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Sample GSM450760 Query DataSets for GSM450760
Status Public on May 24, 2012
Title cDNA array TM-1/Hai7124 20 DPA fiber set1
Sample type RNA
 
Channel 1
Source name 20 DPA cotton fiber
Organism Gossypium hirsutum
Characteristics strain: TM-1
tissue type: fibers
developmental stage: 20 days post anthesis (DPA)
Treatment protocol Developing ovules of TM-1 and Hai7124 were excised from each boll at 5, 10, 15, 20 and 25 DPA, and fiber cells in 10-25 DPA ovules were carefully dissected from the ovules. All harvested plant materials were immediately frozen in liquid nitrogen and stored at –70°C.
Growth protocol G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 plants were grown in the field (Nanjing, China) in 2006.
Extracted molecule total RNA
Extraction protocol Total RNA of cotton was extracted from 5 DPA ovules and 10 to 25 DPA fibers of TM-1 and Hai7124 using a modified hot-borate method.
Label Cy5
Label protocol Total RNA was labeled with Cy3 and Cy5 during cDNA synthesis using Klenow enzyme.
 
Channel 2
Source name 20 DPA cotton fiber
Organism Gossypium barbadense
Characteristics cultivar: Hai7124
tissue type: fibers
developmental stage: 20 days post anthesis (DPA)
Treatment protocol Developing ovules of TM-1 and Hai7124 were excised from each boll at 5, 10, 15, 20 and 25 DPA, and fiber cells in 10-25 DPA ovules were carefully dissected from the ovules. All harvested plant materials were immediately frozen in liquid nitrogen and stored at –70°C.
Growth protocol G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 plants were grown in the field (Nanjing, China) in 2006.
Extracted molecule total RNA
Extraction protocol Total RNA of cotton was extracted from 5 DPA ovules and 10 to 25 DPA fibers of TM-1 and Hai7124 using a modified hot-borate method.
Label Cy3
Label protocol Total RNA was labeled with Cy3 and Cy5 during cDNA synthesis using Klenow enzyme.
 
 
Hybridization protocol Cy3 and Cy5-labeled cDNA resolved in 80 µL hybridization solution (3×SSC, 0.2% SDS, 5 × Denhart’s, 25% formamide). DNA in hybridization solution was denatured at 95°C for 3 min prior to loading onto a microarray. Slides were hybridized at 42°C overnight and transferred to fresh containers with Wash Solution 1 (0.2% SDS, 2 × SSC) at 42°C for 5 min and then immersed in Wash Solution 2 (0.2 × SSC) at room temperature for 5 min.
Scan protocol All microarrays were scanned with a LuxScan scanner using the LuxScan 3.0 software (Captalbio Corp).
Description Comparison of gene expression profiles of G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 fiber at 20DPA
Data processing All microarrays were analyzed using the LuxScan 3.0 software (Captalbio Corp). We quantified signal intensities of individual spots from the 16-bit TIFF images using LuxScan 3.0 software (Captalbio Corp). The nonlinear global-intensity-based LOWESS program (Yang et al., 2002) was applied for normalization.
 
Submission date Sep 09, 2009
Last update date May 24, 2012
Contact name Tianzhen Zhang
E-mail(s) cotton@njau.edu.cn
Phone 862584395307
Fax 862584395307
Organization name National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute
Lab CRI NJAU
Street address Weigang#1
City Nanjing
State/province Jiangsu
ZIP/Postal code 210095
Country China
 
Platform ID GPL2610
Series (1)
GSE18028 cDNA microarray expression profile during fiber elongation between G. hirsutum and G. barbadense

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE
PRE_VALUE lowess normalized ratio (TM-1/Hai7124)

Data table
ID_REF VALUE PRE_VALUE
CM001A01 0.0019 1.0013
CM001A02 0.0081 1.0056
CM001A03 0.2510 1.19
CM001A04 0.8210 1.7666
CM001A05 -0.0564 0.96165
CM001A06 0.6181 1.5349
CM001A07 -0.8408 0.55835
CM001A08 -1.4440 0.36755
CM001A09 -0.2511 0.84025
CM001A10 -0.1478 0.9026
CM001A11 0.1059 1.0762
CM001A12 0.1204 1.087
CM001B01 -0.5653 0.6758
CM001B02 0.1475 1.10765
CM001B03 -0.0960 0.9356
CM001B04 0.2245 1.1684
CM001B05 0.0013 1.0009
CM001B06 0.1502 1.1097
CM001B07 0.1085 1.0781
CM001B08 0.0604 1.04275

Total number of rows: 11706

Table truncated, full table size 273 Kbytes.




Supplementary file Size Download File type/resource
GSM450760.txt.gz 1.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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