|
| Status |
Public on Mar 01, 2015 |
| Title |
Root grown under +Fe of ys3 mutant plants Replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Fe sufficient root
|
| Organism |
Zea mays |
| Characteristics |
genotype/variation: ys3
treatment: Fe sufficient
tissue: root
|
| Treatment protocol |
Fe deficiency treatment was initiated 8 days after germination by transfer of the plants to Fe(III)-EDTA-free culture medium.
|
| Growth protocol |
Maize plants were germinated in a 5-L plastic container for 4 days, and then transferred to a 20-L plastic container with air bubbling. Fe deficiency was initiated 8 days after germination by transfer of the plants to Fe(III)-EDTA-free culture medium. Maize plants grown hydroponically under Fe-sufficient or Fe-deficient conditions for 5 days were harvested at the same time.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
SYBR Green
|
| Label protocol |
Total RNA (3 ug) was treated with RNase-free DNase I (Takara, Kyoto, Japan) to remove contaminating genomic DNA. First-strand cDNA was synthesized using ReverTra Ace reverse transcriptase (Toyobo, Tokyo, Japan) by priming with oligo-d(T)30. For quantitative RT-PCR, a fragment was amplified by PCR in a StepOnePlus Real-Time PCR system (Applied Biosystems, Foster City, CA, USA) with SYBR Green I and ExTaqTM Real-Time PCR Version (Takara) following the manufacturer’s instructions with 40 cycles at 95 oC for 15 seconds, 60C for 30 seconds and 72 oC for 30 seconds. The template concentration was adjusted to 30 ng per each reaction.
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
test
|
| Data processing |
For the normalization it uses the average of five housekeeping genes: ZmUbiquitin; GRMZM2G118637.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_ZmUbiquitin)]
|
| |
|
| Submission date |
Feb 21, 2013 |
| Last update date |
Mar 01, 2015 |
| Contact name |
Tomoko Nozoye |
| E-mail(s) |
[email protected]
|
| Phone |
+81 3 5841 5236
|
| Organization name |
The University of Tokyo
|
| Street address |
1-1-1 yayoi bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-8657 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16711 |
| Series (1) |
| GSE44557 |
Maize plants (Zea may) : WT (Alice) vs. Yellow stripe mutants (ys1 or ys3) (qPCR) |
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