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Sample GSM172122 Query DataSets for GSM172122
Status Public on Apr 30, 2007
Title Fruit6_woolly_rep2
Sample type RNA
 
Source name Mesocarp tissue of O´Henry cultivar peach
Organism Prunus persica
Characteristics Woolly fruit (0% juice)
Biomaterial provider Chilean Functional Genomics in Prunus persica Consortium: Universidad de Chile, Instituto de Investigaciones Agropecuarias, Asociacion de Exportadores, Fundacion para el Desarrollo Fruticola and Fundacion Chile. Supported by FDI-CORFO (FDI G02 P1001)
Treatment protocol Peach sampled from commercial harvest and exposed 7 days at 21 ºC after 15 days at 4ºC
Extracted molecule polyA RNA
Extraction protocol mRNA was purified using an Oligotex Mini kit (Qiagen), following manufacturer recommendations
Label 32P
Label protocol The 32P-labeled target DNA samples were prepared from poly(A)+ RNAs by incorporation of [α-32P]dCTP during first-strand cDNA synthesis, according to the protocol described by Bernard et al. (1996), unincorporated radioactive nucleotides were removed using the QIAquick Nucleotide Removal according to the manufacturer’s instructions (Qiagen).
 
Hybridization protocol Pre-hybridization in 5 ml of hybridization buffer (5X SSC, 5 X Denhardt solution, 1% SDS, and 50% formamide) for 1-3 h at 42 ºC. Hybridization was performed in the same buffer for 16-18 h at 42 ºC.
Scan protocol After washing, the membranes were sealed with a plastic film and exposed for 72-96 h to Phosphor screens (Kodak).
Description Woolly fruit (0% juice)
Data processing Quantification of the signal intensity was performed using the VersArray Analyzer software (BioRad). Raw values were measured as the volume of pixels within a circle encompassing the spot. Local background values were measured in the corners of spot and were subtracted from the signal intensity values for each spot. Spots that showed: (1) Signal Mean < (Background Mean + (1 x Background Standard Deviation; and (2) qcom < 0.8, were considered as low-quality spots and were removed. Qcom values were calculated as described in Wang et al., 2001. Then, the net intensity value of each spot was normalized by that of dap, a spike mRNA control.
 
Submission date Feb 27, 2007
Last update date Mar 02, 2007
Contact name Mauricio Gonzalez
E-mail(s) maugonzalez@inia.cl
Organization name Instituto de Investigaciones Agropecuarias
Lab Postcosecha
Street address Santa Rosa 11610
City Santiago
State/province Region Metropolitana
ZIP/Postal code 439-3
Country Chile
 
Platform ID GPL4889
Series (1)
GSE7145 Transcriptional changes associated with woolliness during fruit ripening in Prunus persica

Data table header descriptions
ID_REF
SIGNAL_RAW Raw intensity signal (mean)
BKD_RAW Background signal (mean)
VALUE Net intensity (mean) normalized

Data table
ID_REF SIGNAL_RAW BKD_RAW VALUE
101_G01 0.043617 0.037249
102_D02 0.038566 0.029224
102_D07 0.054862 0.045338
102_E01 0.054357 0.043441
102_F12 1.247564 0.293065 6.031531414
102_G08 0.053027 0.040058 0.329397906
102_H04 0.053721 0.051128
103_B04 0.05379 0.049271
103_B10 0.038019 0.03113 0.256361257
103_C07 0.039856 0.039777
103_C12 0.063825 0.054628
103_F09 0.044664 0.032335
103_G02 0.040144 0.029904 0.188115183
103_G03 0.073194 0.061844
103_G07 0.52775 0.092423 0.287709424
104_A08 0.028927 0.026984
104_C04 0.029832 0.027037
104_C10 0.038434 0.028621 0.162212042
104_D12 0.028484 0.027394
104_F02 0.035334 0.027374

Total number of rows: 847

Table truncated, full table size 25 Kbytes.




Supplementary file Size Download File type/resource
GSM172122.jpg.gz 420.6 Kb (ftp)(http) JPG

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