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Sample GSM158681 Query DataSets for GSM158681
Status Public on Jun 24, 2007
Title Col_dark_late_rep1
Sample type RNA
Source name Columbia 5 day old seedling, 120 minutes after transfer to darkness, night time
Organism Arabidopsis thaliana
Characteristics Strain: Columbia
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 27, 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 GSM540908
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 2.275370734
244902_at no 2.923556989
244903_at no 4.230661009
244904_at no 3.270004391
244905_at no 2.041708419
244906_at no 2.549683127
244907_at no 2.050167009
244908_at no 2.128037497
244909_at no 1.828479039
244910_s_at no 1.818564074
244911_at no 1.614322571
244912_at no 5.731670307
244913_at no 2.366921452
244914_at no 1.936494091
244915_s_at no 2.608556347
244916_at yes 1.773789471
244917_at yes 1.881230875
244918_at no 1.808503563
244919_at no 2.616379395
244920_s_at yes 5.415296127

Total number of rows: 22810

Table truncated, full table size 556 Kbytes.

Supplementary file Size Download File type/resource
GSM158681.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM158681.txt.gz 264.6 Kb (ftp)(http) TXT

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