Affymetrix GeneChip Arabidopsis Genome [ATH1-121501]

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Comparison of Arabidopsis wild-type developing seeds grown under sulfur-deficient condition vs Arabidopsis wild-type developing seeds grown under control condition.

growth_condition

Transcription profiling of Arabidopsis wild type seeds grown under sulfur-deficient conditions

Comparison of Arabidopsis wild-type developing seeds grown under sulfur-deficient condition vs Arabidopsis wild-type developing seeds grown under control condition.


Affymetrix:Protocol:Hybridization-EukGE-WS2v4_450

Title: Affymetrix EukGE-WS2v4_450 Hybridization. Description:

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-CAGE-24517

For two-weeks, on an agar-solidified MGRL medium containing 1.5 mM (control) or 30 uM (sulfur-deficient) sulfate as MgSO4 in a growth chamber controlled at 22 C and 16 h light cycles).  After two weeks growth, transfer the plants to rockwool bricks (Nittobo, Tokyo, Japan) in a greenhouse controlled at 22 C.  - Day cycle (sunlight and 16 h of lamps per day)  - Irrigated twice a week with a liquid medium, keeping the ratio of nutrition at 1.5 mM sulfate/ 7 mM nitrate (control) or 30 uM sulfate/ 7 mM nitrate (sulfur-deficient) in the plant pods.  

P-CAGE-24520

SCANPRTCL24521

Scanning: GeneArray Scanner (Agilent Technologies, Palo Alto, CA, USA)

P-CAGE-24526

For two-weeks, on an agar-solidified MGRL medium containing 1.5 mM (control) sulfate as MgSO4 in a growth chamber controlled at 22 C and 16 h light cycles.  After two weeks growth, transfer the plants to rockwool bricks (Nittobo, Tokyo, Japan) in a greenhouse controlled at 22 C.  Day cycle (sunlight and 16 h of lamps per day)  Irrigated twice a week with a liquid medium, keeping the ratio of nutrition at 1.5 mM sulfate/ 7 mM nitrate (control) in the plant pods.  Harvest developing siliques at 10 and 11 day after flowering in the morning. Frozen by liquid nitrogen. Harvesting date is only once for each plant.  

P-CAGE-24527

For two-weeks, on an agar-solidified MGRL medium containing  30 uM (sulfur-deficient) sulfate as MgSO4 in a growth chamber controlled at 22 C and 16 h light cycles.  After two weeks growth, transfer the plants to rockwool bricks (Nittobo, Tokyo, Japan) in a greenhouse controlled at 22 C.  Day cycle (sunlight and 16 h of lamps per day)  Irrigated twice a week with a liquid medium, keeping the ratio of nutrition at 30 uM sulfate/ 7 mM nitrate (sulfur-deficient) in the plant pods.  Harvest developing siliques at 10 and 11 day after flowering in the morning. Frozen by liquid nitrogen. Harvesting date is only once for each plant.  

P-CAGE-24529

Labeled target cRNA was prepared according to the GeneChip Expression Analysis Technical Manual (701025 Rev. 3) of Arabidopsis Genome ATH1 DNA array (Affymetrix, Santa Clara, CA, USA).  - Double-stranded cDNA was prepared from 12 ug of total RNA.  - Double strand cDNA synthesis using SuperScript Choice System (Invitrogen, Carlsbad, CA, USA)  - Synthesis of biotin-labeled cRNA through in vitro transcription using BioArray HighYield RNA Transcript Kit (Enzo, New York, NY, USA) - Purification labeled cRNA with RNeasy column (Qiagen, Hilden, Germany) - Fragmentation of labeled cRNA. 94 C, 35 min in Fragmentation Buffer (Affymetrix).  

P-CAGE-24558

GeneSpring 7.0 (Silicon Genetics, Redwood City, CA, USA)  The minus values of difference between back-ground to signal were converted to 0.01 signal value. Perform per chip normalization with the median of all measurements on the chip. To reduce false positives, genes with present or marginal values in the absolute call of the baseline data in all array sets were selected for the analysis.

Transcription profiling of Arabidopsis wild type seeds grown under sulfur-deficient conditions

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