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Sample GSM679199 Query DataSets for GSM679199
Status Public on Mar 07, 2012
Title IC1179
Sample type genomic
 
Source name mycelia
Organism Aspergillus flavus
Characteristics strain: IC1179
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: 18543 (=IC1179, AF36)
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
IC1179 loess normalized loess normalized data

Data table
ID_REF VALUE IC1179 loess normalized
aflJ-adhA_at0 11.12109375 2230
aflJ-adhA_at1 10.69335938 1658
aflJ-adhA_at2 6.844726563 115
aflJ-adhA_at3 6.870117188 117
aflJ-adhA_at4 10.01757813 1037
aflJ-adhA_at5 10.90039063 1912
aflJ-adhA_at6 12.765625 6968
aflJ-adhA_at7 10.59570313 1549
aflJ-adhA_at8 12.33789063 5179
aflJ-adhA_at9 10.92773438 1948
aflJ-adhA_at10 11.89648438 3817
aflJ-adhA_at11 11.24414063 2426
aflJ-adhA_at12 10.9453125 1974
aflJ-adhA_at13 8.966796875 501
aflJ-adhA_at14 11.41601563 2733
aflJ-adhA_at15 12.05859375 4270
aflJ-adhA_at16 7.577148438 191
aflJ-adhA_at17 10.6015625 1554
aflJ-adhA_at18 12.84179688 7348
aflJ-adhA_at19 11.7578125 3465

Total number of rows: 150338

Table truncated, full table size 4736 Kbytes.




Supplementary file Size Download File type/resource
GSM679199.CEL.gz 2.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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