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Sample GSM1121336 Query DataSets for GSM1121336
Status Public on Mar 03, 2014
Title wild type early stationary phase
Sample type RNA
 
Channel 1
Source name Δura3 knockout at OD600 = 1.2401
Organism Halobacterium salinarum NRC-1
Characteristics strain: NRC-1
genotype: Δura3
temperature: 37°C
od: 1.2401
Treatment protocol Culture aliquots (2 ml) were collected over mid-log (OD600: ~0.4), late-log (OD600: ~0.8), early stationary, and late stationary phases of growth (as the carrying capacity differs for the two strains, stationary phase points were determined as occurring after an equivalent proportion of the duration of stationary phase.) Cells were centrifuged (16 000 g, 60 s) and flash frozen.
Growth protocol The wild type (Dura3) and VNG2099C in-frame deletion strain (D2099) were batch cultured in flasks at 37°C with constant shaking (~220 rpm) in a complex media (CM: 250 g/l NaCl, 20 g/l MgSO4, 2 g/l KCl, 3 g/l sodium citrate, 10 g/l Oxoid brand bacteriological peptone). This standard CM was supplemented with 50mg/l uracil to compensate for the uracil deficiency caused by the Dura3 marker.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from the cell pellets using the mirVANA RNA kit (Ambion, Austin, TX) according to manufacturer's instructions and then treated with RNase-free DNase (Promega).
Label Cy3, Cy5
Label protocol RNAs were direct labeled with Alexa547 and Alexa647 dyes (Kreatech). 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):1025-35.
 
Channel 2
Source name Halobacterium salinarum NRC-1 reference sample
Organism Halobacterium salinarum NRC-1
Characteristics strain: NRC-1
genotype: wild type
temperature: 37°C
od: 0.5-0.6
Treatment protocol Culture aliquots (2 ml) were collected over mid-log (OD600: ~0.4), late-log (OD600: ~0.8), early stationary, and late stationary phases of growth (as the carrying capacity differs for the two strains, stationary phase points were determined as occurring after an equivalent proportion of the duration of stationary phase.) Cells were centrifuged (16 000 g, 60 s) and flash frozen.
Growth protocol The wild type (Dura3) and VNG2099C in-frame deletion strain (D2099) were batch cultured in flasks at 37°C with constant shaking (~220 rpm) in a complex media (CM: 250 g/l NaCl, 20 g/l MgSO4, 2 g/l KCl, 3 g/l sodium citrate, 10 g/l Oxoid brand bacteriological peptone). This standard CM was supplemented with 50mg/l uracil to compensate for the uracil deficiency caused by the Dura3 marker.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from the cell pellets using the mirVANA RNA kit (Ambion, Austin, TX) according to manufacturer's instructions and then treated with RNase-free DNase (Promega).
Label Cy5, Cy3
Label protocol RNAs were direct labeled with Alexa547 and Alexa647 dyes (Kreatech). 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):1025-35.
 
 
Hybridization protocol Whole-genome tiling arrays were designed using e-Array (Agilent Technologies) for the H. salinarum NRC-1 main chromosome (NC_002607), and pNRC100 (NC_001869) and pNRC200 (NC_002608) plasmids using a 60k feature design of 60-mer strand-specific probes spaced at 24 bp. Arrays included manufacturer’s control probes and were printed by Agilent Technologies. Hybridization and washing was performed as described (Turkarslan et al 2011), with dye flip experiments performed for each sample. See http://www.chem.agilent.com/Scripts/PDS.asp?lPage=34519 for details.
Scan protocol Arrays were scanned in ScanArray 5000 (Perkin Elmer) using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details.
Description Normalized log10 intensity of X_INT/Y_INT (sample/reference) averaged over dye flip between sample and reference RNA.
Data processing Spot finding was performed using Feature Extraction (Agilent Technologies). See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details.
Normalization and statistical analysis were performed as described before (Koide et al, 2009). Values are normalized log10 ratios representing test/reference. Interarray comparisons were normalized relative to a reference RNA sample generated from unperturbed H. salinarum NRC-1 batch culture in rich medium at OD600 0.5-0.6.
 
Submission date Apr 11, 2013
Last update date Mar 03, 2014
Contact name Elisabeth Wurtmann
Organization name Institute for Systems Biology
Street address 401 Terry Ave N
City Seattle
State/province Washington
ZIP/Postal code 98109
Country USA
 
Platform ID GPL17005
Series (1)
GSE45988 H. salinarum NRC-1 vs VNG2099C knockout

Data table header descriptions
ID_REF
VALUE normalized log10 ratios representing test/reference.

Data table
ID_REF VALUE
HALCHR_fwd_000001 -0.7126
HALCHR_fwd_000002 0.2419
HALCHR_fwd_000003 -0.0553
HALCHR_fwd_000004 -0.0297
HALCHR_fwd_000005 0.0056
HALCHR_fwd_000006 0.0822
HALCHR_fwd_000007 0.13
HALCHR_fwd_000008 -0.0444
HALCHR_fwd_000009 -0.1366
HALCHR_fwd_000010 -0.165
HALCHR_fwd_000011 -0.1533
HALCHR_fwd_000012 -0.0964
HALCHR_fwd_000013 -0.046
HALCHR_fwd_000014 -0.121
HALCHR_fwd_000015 -0.1861
HALCHR_fwd_000016 -0.0759
HALCHR_fwd_000017 -0.0326
HALCHR_fwd_000018 -0.1396
HALCHR_fwd_000019 -0.1454
HALCHR_fwd_000020 -0.1344

Total number of rows: 61467

Table truncated, full table size 1527 Kbytes.




Supplementary file Size Download File type/resource
GSM1121336_Dura3_od-1.2401_Cy3_v_NRC-1_Cy5.txt.gz 18.3 Mb (ftp)(http) TXT
GSM1121336_NRC-1_Cy3_v_Dura3_od-1.2401_Cy5.txt.gz 18.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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