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Sample GSM186756 Query DataSets for GSM186756
Status Public on Jan 03, 2008
Title Halobacterium NRC-1 dark diurnal experiment 1, 20.0 hours post entrainment, Array 7370
Sample type RNA
 
Channel 1
Source name Halobacterium NRC-1 dark diurnal experiment 1, 20.0 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 darkness20.0 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 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):1025-45
 
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 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):1025-45
 
 
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):1025-45
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, 20.0 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 0.6773363688303679 4.7583723 559.5753 117.59805 I 0.6773363688303679
2 0.6640813227182226 4.615311 554.6774 120.18202 I 0.6640813227182226
3 0.8287649058905896 6.7439485 500.53745 74.22024 I 0.8287649058905896
4 0.7358494438290332 5.4448013 451.41708 82.907906 I 0.7358494438290332
5 0.721795790609587 5.2713985 442.7225 83.98578 I 0.721795790609587
6 0.871393569312283 7.439617 510.54346 68.62496 I 0.871393569312283
7 0.4401526043068775 2.7556999 508.76492 184.62276 I 0.4401526043068775
8 0.4579710901989077 2.871135 555.5083 193.48038 I 0.4579710901989077
9 0.2767452279663176 1.891451 860.09033 454.72516 I 0.2767452279663176
10 0.29805243355659905 1.9865804 843.02435 424.35956 I 0.29805243355659905
11 0.347918003295836 2.228336 517.79504 232.36847 I 0.347918003295836
12 0.3945618348039904 2.4810352 522.01697 210.4029 I 0.3945618348039904
13 0.3620500749034871 2.302053 626.161 272.00113 I 0.3620500749034871
14 0.3824908653177408 2.4130137 651.70264 270.0783 I 0.3824908653177408
15 0.361604815416581 2.2996936 461.49066 200.67485 I 0.361604815416581
16 0.5093191659227128 3.2315505 545.90295 168.92911 I 0.5093191659227128
17 0.06457682190068047 1.1603485 819.0954 705.9046 J 0.06457682190068047
18 0.18116746729990393 1.5177495 862.5915 568.3359 J 0.18116746729990393
19 0.739209421258919 5.487097 995.6424 181.45158 I 0.739209421258919
20 0.7637013055284099 5.8054905 1052.2037 181.24286 I 0.7637013055284099

Total number of rows: 10752

Table truncated, full table size 775 Kbytes.




Supplementary file Size Download File type/resource
GSM186756.csv.gz 1.1 Mb (ftp)(http) CSV

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