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Sample GSM159301 Query DataSets for GSM159301
Status Public on Jun 24, 2007
Title CCA1-34_dark_late_rep1
Sample type RNA
Source name cca1-34 5 day old seedling, 120 minutes after transfer to darkness, night
Organism Arabidopsis thaliana
Characteristics Strain: CCA1-34 (CCA1-OX)
Age: 5 Days
Tissue: Whole Seedling
Growth protocol About 100 seedlings were grown on a filter paper laid on 1xMSMO, 3% sucrose, 0.9% agar (Cat # A1296, Sigma) in 6 cm round Petri dishes. Seeds were stratified for four days at 4 ˚C and then incubated for four days at 20˚C under short day (8 hours light: 16 hours dark) conditions. The Petri dishes were tilted about 30˚ from vertical in a growth chamber equipped with red and blue LEDs (70.7 µE red light and 15.3 µE blue light). Starting from subjective dawn at day five, cycles of 160 min light and 320 min dark were given for three days. This sample was collected 1240 minutes after subjective dawn on the fifth day; 120 minutes after lights-off.
Extracted molecule total RNA
Extraction protocol Samples were transferred to 1.5 ml tube and immediately frozen by liquid nitrogen and stored at –80˚C. Samples were collected using infra-red (IR) goggles (Night Vision model NCB4, Night Owl Optics, NY) to avoid light exposure. 100 mg frozen tissue samples were ground by pestle and electric motor. Total RNA was extracted using RNeasy Plant Mini kit (Qiagen, CA).
Label biotin
Label protocol From 5 µg of total RNA, cRNA was made and labeled with biotin (Affymetrix, CA) according to protocol described by Schmid, M. et al. Nat. Genet. 37, 501-506 (2005).
Hybridization protocol Hybridization was performed in a Affymetrix 640 Hybridization Oven using standard Affymetrix protocols.
Scan protocol Scans were performed on a Affymetrix GeneChip 3000 scanner.
Description Seedlings were entrained in short days for four days and then transferred to cycles of 160 min light and 320 min dark for three days. This sample was collected two hours after lights off, 1240 minutes after dawn on the fifth day.
Data processing Data was normalized using the RMA protocol.
Submission date Jan 29, 2007
Last update date Aug 28, 2018
Contact name Julin N Maloof
Phone (530) 752-8077
Fax (530) 752-5410
Organization name University of California, Davis
Department Plant Biology
Street address One Shields Ave
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platform ID GPL198
Series (1)
GSE6906 Rhythmic growth explained by coincidence between internal and external cues
Reanalyzed by GSM540920
Reanalyzed by GSE118579
Reanalyzed by GSE119083

Data table header descriptions
is_ambiguous Indicates whether or not the probeset hybridizes to more than one gene
VALUE log2 corrected values from RMA

Data table
ID_REF is_ambiguous VALUE
244901_at no 2.343330693
244902_at no 3.087285939
244903_at no 4.925084306
244904_at no 3.683317887
244905_at no 1.963854348
244906_at no 2.706576825
244907_at no 2.198178223
244908_at no 2.021562827
244909_at no 2.286500591
244910_s_at no 1.896891302
244911_at no 1.796374948
244912_at no 5.602562811
244913_at no 2.753684905
244914_at no 1.991568846
244915_s_at no 2.427973978
244916_at yes 2.027651208
244917_at yes 2.084229628
244918_at no 1.829743531
244919_at no 2.552251261
244920_s_at yes 5.590678678

Total number of rows: 22810

Table truncated, full table size 556 Kbytes.

Supplementary file Size Download File type/resource
GSM159301.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM159301.txt.gz 264.5 Kb (ftp)(http) TXT

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