutants at transcript levels compared with wild type. Seedlings of two-week-old plants grown in liquid MS media were harvested for total RNA isolation by RNeasy Plant Mini Kit (Qiagen). Libraries were prepared and sequenced using the Illumina platform by Novogene (Cambridge, UK). For RNA-seq data analysis, raw reads were first filtered by CutAdapt 2.1 to remove adaptors and low-quality reads. The filtered reads were mapped to Arabidopsis thaliana Col-0 reference genome (Tair 10). Read counts were determined by Qualimap2. Differentially expressed genes were identified using the R package DESeq2.

2024-03-01 | E-MTAB-13779 | biostudies-arrayexpress

The comparison for the transcript levels of chloroplast-encoded genes between wild type (Col-0) and pbf8 mutants

Project description:We found that thylakoid-anchored protein PBF8 is a key regulator for Photosystem I (PSI) biogenesis. To explore the role of PBF8 in regulating chloroplast gene expression, we performed the RNA-seq to compare the the transcript levels of chloroplast-encoded genes between wild type (Col-0) and pbf8 mutants. To this end, we isolated the total RNA form 12-day-old wild type and pbf8 seedlings grown on the MS medium under long-day conditions (14 h light, 10 h dark) at 22 ºC and with a light intensity of 80 µmol m-2 s-1. The rRNAs were deleted using the Ribo-Zero Kit (Epicentre). The resulting rRNA-depleted RNA was used for preparing the sequencing library with NEBNext Single Cell/Low input library Prep Kit. The libraries were pooled and sequenced on an Illumina Nova 6000 system with 150-bp pair-end reads. Finally, our results show that the transcript accumulation for chloroplast-encoded PSI subunit and assembly factor genes between the wild type (Col-0) and pbf8 samples, suggesting PBF8 may not affect the transcript levels of chloroplast-encoded PSI subunits and assembly factors in chloroplasts.

2024-01-24 | GSE239827 | GEO

Col versus Col_Rose Bengal

Project description:MS treated wild-type Arabidopsis seedlings versus MS Rose Bengal (RB)-containing medium (10 microM) wild type treated seedlings

2011-03-01 | E-MEXP-3009 | biostudies-arrayexpress

High temperature transcriptomes of mutants in HDA9, PIF4 and Col-0 wild type of young Arabidopsis seedlings

Project description:We determined the transcriptomes of hda9-1, pif4-2 and wild type Col-0 seedlings of 2 day old and 7 day old, at control and high temperature conditions (22oC vs 27oC), in short day (8h) photoperiod

2019-01-01 | GSE121383 | GEO

RNA-seq of Arabidopsis Col-0, snrk2.4, double snrk2.4/2.10 and quintuple snrk2.1/2.4/2.5/2.9/2.10 mutants from control (0mM) and salt stress (150mM NaCl for 1hour) treatment.

Project description:The purpose of this experiment was to investigate the downstream evens of Arabidopsis subclass 1 SnRK2 protein kinases signaling pathway. Seedlings were grown in 100 ml liquid media containing 0.5xMurashi-Skoog basal salt, 0.5% sucrose, 1% M.E.S. monohydrate, pH 5.8 (KOH) with shaking (120 rpm). Ten days-old seedlings were treated with 150 mM NaCl in 0.1xMS media (salt stress) or 0.1xMS media (control) for 1hour.

2019-07-11 | E-MTAB-8073 | biostudies-arrayexpress

treatment g-butyrobetaine wt col.0-Effect of carnitine on the transcriptome of A. thaliana

2009-02-18 | E-GEOD-10677 | biostudies-arrayexpress

Transcriptome analysis of vtc1, abi4-102 and wild type Col 0

Project description:The role of abscisic acid (ABA) signalling in the ascorbic acid (AA)-dependent control of plant growth and defence was determined using the vtc1 and vtc2 mutants, which have impaired ascorbic acid synthesis, and in the abi4 mutant that is impaired in ABA-signalling. ABA levels were increase in the mutants relative to the wild type (Col0). Like vtc1 the vtc2 mutants have a slow growth relative to Col0. However, the wild type phenotype is restored in the abi4vtc2 double mutant. Similarly, the sugar sensing phenotype of in the abi4 is reversed in the abi4vtc2 double mutant. The vtc1 and vtc2 leaf transcriptomes show up to 70 % homology with abi4. Of the transcripts that are altered in the mutants a relative to Col0, only a small number are reversed in the abi4vtc2 double mutants relative to either abi4 or vtc2. We conclude that AA controls growth via an ABA and abi4-dependent signalling pathway. The vtc and abi4 mutants have enhanced glutathione levels and common redox signalling pathways leading to similar gene expression patterns.

2011-08-26 | GSE23330 | 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