NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM679193 Query DataSets for GSM679193
Status Public on Mar 07, 2012
Title IC278
Sample type genomic
 
Source name mycelia
Organism Aspergillus flavus
Characteristics strain: IC278
Growth protocol Isolates were grown in Potato Dextrose Broth (DifcoTM) for up to 5 days before the mycelia was harvested and lyophilized.
Extracted molecule genomic DNA
Extraction protocol Total genomic DNA was extracted from freeze-dried mycelia using either the Qiagen maxiprep kit (Qiagen, Valencia, CA) or the MasterPure Yeast DNA Purification Kit (Epicentre Technologies, Madison, WI) following the manufacturer’s protocol.
Label biotin
Label protocol Genomic DNA was labeled using the BioPrime DNA labeling System (Invitrogen Catalogue No. 18094-011) as follows: (1) fungal DNA in the amount of 300-350 ng was mixed with 60 μl of 2.5X random primers (BioPrime kit) and 132 μl of dH2O, (2) the reaction mixture was denatured in an Eppendorf thermocycler at 99°C for 10 min, and then cooled at 4°C for 15 min, (3) 15 μl of 10X dNTPs containing biotin dCTP and 3 μl Klenow polymerase were added and incubated at 25°C in a thermocycler for 18 h, (4) the reaction mixture was precipitated by adding 15 μl of 3M NaOAc and 400 μl of cold 95% ethanol, followed by incubation at 20°C for 15 min, (5) samples were centrifuged at high speed in a refrigerated microcentrifuge for 20 min, and (6) the pellets were washed with 500 μl ice-cold 70% ethanol, centrifuged, and then vacuum dried with heating for 10 min. DNA was resuspended in 100 μl of dH2O and 5 μl was used to check the quality of the labeled DNA on a gel.
 
Hybridization protocol Each sample was analyzed by the Microarray Laboratories of Expression Analysis (Raleigh-Durham NC). Briefly, 300-350 ng of fragmented genomic DNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with streptavidin-phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
Scan protocol Fluorescent images were detected in a GeneChip® Scanner 3000 and array data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). Arrays images were further inspected for defects or debris. Quality control was based on a comparison of the conformity of hybridization controls, scaling factor, and noise; percent detection metrics were analyzed to determine if any outliers were present.
Description NRRL: 29507
Data processing For the parent-offspring trio heat maps, array data for all strains examined using aCGH were imported into JMP genomics (SAS, Cary, NC, USA) for further transformation and normalization. Data were log2 transformed and normalized using Loess normalization. Because we are interested in detecting differences in hybridization intensities no background correction was applied. For the genome-wide parentage plots, the A. flavus probe data were normalized using Loess normalization but not log2 transformed.
 
Submission date Feb 24, 2011
Last update date Mar 07, 2012
Contact name Ignazio Carbone
E-mail(s) ignazio_carbone@ncsu.edu
Phone 919-513-4866
Organization name North Carolina State University - Center for Integrated Fungal Research
Department Plant Pathology
Lab Ignazio Carbone
Street address 851 Main Campus Drive, Suite 233
City Raleigh
State/province NC
ZIP/Postal code 27606
Country USA
 
Platform ID GPL13221
Series (1)
GSE27484 Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis

Data table header descriptions
ID_REF
VALUE log2 loess normalized data
IC278 loess normalized loess normalized data

Data table
ID_REF VALUE IC278 loess normalized
aflJ-adhA_at0 10.38867188 1342
aflJ-adhA_at1 10.07421875 1079
aflJ-adhA_at2 6.021484375 65
aflJ-adhA_at3 6.28515625 78
aflJ-adhA_at4 9.42578125 688
aflJ-adhA_at5 10.41210938 1364
aflJ-adhA_at6 12.34570313 5209
aflJ-adhA_at7 9.509765625 729
aflJ-adhA_at8 11.4921875 2881
aflJ-adhA_at9 10.0859375 1088
aflJ-adhA_at10 10.921875 1941
aflJ-adhA_at11 10.81054688 1796
aflJ-adhA_at12 10.5 1449
aflJ-adhA_at13 8.548828125 375
aflJ-adhA_at14 10.37695313 1331
aflJ-adhA_at15 11.578125 3061
aflJ-adhA_at16 7.713867188 210
aflJ-adhA_at17 9.7734375 876
aflJ-adhA_at18 12.5 5794
aflJ-adhA_at19 10.86132813 1862

Total number of rows: 150338

Table truncated, full table size 4701 Kbytes.




Supplementary file Size Download File type/resource
GSM679193.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap