|
| Status |
Public on Apr 24, 2008 |
| Title |
Arabidopsis, root cells, -Fe, replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Protoplasted and FACS sorted root cells
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Ecotype: Columbia
Age: Seedling roots, 6 days after germination
Growth Media: Standard media, transferred to -Fe media for 24 hours prior to harvesting tissue
|
| Treatment protocol |
Samples were prepared as in Birnbaum et al. (2005) except that roots were transferred to -Fe media for 24 hours before protoplasting or harvested without protoplasting. Protoplasted cells were passed through the FACS device with all cells being collected.
|
| 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 for 4˚C for 2 days, then placed on standard media. Standard media is 1X Murashige and Skoog salt mixture in which ferrous sulfate is replaced with 100mM Fe(III)-EDTA, 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. –Fe media is 1X Murashige and Skoog salt mixture in which ferrous sulfate is replaced with 0.3mM Ferrozine. 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 |
RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).
|
| Label |
biotin
|
| Label protocol |
Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.
|
| |
|
| Hybridization protocol |
Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
|
| Scan protocol |
Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
|
| Description |
Gene expression data from FACS sorted cells from roots treated for 24 hours with -Fe media
|
| Data processing |
MAS5.0
|
| |
|
| Submission date |
Feb 12, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Terri Anita Long |
| E-mail(s) |
[email protected]
|
| Phone |
919-613-8202
|
| Fax |
919-613-8177
|
| Organization name |
Duke University
|
| Department |
Biology
|
| Lab |
Philip Benfey
|
| Street address |
Box 90338
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27707 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (2) |
| GSE10496 |
Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe) |
| GSE10576 |
Iron deficiency (-Fe) effect: Arabidopsis roots |
|
| Relations |
| Reanalyzed by |
GSE119083 |
