Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

HAP5 Triple Mutant vs. Constans Mutant

ABSTRACT: Aims: To compare the transcriptional profiles of an AtHAP5 (AtNF-YC, AtCBF-C) triple mutant vs. a Constans mutant. Background Information on Mutants: AtHAP5 triple mutant created by cross between the following SALK TDNA inserts: SALK_034838, SALK_058903, SALK_032163; these correspond to At1G54830, At1G08970, At5G63470, respectively. co-SAIL TDNA insertion SAIL_24_H04 corresponds to AT5G15840. Tissue: Above-ground whole plants grown for 10 days, under 16 hr light 8 hrs dark at constant 22C. Tissue collected 14 hrs after lights on. RT-PCR analysis on test RNA confirmed FT levels reduced in mutants lines compared to wild-type. 9 samples were used in this experiment.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Nottingham Arabidopsis Stock Centre (NASC)

PROVIDER: E-GEOD-20258 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. The efficiency (specificity, detection sensitivity) of the developed array was evaluated using the labeled genomic DNA of pure bacterial strains, Escherichia coli DH5M-NM-1 and Sphingomonas sp. strain NM-05 (involved in the biodegradation of M-NM-3-hexachlorohexane isolated from IPL, Lucknow) at different concentrations of 300ng, 500ng, 800ng, 1000ng and 1250ng. The specificity of the developed array was further validated using mixed cultures containing three strains (Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1 and Bordetella sp. strain IITR-02) involved in biodegradation of M-NM-3-hexachlorohexane, biphenyl and chlorobenzenes respectively. The mixed culture also contained non-target/non-degrader strains (E. coli DHM-NM-1, E.coli BL21 and E.coli K12 NCTC50192). The developed array was applied for profiling using the total soil DNA in five contaminated habitats of north India, viz. chloroaromatic chemicals contaminated site (India Pesticide Limited, Chinhat, Lucknow), a river sediments (Gomti river sediment, Lucknow), heavy metal industry dump site (Jajmau industrial area Kanpur), a effluent treatment plant (CETP along Ganges river near Kanpur), and an oil refinery (Mathura oil refinery). Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well characterized genera involved in biodegradation of pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph), biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal) and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to hydroxylases, monooxygenases and dehydrogenases which were present in all the five samples. Many compound specific genes which initiate the degradation pathway were also detected. Thus, the array developed and validated here may be useful in assessing the biodegradative potential and composition of environmentally useful bacteria in hazardous ecosystems. Agilent one-color CGH experiment,Organism: Genotypic designed Agilent-17159 Genotypic designed Agilent Multibacterial 8x15k Array , Labeling kit: Agilent Genomic DNA labeling Kit (Part Number: 5190-0453)

Dataset Information

HAP5 Triple Mutant vs. Constans Mutant

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure