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Sample GSM186765 Query DataSets for GSM186765
Status Public on Jan 03, 2008
Title Halobacterium NRC-1 dark diurnal experiment 1, 36.0 hours post entrainment, Array 7343
Sample type RNA
 
Channel 1
Source name Halobacterium NRC-1 dark diurnal experiment 1, 36.0 hours post entrainment.
Organism Halobacterium salinarum NRC-1
Characteristics Halobacterium NRC-1 dark diurnal experiment 1 with cells grown at 42degrees C in aerobic conditions and entrained for 72 hours with 12:12hr light:dark cycle and sampled in darkness.0_h hours post entrainment.
Biomaterial provider Baliga Lab, Institute for Systems Biology
Growth protocol Halobacterium NRC-1 were grown in aerobic conditions (shaking at 100RPM) at 42degrees C and entrained for 72 hours with 12:12hr light:dark cycle at a light intensity of 150µE/M^2/sec. and sampled in darkness36.0 minutes post entrainment.
Extracted molecule total RNA
Extraction protocol Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.
Label Alexa 647
Label protocol see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-54
 
Channel 2
Source name Standard mid-log Halobacterium NRC-1 reference sample.
Organism Halobacterium salinarum NRC-1
Characteristics Halobacterium NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).
Biomaterial provider Baliga Group, Institute for Systems Biology
Growth protocol Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.
Extracted molecule total RNA
Extraction protocol Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.
Label Alexa 532
Label protocol see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-54
 
 
Hybridization protocol see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-54
Scan protocol ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details
Description Halobacterium NRC-1 dark diurnal experiment 1, 36.0 hours post entrainment versus standard reference.
Data processing AnalyzerDG software for spotfinding. see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details
 
Submission date May 02, 2007
Last update date Jan 03, 2008
Contact name Marc Facciotti
E-mail(s) mfacciotti@systemsbiology.org
Organization name Institute for Systems Biology
Street address 1441 North 34th Street
City Seattle
State/province WA
ZIP/Postal code 98103
Country USA
 
Platform ID GPL3739
Series (2)
GSE7709 Halobacterium NRC-1 Diurnal experiment Dark 1
GSE7739 Halobacterium NRC-1 Diurnal experiment

Data table header descriptions
ID_REF
VALUE normalized log 10 ratio (treatment/reference) with FLAG=K removed
RATIO standard ratio (not log10)
X_INT Background subtracted, normalized intensity value of channel 1
Y_INT Background subtracted, normalized intensity value of channel 2
FLAG Internal Quality Control Flag(s)
UNF_VALUE normalized log10 ratio (treatment/reference)

Data table
ID_REF VALUE RATIO X_INT Y_INT FLAG UNF_VALUE
1 0.2699503548113946 1.8620828 551.54474 296.19775 I 0.2699503548113946
2 0.23546456353887305 1.719915 559.73706 325.4446 I 0.23546456353887305
3 0.33181003031082895 2.1471868 515.0264 239.86102 I 0.33181003031082895
4 0.27387408441086425 1.8789855 534.6203 284.52603 I 0.27387408441086425
5 0.23100230876905145 1.7023307 484.72125 284.73978 I 0.23100230876905145
6 0.26102125365156986 1.8241825 493.94205 270.77448 I 0.26102125365156986
7 0.24506535157434942 1.758367 611.9523 348.02307 I 0.24506535157434942
8 0.23194022991258428 1.7060118 554.6214 325.09824 I 0.23194022991258428
9 -0.027227315703716524 0.93922096 692.0661 736.8512 I -0.027227315703716524
10 0.010554634708367722 1.0246052 663.83185 647.89044 I 0.010554634708367722
11 0.24414396969365676 1.7546397 671.6171 382.7664 I 0.24414396969365676
12 0.23363750774204475 1.7126933 622.27185 363.3294 I 0.23363750774204475
13 0.26855442124186346 1.8561062 691.2328 372.41016 I 0.26855442124186346
14 0.15788035187804667 1.4384965 675.4773 469.57175 I 0.15788035187804667
15 0.2526284306680849 1.789262 667.2339 372.9101 I 0.2526284306680849
16 0.2856829613969759 1.9307873 664.2517 344.03152 I 0.2856829613969759
17 0.21555630835976974 1.6428396 741.7495 451.50455 I 0.21555630835976974
18 0.22662590718285516 1.6852593 818.645 485.76797 I 0.22662590718285516
19 0.049534770019923964 1.1208402 599.8526 535.1812 I 0.049534770019923964
20 0.0778210706881814 1.1962862 650.10913 543.43945 I 0.0778210706881814

Total number of rows: 10752

Table truncated, full table size 783 Kbytes.




Supplementary file Size Download File type/resource
GSM186765.csv.gz 1.2 Mb (ftp)(http) CSV

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