|
| Status |
Public on Jul 19, 2010 |
| Title |
Arabidopsis ATH1_cortex/endodermis initial cell type_CYCD6 marker GFP line_second biological replicate |
| Sample type |
RNA |
| |
|
| Source name |
CEI sorted cells
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
age: Seedling roots, 5 days after germination
treatment: Standard media
|
| Treatment protocol |
Seedlings were grown for 5 days before transfer to Dex media. Roots were cut with a razor blade 0.5 mm below the root/hypocotyl junction and collected into RNA extraction buffer.
|
| Growth protocol |
Seeds were surface sterilized for 2 minutes in 70% ethanol, the ethanol was removed, then replaced with 30% Bleach and 0.02% Triton X-100 for 15 minutes. Seeds were rinsed 3 times with sterile water, stratified at 4˚C for 2 days, then placed on standard media. Standard media is 1X Murashige and Skoog salt mixture, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. Dex media is 1X Murashige and Skoog salt mixture in which 1micromolar of Dex is added. Nylon mesh was placed on top of the solidified media and seeds were planted at ~20 seeds/cm in two rows.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 1000 roots were collected per replicate, with two biological replicates being performed per time point. Samples were briefly sonicated to disrupt the tissue. RNA was extracted using the RNAeasy Plant Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.
|
| |
|
| Hybridization protocol |
Samples were submitted to Duke Microarray Facility (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
|
| Scan protocol |
Samples were submitted to Duke Microarray Facility (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
|
| Description |
Gene expression data from CEI sorted cells under standard conditions for 5 days
|
| Data processing |
MAS 5.0
|
| |
|
| Submission date |
Apr 28, 2009 |
| Last update date |
Jul 19, 2010 |
| Contact name |
Rosangela Sozzani |
| E-mail(s) |
[email protected]
|
| Phone |
919 6138202
|
| Organization name |
Duke University
|
| Department |
Biology
|
| Lab |
Benfey
|
| Street address |
124 Science Dr
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE15876 |
The SHR/SCR pathway directly activates genes involved in asymmetric cell division in the Arabidopsis root |
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