Investigation Title Transcription profiling of M.graminicola between growth in vitro and late-stage infection in planta
Comment[Submitted Name] Rothamsted-M.graminicola-Expt2-PDB v. 28d Infected Plant
Experimental Design cell_type_comparison_design transcription profiling by array
Experimental Design Term Source REF mo EFO
Comment[ArrayExpressReleaseDate] 2006-02-28
Comment[AEMIAMESCORE] 4
Comment[ArrayExpressAccession] E-MEXP-523
Comment[MAGETAB TimeStamp_Version] 2010-08-11 15:12:37 Last Changed Rev: 13058
Experimental Factor Name cell type
Experimental Factor Type cell_type
Experimental Factor Term Source REF
Person Last Name Hammond-Kosack Antoniw Keon Rudd Hargreaves Skinner
Person First Name Kim John John Jason John Wendy
Person Mid Initials J
Person Email john.keon@bbsrc.ac.uk
Person Phone 01582 763133
Person Fax
Person Address Harpenden, St Albans, Hertfordshire, AL5 2JQ, United Kingdom
Person Affiliation Rothamsted Research Rothamsted Research Plant Pathogen Interactions, Rothamsted Research Rothamsted Research Rothamsted Research Rothamsted Research
Person Roles submitter
Person Roles Term Source REF
Quality Control Type technical_replicate
Quality Control Term Source REF mo
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date 2006-02-28
PubMed ID
Publication DOI
Publication Author List John Keon; Jason Rudd; John Antoniw; Wendy Skinner; John Hargreaves; Kim Hammond-Kosack
Publication Title Metabolic and stress adaptation by Mycosphaerella graminicola during sporulation in its host revealed through microarray transcription profiling
Publication Status
Publication Status Term Source REF
Experiment Description Comparison of gene expression in M.graminicola between growth in vitro and late-stage infection in planta.
Protocol Name P-MEXP-7130 P-MEXP-7132 P-MEXP-7133 P-MEXP-7234 P-MEXP-8015 P-MEXP-15806 P-MEXP-15656 P-MEXP-15655 P-MEXP-15807 P-MEXP-15658
Protocol Type grow grow pool pool nucleic_acid_extraction nucleic_acid_extraction labeling labeling hybridization feature_extraction
Protocol Description A virulent isolate of M. graminicola (LA951) recovered from the UK wheat cultivar Riband grown in experimental plots at IACR - Long Ashton Research Station was used. The isolate was stored at -80 C in 50% v/v glycerol. Fungal spores for plant and culture inoculation were harvested from 5 day old cultures growing in the budding form on potato dextrose agar plates (Oxoid Ltd., Hampshire, UK) at 17 C under near UV light (Sylvania, F8T5/BLB).
For fungal cultures grown in vitro, 100mls of growth medium, Potato Dextrose Broth [PDB](Sigma) was seeded with 4x105 cells/ml. Cultures were grown with shaking (220rpm) at 23 C. Tissue was harvested by filtration when the cell density reached c. 5x106 cells/ml. This density was achieved in c.72 hrs for cultures grown in PDB. Filtered tissue was stored at -80 C until required. Potato Dextrose Broth was used as a complex nutrient-rich condition typically containing 20g/L glucose and 4g/L potato extract. A virulent isolate of M. graminicola (LA951) recovered from the UK wheat cultivar Riband grown in experimental plots at IACR - Long Ashton Research Station was used. The isolate was stored at -80 C in 50% v/v glycerol. Fungal spores for plant and culture inoculation were harvested from 5 day old cultures growing in the budding form on potato dextrose agar plates (Oxoid Ltd., Hampshire, UK) at 17 C under near UV light (Sylvania, F8T5/BLB). To generate late stage plant infected material the second leaf of 17 day old wheat plants (cultivar Riband) was attached, adaxial side up to Perspex sheets, using double sided tape. The leaves were inoculated with 10 ul spore droplets containing 105 cells/ml, (5 drops per leaf). Following an initial 72 hour incubation at 100% relative humidity, inoculated plants were incubated at 16 C with a 16hr light period at 88% relative humidity for up to 28 days during symptom development. After 28 days many pycnidia were visible within diseased lesions, and the surrounding leaf tissue was senescent. Infected tissue was excised and stored at -80 C. Each 100ml fungal culture yielded approximately 3-400mgs w/w after harvesting by filtration. Typically the fungus from 6 flasks was pooled to yield a single biological replicate of c. 1,800mgs which was used for RNA extraction. Plants were grown in half seed trays with 20 leaves inoculated in one experimental treatment. Typically 18 leaf segments c. 7cm long were harvested and pooled for extraction. 