Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Affy_ath_2012_05-Arabidopsis Ubiquitin-Like Proteases characterization

ABSTRACT: affy_ath_2012_05 - affy_ath_2012_05 - The main objective is to determinate the influence of Ubiquitin-Like Proteases in plant transcriptional modulation. The experiment will also allow us to find what transcriptional cues are particularly affected in the mutants relatively to wild-type.-Seeds were stratified for 3 days at 4ºC in the dark. Afterwards, seeds were surface sterilized, sown onto MS media and grown at 23ºC, with 100 µE light condition, in long days (16h L/8h D). Each MS plate was dived in four, corresponding to a genotype (Col, AB, SIZ1 or SAB), and 10 seeds were sown per genotype. After 10 days, seedlings were collected and frozen in liquid nitrogen. Each replicate was made of ~40 seedlings coming from 4 different MS plates. Frozen plant material was grounded in an eppendorf tube using a mini pestle. RNA was extracted using RNeasy Plant Mini kit (QIAGEN cat.74904), following the manufacturer instructions (QIAGEN, Hilden, Germany). The RNA samples were DNase treated (Recombinant DNase I, Takara Biotechnology, Dalian, China) and subsequently cleaned by column using RNeasy Plant Mini kit (QIAGEN, Hilden, Germany).

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE43883 | GEO | 2013/09/01

SECONDARY ACCESSION(S): PRJNA188668

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

affy_ath_2012_05-Arabidopsis Ubiquitin-Like Proteases characterization

Project description:affy_ath_2012_05 - affy_ath_2012_05 - The main objective is to determinate the influence of Ubiquitin-Like Proteases in plant transcriptional modulation. The experiment will also allow us to find what transcriptional cues are particularly affected in the mutants relatively to wild-type.-Seeds were stratified for 3 days at 4ºC in the dark. Afterwards, seeds were surface sterilized, sown onto MS media and grown at 23ºC, with 100 µE light condition, in long days (16h L/8h D). Each MS plate was dived in four, corresponding to a genotype (Col, AB, SIZ1 or SAB), and 10 seeds were sown per genotype. After 10 days, seedlings were collected and frozen in liquid nitrogen. Each replicate was made of ~40 seedlings coming from 4 different MS plates. Frozen plant material was grounded in an eppendorf tube using a mini pestle. RNA was extracted using RNeasy Plant Mini kit (QIAGEN cat.74904), following the manufacturer instructions (QIAGEN, Hilden, Germany). The RNA samples were DNase treated (Recombinant DNase I, Takara Biotechnology, Dalian, China) and subsequently cleaned by column using RNeasy Plant Mini kit (QIAGEN, Hilden, Germany). 12 arrays - ATH1; gene knock out Col [wild type] AB [knock out / insertional mutagen /T-Dna] SIZ1 [knock out / insertional mutagen /T-Dna] SAB [knock out / insertional mutagen /T-Dna] . More information about this study can be found at : http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/consult_project.pl?project_id=326

2013-09-01 | E-GEOD-43883 | biostudies-arrayexpress

Transcription profiling by array of wheat after inoculation with an adapted and a non-adapted Magnaporthe isolate or mock-inoculation to identify candidate genes for nonhost resistance against blast disease

Project description:In this experiment the transcriptome reprogramming in wheat during host and nonhost interaction with Magnaporthe sp. was analyzed in a time-series approach. Seven days old wheat plants of cv. Renan were mock-inoculated or inoculated with adapted Magnaporthe isolate Br116.5 from wheat or non-adapted isolate CD180 from Pennisetum. After 6, 12, 24 and 48 hours the abaxial epidermis was sampled. Total RNA was extracted using the RNeasy Plant Mini Kit with on-column DNase digestion (Qiagen, Hilden, Germany), and hybridized to Agilent 44k oligonucleotide arrays.

2017-12-02 | E-MTAB-5635 | biostudies-arrayexpress

Transcription profiling by array of barley after inoculation with an adapted and a non-adapted Magnaporthe isolate or mock-inoculation to identify candidate genes for nonhost resistance against blast disease

Project description:In this experiment the transcriptome reprogramming in barley during host and nonhost interaction with Magnaporthe sp. was analyzed in a time-series approach. Seven days old barley plants of cv. Vada were mock-inoculated or inoculated with adapted Magnaporthe isolate TH6772 from rice or non-adapted isolate CD180 from Pennisetum. After 6, 12, 24 and 48 hours the abaxial epidermis was sampled. Total RNA was extracted using the RNeasy Plant Mini Kit with on-column DNase digestion (Qiagen, Hilden, Germany), and hybridized to Agilent 44k oligonucleotide arrays.

2017-12-02 | E-MTAB-5634 | biostudies-arrayexpress

Transcription profiling by array of wheat after inoculation with Puccinia triticina, Puccinia hordei or mock-inoculation to identify candidate genes for nonhost resistance against rust disease

Project description:In this experiment the transcriptome reprogramming in wheat during host and nonhost interaction with Puccinia sp. was analyzed in a time-series approach. Ten days old wheat plants of cv. Renan were mock-inoculated or inoculated with P. triticina (Pt), BRW96258 isolate, or P. hordei (Ph), 1.2.1 isolate. After 12, 24, 36 and 48 hours first leaves were sampled. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), the Ambion TURBO DNA-free DNase Kit was used for DNA elimination, and RNA was hybridized to Agilent 44k oligonucleotide arrays.

