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Sample GSM182484 Query DataSets for GSM182484
Status Public on Jan 03, 2008
Title Halobacterium EMS exposure experiment, Array 8169
Sample type RNA
 
Channel 1
Source name Halobacterium NRC1, no EMS control, 30 minutes post mock EMS dose.
Organism Halobacterium salinarum NRC-1
Characteristics No EMS control sample grown in standard conditions and sampled 30 minutes post mock EMS treatment
Biomaterial provider DiRuggiero Group, University of Maryland
Growth protocol Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 30 minutes post 30min mock EMS treatment.
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):1025-42
 
Channel 2
Source name Standard mid-log Halobacterium NRC-1 reference sample.
Organism Halobacterium salinarum NRC-1
Characteristics Halobacterium NRC-1 grown in standard growth media
Biomaterial provider DiRuggiero Group, University of Maryland
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 546
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):1025-42
 
 
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):1025-42
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 No EMS control sample grown in standard conditions and sampled 30 minutes post mock EMS treatment 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 Apr 17, 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 (1)
GSE7609 Halobacterium NRC-1, EMS Stress Response

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 log 10 ratio (treatment/reference)

Data table
ID_REF VALUE RATIO X_INT Y_INT FLAG UNF_VALUE
1 0.20069005504450693 1.5875456 325.64328 205.12373 I 0.20069005504450693
2 0.22917408143458906 1.6951783 347.48196 204.98254 I 0.22917408143458906
3 0.38810697132929384 2.444426 230.4029 73.90207 I 0.38810697132929384
4 0.43936887453232165 2.7507305 281.20224 102.2282 I 0.43936887453232165
5 0.47402145704339915 2.9792495 294.58496 98.878914 I 0.47402145704339915
6 0.4450904909460645 2.7872164 262.7131 70.57696 I 0.4450904909460645
7 0.2253113170312384 1.6801649 333.62842 198.56885 I 0.2253113170312384
8 0.23160883720776546 1.7047102 365.1057 214.17465 I 0.23160883720776546
9 -0.09273619902036133 0.80769444 607.5382 752.1882 I -0.09273619902036133
10 -0.08273437354128689 0.82651496 698.6621 845.3109 I -0.08273437354128689
11 0.20741825075378778 1.6123363 408.33923 253.25935 I 0.20741825075378778
12 0.254478465317783 1.7969017 375.46954 208.95386 I 0.254478465317783
13 0.04353740747922359 1.1054657 458.83817 415.06323 I 0.04353740747922359
14 0.08324809104058731 1.2113317 472.18237 389.80435 I 0.08324809104058731
15 0.33906579013507293 2.1833677 366.43533 167.83034 I 0.33906579013507293
16 0.4325637094012648 2.7079563 429.2469 158.51323 I 0.4325637094012648
17 0.16165097878910376 1.4510424 569.626 392.5633 I 0.16165097878910376
18 0.14033823219541855 1.3815402 590.43396 427.37372 I 0.14033823219541855
19 -0.05734525587218445 0.87628305 385.86575 440.34375 I -0.05734525587218445
20 -0.00961614555916146 0.97809744 464.33286 474.73068 I -0.00961614555916146

Total number of rows: 10752

Table truncated, full table size 783 Kbytes.




Supplementary file Size Download File type/resource
GSM182484.csv.gz 1.2 Mb (ftp)(http) CSV

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