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Sample GSM377075 Query DataSets for GSM377075
Status Public on Mar 06, 2009
Title Genomic DNA - 45 day old leaf sample - mutant g650
Sample type genomic
 
Channel 1
Source name 45 day old leaf tissue - g650
Organism Oryza sativa Indica Group
Characteristics tissue: leaf tissue
genotype: IR64 mutant g650
mutant type: gamma ray
Treatment protocol Mutagenesis was induced by treatment of the indica variety IR64 with DEB-treatment, Fast Neutron, or gamma ray (GR) exposure. These mutagenized lines were advanced to M4 or M5 lines prior to DNA extraction by single seed descent
Growth protocol A total of 16 mutant populations were grown under greenhouse conditions (standard for rice growth) until 45 days after sowing.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from leaves of 45 day-old greenhouse-grown plants by CTAB extraction and purified by cesium chloride gradient centrifugation. The genomic DNA samples were assayed and quantified by spectrophotometry.
Label biotin
Label protocol Each sample was biotin labeled using the random priming method with BioPrime® Array CGH Genomic Labeling System (Invitrogen, Carlsbad, CA) following the manufacturer's instruction; a total of 3 µg of genomic DNA from each sample was mixed with 40 µl of 2.5X random primer solutions.
 
Channel 2
Source name 45 day old leaf tissue - wtcheck
Organism Oryza sativa Indica Group
Characteristics tissue: leaf tissue
genotype: wildtype
Growth protocol Wildtype samples were grown under greenhouse conditions (standard for rice growth) until 45 days after sowing.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from leaves of 45 day-old greenhouse-grown plants by CTAB extraction and purified by cesium chloride gradient centrifugation. The genomic DNA samples were assayed and quantified by spectrophotometry.
Label biotin
Label protocol Each sample was biotin labeled using the random priming method with BioPrime® Array CGH Genomic Labeling System (Invitrogen, Carlsbad, CA) following the manufacturer's instruction; a total of 3 µg of genomic DNA from each sample was mixed with 40 µl of 2.5X random primer solutions.
 
 
Hybridization protocol Hybridizations were conducted according to Affymetrix standard protocol for eukaryotic target hybridization. Ten µg of biotinylated fragments were mixed in 200 µl with a final concentration of 0.1 mg/ml sonicated herring sperm DNA in a hybridization buffer with 100 mM 2-N-morpholino-ethane-sulphonic acid (MES), 1 M NaCl, 20 mM EDTA and 0.01% Tween 20, denatured at 99ºC for 5 min and equilibrated at 45ºC for 5 min prior to hybridization. The hybridization mix was then transferred into the Rice GeneChip® cartridge and hybridized at 45ºC for 16 h. The hybridized arrays were washed and stained using EukGE-WS2v5_450 protocol with an Affymetrix GeneChip Fluidics Station 450.
Scan protocol The arrays were scanned twice and the intensities averaged with an Affymetrix GeneChip Scanner 3000 using GCOS 1.4.0.036 software (Affymetrix, Santa Clara, CA).
Description Genome hybridization using total DNA from g650
Data processing The "affy" package (R/Bioconductor) was used to extract probe level information and examine diagnostics. Perfect match probe data was scale-normalized to the average of the wild type arrays, using a log2 ratio calculation versus wild type at the probe level.
For arrays with replicates, the average probe level intensity was taken prior to data analysis. Similarly, the wild type average probe level intensity was taken prior to data analysis (note: scale normalization occurs AFTER averaging of the intensity for wild type arrays but BEFORE averaging the replicated mutant arrays (G650 and N1856)).
 
Submission date Mar 03, 2009
Last update date Mar 06, 2009
Contact name Ramil Paner Mauleon
E-mail(s) r.mauleon@cgiar.org
Organization name International Rice Research Institute
Department Crop Research Informatics Laboratory
Lab Bioinformatics team
Street address IRRI Campus, Pili Drive
City Los Banos
State/province Laguna
ZIP/Postal code 4031
Country Philippines
 
Platform ID GPL2025
Series (1)
GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays

Data table header descriptions
ID_REF
VALUE R/Bioconductor affy package derived signal (log2 ratio at fold change cut-off < -0.6, from probe-level scaled differences of mutant with wildtype).
gr650_FC_<_-0.8
gr650_FC_<_-1.0

Data table
ID_REF VALUE gr650_FC_<_-0.8 gr650_FC_<_-1.0
Os.10001.1.S1_at 0 0 0
Os.1000.1.S1_at 0 0 0
Os.10002.1.S1_at 0 0 0
Os.10003.1.S1_at 0 0 0
Os.10004.1.S1_s_at 0 0 0
Os.10006.1.S1_at 0 0 0
Os.10006.2.S1_x_at 0 0 0
Os.10007.1.A1_a_at 0 0 0
Os.10007.2.S1_a_at 0 0 0
Os.10010.1.S1_at 0 0 0
Os.10011.1.S1_at 0 0 0
Os.10013.1.S1_at 0 0 0
Os.10014.1.S1_at 0 0 0
Os.10015.1.S1_at 0 0 0
Os.10015.1.S1_s_at 0 0 0
Os.10016.1.S1_a_at 0 0 0
Os.10017.1.S1_at 0 0 0
Os.10018.1.S1_at 0 0 0
Os.10019.1.S1_a_at 0 0 0
Os.10020.1.S1_at 0 0 0

Total number of rows: 57194

Table truncated, full table size 1425 Kbytes.




Supplementary file Size Download File type/resource
GSM377075_gr650a.CEL.gz 5.4 Mb (ftp)(http) CEL
GSM377075_gr650b.CEL.gz 5.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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