2017-12-02 | E-MTAB-5656 | biostudies-arrayexpress

Transcription profiling by array of barley after inoculation with Puccinia hordei, Puccinia triticina or mock-inoculation to identify candidate genes for nonhost resistance against rust disease

Project description:In this experiment the transcriptome reprogramming in barley during host and nonhost interaction with Puccinia sp. was analyzed in a time-series approach. Ten days old barley plants of cv. Vada were mock-inoculated or inoculated with P. hordei (Ph), 1.2.1 isolate, or P. triticina (Pt), BRW96258 isolate. After 12, 24, 36 and 48 hours first leaves were sampled. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), the Ambion TURBO DNA-free DNase Kit was used for DNA elimination, and RNA was hybridized to Agilent 44k oligonucleotide arrays.

2017-12-02 | E-MTAB-5655 | biostudies-arrayexpress

Identification of candidate non-host resistance genes for powdery mildew in barley

Project description:To identify the non-host responsive genes, a time-series based global expression profiling was performed in barley using Agilent chip. Seven-day-old barley plants of cv. Vada were inoculated with spore density of 50-80 conidia mm-2 of Bgh or Bgt, and the abaxial epidermis of inoculated primary leaves or from non-inoculated control leaves was peeled 6, 12, 24 and 74 h after inoculation. Total RNA was extracted by using the RNeasy plant mini kit with on-Column DNase digestion (Qiagen, Hilden, Germany), and hybridized to a 44K Agilent oligonucleotide custom array of barley.

2014-10-24 | E-MTAB-2916 | biostudies-arrayexpress

2-week-old Arabidopsis seedlings (Columbia ecotype)

Project description:Comparison of TopHat alignments and assessment of spurious splice junctions for 32nt and 76nt read lengths. Total RNA from 2-week-old Arabidopsis thaliana (ecotype Columbia) seedlings grown on MS plates was isolated using RNeasy Plant Mini Kit from Qiagen. To remove any contaminating DNA, RNA was treated with DNAse. Isolation of poly (A) mRNA and preparation of cDNA library were carried out using the Illumina TrueSeq RNA kit. Sequencing (72 cycle) was done on Illumina Genome Analyzer II.

2011-09-24 | GSE32318 | GEO

Identification of candidate genes for nonhost resistance to powdery mildew in wheat

Project description:To identify the nonhost resistance genes, a time-series based global expression profiling was performed in wheat using Agilent gene expression 44K microarray array. Seven-day-old wheat plants of cv. Renan was inoculated with spore density of 50-80 conidia mm-2 of adapted (Bgt) or non-adapted (Bgh) powdery mildew pathogen, and the abaxial epidermis of inoculated primary leaves or from non-inoculated control leaves was peeled at 6, 12, 24 and 74 h after inoculation. Total RNA was extracted by using the RNeasy plant mini kit with on-Column DNase digestion (Qiagen, Hilden, Germany), and hybridized to a 44K Agilent oligonucleotide custom array of wheat.

2016-06-30 | E-MTAB-3803 | biostudies-arrayexpress

Transcriptome differences between two vitamin C-deficient mutants and wild type

Project description:The Arabidopsis mutant vtc2 is vitamin C-deficient and high light sensitive (Mueller-Moule et al., 2002. Plant Physiol 128: 970-977; Mueller-Moule et al., 2003. Plant Physiol 133: 748-760). Even though the VTC2 gene has been cloned (Jander et al., 2002. Plant Physiol 129: 440-450), its function is still unclear. The goal of this experiment is to learn more about the function of the VTC2 gene by determining differences in the transcriptomes of wild type and the vtc2-1 mutant. In order to differentiate between VTC2 gene-specific differences and vitamin C-induced differences, a second vitamin C-deficient mutant vtc1-1 (Conklin et al., 1996. PNAS 93: 9970-9974) is included in the experiment. The plants will be grown on agar plates in a growth chamber with a 16 hour light (about 40 umol photons m(-2)s(-1))/8 hour dark regime at 20C for 14 days to stage 1.04. Whole plants will be collected and total RNA will be isolated using the Qiagen Rneasy plant mini kit (Qiagen, Hilden, Germany).

2009-12-05 | GSE19257 | GEO

Gene expression profiles of human retinal microvascular pericytes (HRMVPC) and human lipoaspirate derived mesenchymal stromal cells (adipose stromal cells, ASC)

Project description:Comparative gene expression profiles of human retinal pericytes (HRMPC) and lipoaspirate derived mesenchymal stromal cells (adipose stromal cells, ASC) cultivated either in normal (1g/l) or high (4.5g/l) glucose medium to identify similarities and discrepancies and elucidate high glucose effects considering cell-based therapies in diabetic retinopathy. A hallmark of diabetic retinopathy is pericyte- dropout increased vascular permeability and progressive vascular occlusion. ASC and HRMVPC were cultured in NG or HG for 7 days. Then cells were trypsinized, washed and RNA isolated using Qiagen RNeasy mini Kit (Qiagen, Hilden, Germany). RNA quality was tested by capillary electrophoresis on an Agilent 2100 Bioanalyzer (Agilent) and high quality (RNA integrity values ≥ 9) was confirmed.

2020-05-26 | GSE144605 | GEO

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