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Browse MaizePLEX Experiment Data

Choose an experiment:
Circadian clock-mediated transcriptional regulation in maize
Frank G. Harmon, Plant Gene Expression Center (fharmon@berkeley.edu,sadaf_pbs@yahoo.com)
Experiment design (12 hybridizations)
Continuous Light
•ZT0 •ZT4 •ZT8 •ZT12 •ZT16 •ZT20 •ZT24 •ZT28 •ZT32 •ZT36 •ZT40 •ZT44

The goal of the experiment was to perform a large scale study of circadian regulation of gene expression in maize. To identify maize genes with exp...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Circadian clock-mediated transcriptional regulation in maize
Accession No: ZM28
Microarray: maize18k
Visibility: public
Experiment Type:
Experiment Factor(s):
Continuous Light
•ZT0   •ZT4   •ZT8   •ZT12   •ZT16   •ZT20   •ZT24   •ZT28   •ZT32   •ZT36   •ZT40   •ZT44
Quality Control: biological replicates
Treatment summary:
 Continuous Light  # replicates
 ZT0  1
 ZT4  1
 ZT8  1
 ZT12  1
 ZT16  1
 ZT20  1
 ZT24  1
 ZT28  1
 ZT32  1
 ZT36  1
 ZT40  1
 ZT44  1
Total hybridizations: 12
Description: The goal of the experiment was to perform a large scale study of circadian regulation of gene expression in maize. To identify maize genes with expression regulated by the circadian clock, transcript levels in the aerial tissues of young maize seedlings were determined by transcriptional profiling with the Affymetrix GeneChip Maize Genome Array. Maize inbred B73 seedlings were grown inside Conviron growth chamber. B73 seedlings were grown for 7 days under 12 h light:12 h dark (LD) photocycles, 26° C temperature and 70% humidity. At the 8th day, seedlings were transferred to continuous light (LL) and were allowed to entrain completely for 24 h prior to tissue harvest following which tissue was harvested every 4 hours under LL conditions for a period of 48h. Therefore, for the circadian LL time course 12 time points were collected as follows (also defined as factors in the treatment section):
ZT0 - 8:00 am/ subjective dawn/ Day1
ZT4 - 12:00 pm/ subjective mid-day/ Day1
ZT8 - 4:00 pm/ subjective late-day/ Day1
ZT12 - 8:00 pm/ subjective dusk/ Day1
ZT16 - 12:00 am/ subjective mid-night/ Day1
ZT20 - 4:00 am/ subjective pre-dawn/ Day1
ZT24- 8:00 am/ subjective dawn/ Day2
ZT28 - 12:00 pm/ subjective mid-day/ Day2
ZT32 - 4:00 pm/ subjective late-day/ Day2
ZT36 - 8:00 pm/ subjective dusk/ Day2
ZT40 - 12:00 am/ subjective mid-night/ Day2
ZT44 - 4:00 am/ subjective pre-dawn/ Day2

Tissue comprised of aerial portion of the seedlings (corresponding to tissue from the prop roots and up) for RNA isolation. Total RNA was isolated from the entire aerial portion of 7 day-old seedlings (corresponding to tissue from the prop roots and up) by Trizol extraction followed by Qiagen RNeasy columns and treatment with RNase-free DNase I (Qiagen; qiagen.com). RNA was isolated from 3 independent biological replicates was pooled. cRNA was generated from pooled total RNA from 3 biological replicates with the GeneChip One-Cycle Target Labeling kit according to the manufacturer’s recommendations (Affymetrix, affymetrix.com). The University of California, Berkeley Functional Genomics Laboratory hybridized samples to Affymetrix GeneChip Maize Genome Arrays and scanned the washed arrays as suggested by manufacturer. Probe sets called “Not Present” or “Marginal” on one or more microarrays were removed from the downstream analysis, as is common practice with circadian studies. Raw hybridization intensities were normalized across all twelve arrays using RMA express in Perfect Match mode.

Submitted at NCBI GEO via PLEXdb.

Publication: none
Created: 2010-04-06 20:04:10
Last Update: 2010-05-24 16:14:56
Released: 2010-06-23
GEO Accession GSE31763
Submitter: Frank G Harmon
Name: Frank G. Harmon
Institution: Plant Gene Expression Center
Head of Laboratory: Frank G. Harmon
email(s):
Homepage:

 
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