|
| Status |
Public on Apr 24, 2008 |
| Title |
Arabidopsis, whole roots, standard conditions, rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
whole roots
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Ecotype: Columbia
Age: Seedling roots, 5 days after germination
Growth Media: Standard media for 5 days then transferred to fresh standard media for 3 hours
Iron deficiency Treatment length: none
|
| Treatment protocol |
Seedlings were grown for 5 days before transfer to -Fe media. Transfers were staggered such that all roots were harvested within 3 hours of each other on the sixth day of growth. Roots were cut with a razor blade 0.5 mm below the root/hypocotyl junction and collected into RNA extraction buffer. Approximately 320 roots were collected per replicate, with two biological replicates being performed per time point. Samples were briefly sonicated to disrupt the tissue.
|
| 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 |
Approximately 320 roots were collected per replicate. 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 one-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 whole roots grown under standard conditions for 5 days and transferred to fresh standard to media for 3 hours
|
| 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) |
| GSE10502 |
Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots |
| GSE10576 |
Iron deficiency (-Fe) effect: Arabidopsis roots |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
