|
| Status |
Public on May 24, 2012 |
| Title |
cDNA array TM-1/Hai7124 25 DPA fiber set2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
25 DPA cotton fiber
|
| Organism |
Gossypium hirsutum |
| Characteristics |
strain: TM-1
tissue type: fibers
developmental stage: 25 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 |
25 DPA cotton fiber
|
| Organism |
Gossypium barbadense |
| Characteristics |
cultivar: Hai7124
tissue type: fibers
developmental stage: 25 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 25DPA
|
| 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 |
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