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Sample GSM183358 Query DataSets for GSM183358
Status Public on Jul 31, 2007
Title Halobacterium_oxygen3_L2H_000min, Array 10639
Sample type RNA
 
Channel 1
Source name Halobacterium NRC1, aerobic 000 minutes after shift.
Organism Halobacterium salinarum NRC-1
Characteristics Halobacterium NRC-1 in standard growth medium at 37C; at 0% oxygen.
Biomaterial provider Baliga Lab, Institute for Systems Biology
Growth protocol Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr. Sample was harvested at 000 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.
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 547
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):1025-37
 
Channel 2
Source name Halobacterium NRC-1, reference
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 Lab, Institute for Systems Biology
Growth protocol Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm
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):1025-37
 
 
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):1025-37
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 High-oxygen 000 minutes post-shift vs. reference
Data processing AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:288
 
Submission date Apr 19, 2007
Last update date Jul 31, 2007
Contact name Amy K Schmid
E-mail(s) aschmid@systemsbiology.org
Fax 206-1299
Organization name Institute for Systemsbiology
Lab Nitin Baliga Halobacterium Lab
Street address 1441 N 34th St
City Seattle
State/province WA
ZIP/Postal code 98103
Country USA
 
Platform ID GPL3739
Series (1)
GSE7559 Halobacterium NRC-1_oxygen_response_timecourse_set3

Data table header descriptions
ID_REF
VALUE normalized log10 ratio (test/reference)
RATIO standard ratio (not log10)
PROBE_ID Unique probe identifier
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)
ROW Row on array
COL Column on array

Data table
ID_REF VALUE RATIO PROBE_ID X_INT Y_INT FLAG ROW COL
1 0.19190915941863973 1.5557641 HO01H19 591.25653 380.04254 I 0 0
2 0.2504648153132901 1.7803687 HO01H19 504.41992 283.3233 I 0 1
3 0.47641916094492204 2.9957461 HO01H13 671.231 224.06139 I 0 2
4 0.7283747389581136 5.3518753 HO01H13 664.76154 124.21095 I 0 3
5 0.5128173747141984 3.2576902 HO01H07 515.24225 158.16183 I 0 4
6 0.4279659965063287 2.6794343 HO01H07 605.7251 226.06454 I 0 5
7 0.278998322115587 1.901291 HO01H01 586.97516 308.72452 I 0 6
8 0.18742611794831698 1.5397843 HO01H01 524.1099 340.37878 I 0 7
9 -0.30020446017653163 0.50088894 HO01D19 1687.659 3369.3276 I 0 8
10 -0.28059998120523666 0.5240219 HO01D19 1701.0742 3246.1892 I 0 9
11 0.12101231637732758 1.3213995 HO01D13 608.8924 460.7936 I 0 10
12 0.21334477860161713 1.6344936 HO01D13 709.70776 434.2065 I 0 11
13 -0.19086418894067608 0.6443197 HO01D07 582.2582 903.679 I 0 12
14 -0.0693899115910182 0.85231 HO01D07 752.81036 883.25885 I 0 13
15 0.23843981271313733 1.7317404 HO01D01 571.08826 329.77707 I 0 14
16 0.2511948913785666 1.7833647 HO01D01 540.8512 303.27573 I 0 15
17 0.10675497360849019 1.2787163 HO01G19 2211.5593 1729.5151 I 0 16
18 0.14516345299514877 1.3969781 HO01G19 2569.9988 1839.6843 I 0 17
19 0.06816944701452286 1.1699889 HO01G13 1315.2498 1124.1558 I 0 18
20 0.14792497783959624 1.405891 HO01G13 1409.6382 1002.6654 I 0 19

Total number of rows: 10752

Table truncated, full table size 742 Kbytes.




Supplementary file Size Download File type/resource
GSM183358.csv.gz 1.2 Mb (ftp)(http) CSV
Processed data included within Sample table

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