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Browse BrachyPLEX Experiment Data

Choose an experiment:
Brachy leaf, root, and stem
Karen Osmont, University of Massachusetts (
Experiment design (9 hybridizations)
tissue type name
•leaf •root •stem

Plant growth conditions Seeds of the wild-type accession Bd21 were sown directly to humid Farfad potting mix #2 in 10 cm pots. Growth chamber te...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Experiment Name: Brachy leaf, root, and stem
Accession No: BD3
Microarray: Brachy
Visibility: public
Experiment Type:
Experiment Factor(s):
tissue type name
•leaf   •root   •stem
Quality Control: biological replicates
Treatment summary:
 tissue type name  # replicates
 leaf  3
 root  3
 stem  3
Total hybridizations: 9
Description: Plant growth conditions

Seeds of the wild-type accession Bd21 were sown directly to humid Farfad potting mix #2 in 10 cm pots. Growth chamber temperature was maintained at 20°C with 20 h light:4 h dark cycles at a fluence rate of 200 μmol of photons.m-2.s-1 and relative humidity of 68.0-68.5. For plate-grown seedlings, seeds were de-hulled and then imbibed in water for two hours with shaking. Then, seeds were treated with 70% ethanol for 20 sec, rinsed with sterile water, then soaked in 1.3% NaClO for 4 min at room temperature while shaking. Seeds were subsequently rinsed 3 times with sterile H20 and stored in the dark at 4°C for a minimum of 2 days in a sterile Petri dish with filter paper. Seedlings were grown for seven days on 0.5X MS medium containing 0.7% bactoagar adjusted to a pH of 5.8 with KOH.

Tissue sampling and preparation for microarray expression profiling

Approximately 30 days following germination, total leaf and stem were collected when flowers began to emerge from the flag leaf. Leaves were collected from the stems with a curved-tip probe. Nodes and internodes from the second leaf junction to the internode below the inflorescence were placed in a tube cooled with liquid nitrogen. Seven-day-old whole seedlings were flash frozen in liquid nitrogen and then the roots were snapped off into a sterile culture tube. The six time points were collected over the course of one day at ZT2, 6, 10, 14, 18, and 22. Three plants were dissected for each time point and in triplicate for each tissue type. Samples were stored in liquid nitrogen or at -80°C until RNA extraction. Tissue was ground with mortars and pestles in liquid nitrogen. RNA was extracted using the Qiagen (Valencia, CA, USA) Plant RNaeasy Kit according to the manufacturer’s instructions. Labeled sense strand cDNA probes were synthesized using the Ambion WT expression kit.
Publication: none
Created: 2012-05-23 15:25:53
Last Update: 2013-06-04 11:30:52
Submitter: Samuel P Hazen
Name: Karen Osmont
Institution: University of Massachusetts
Head of Laboratory: Sam Hazen

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