7cm uninfected leaf segments weighed approximately 100mg each, although the weight was lower following infection. Total RNA was isolated from freeze-dried M. graminicola cells or senescent wheat leaves containing M. graminicola using the TRIZOL procedure (Invitrogen), following the suppliers protocol and incorporating the suggested additional procedures for polysaccharide containing tissues. TRIZOL was used at the ratio of 1ml. per 100mg fresh/weight of tissue. Tissue was disrupted by 4x 1minute bursts using a Polytron over a 20 minute incubation. Further purification of the total RNA was achieved by precipitation from a solution of 4M Lithium Chloride. Total RNA was used for all microarray analyses. Total RNA was isolated from freeze-dried M. graminicola cells or senescent wheat leaves containing M. graminicola using the TRIZOL procedure (Invitrogen), following the suppliers protocol and incorporating the suggested additional procedures for polysaccharide containing tissues. TRIZOL was used at the ratio of 1ml. per 100mg fresh/weight of tissue. Tissue was disrupted by 4x 1minute bursts using a Polytron over a 20 minute incubation. Further purification of the total RNA was achieved by precipitation from a solution of 4M Lithium Chloride. Total RNA was used for all microarray analyses. Labelling of total RNA isolated from fungal cultures or from 28 day infected plant material was by indirect incorporation of reactive AlexaFluor dyes into amine-modified cDNA synthesised using Superscript III reverse transcriptase (SuperScript Indirect cDNA Labelling System, Invitrogen), following the suppliers protocols. 20 ug of total RNA was used in each labelling reaction. AlexaFluor 555 (equivalent to Cy3 dye) was used in the green channel and AlexaFluor 647 (equivalent to Cy5 dye) was used in the red channel. Following purification, the labelled probe was reduced to dryness in a centrifugal evaporator. Labelling of total RNA isolated from fungal cultures or from 28 day infected plant material was by indirect incorporation of reactive AlexaFluor dyes into amine-modified cDNA synthesised using Superscript III reverse transcriptase (SuperScript Indirect cDNA Labelling System, Invitrogen), following the suppliers protocols. 20 ug of total RNA was used in each labelling reaction. AlexaFluor 555 (equivalent to Cy3 dye) was used in the green channel and AlexaFluor 647 (equivalent to Cy5 dye) was used in the red channel. Following purification, the labelled probe was reduced to dryness in a centrifugal evaporator. Detailed hybridisation and washing conditions were as described at the COGEME website (http://www.cogeme.man.ac.uk). Specifically; Slides were pre-hybridised for 45min. at 42C (5xSSC, 0.1%w/v SDS, 1%w/v BSA) followed by washing in de-ionised water (5x) and briefly in isopropanol before drying in a centrifuge (2,000g for 1min.). Each dried purified probe was dissolved in 20ul of hybridisation buffer (25% formamide, 5xSSC, 0.1%w/v SDS).These were mixed, denatured for 3minutes at 90C and cooled on ice. The 40ul of mixed probe was applied to the slide and covered with a Hybri-slip (SIGMA 22mmx60mm). Slides were incubated overnight at 42C before washing with (1.) 2xSSC, 1%SDS, for 15min. (2.) 1xSSC, 0.2%SDS, for 8min. & (3.) 0.1%SSC, 0.2%SDS, for 5min. (all washes were at room temperature). The fluorescently labelled slides were scanned using an Axon 4000B scanner with a spot size of 5um. Laser power (PMT) values for each block were initially set by eye and refined using the analysis supplied with the scanner. Maximum PMT values in each channel were set to produce fewer than 5 saturating spots
Protocol Parameters media; media; Amplification;Extracted product; Extracted product;Amplification; Amount of nucleic acid labeled;Label used;Amplification; Amplification;Amount of nucleic acid labeled;Label used; Quantity of label target used;Chamber type;temperature;
Protocol Hardware Axon- GenePix4000B
Protocol Software GenePix [Axon Instruments]
Protocol Contact
Protocol Term Source REF
SDRF File E-MEXP-523.sdrf.txt
Term Source Name ncbitax ArrayExpress mo EFO
Term Source File http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html http://www.ebi.ac.uk/arrayexpress http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/efo/
Term Source Version