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Sample GSM1953715 Query DataSets for GSM1953715
Status Public on Nov 26, 2015
Title R. sphaeroides 2.4.1 (lag20) vs. R. sphaeroides 2.4.1 (exp low) 2
Sample type RNA
 
Channel 1
Source name lag phase (20min)_low aeration
Organism Cereibacter sphaeroides 2.4.1
Characteristics growth phase: lag phase (20min)
aeration condition: low aeration
Treatment protocol R. sphaeroides strains grown under low aeration or aerobic conditions and cells were harvested at different growth phases
Growth protocol R. sphaeroides strains grown under low aeration or aerobic conditions
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.
Label Cy3
Label protocol The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation
 
Channel 2
Source name exponential phase_low aeration
Organism Cereibacter sphaeroides 2.4.1
Characteristics growth phase: exponential phase
aeration condition: low aeration
Treatment protocol R. sphaeroides strains grown under low aeration or aerobic conditions and cells were harvested at different growth phases
Growth protocol R. sphaeroides strains grown under low aeration or aerobic conditions
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.
Label Cy5
Label protocol The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation
 
 
Hybridization protocol Total RNA of three independent experiments (biological replicates 1-3 or 4-6) of two different growth phases were pooled and hybridized to one array. Two arrays were hybridized with independent experimental runs. Gene chip hybridization and scanning were performed according to the specifications from Agilent.
Scan protocol Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)
Description 2 lag20 vs exp (low)
biological sample 4-6
Data processing LOESS normalization log2 ratio (Cy3/Cy5) with Limma package (v.3.14.3; release date: 2012/11/29) for Bioconductor in R
 
Submission date Nov 24, 2015
Last update date Nov 26, 2015
Contact name Gabriele Klug
E-mail(s) [email protected]
Organization name Justus-Liebig University Gießen
Department Molecular- and Microbiology
Street address Heinrich-Buff-Ring 26-32
City Gießen
ZIP/Postal code 35392
Country Germany
 
Platform ID GPL15457
Series (1)
GSE75345 Growth-phase dependent gene regulation in the alpha-proteobacterium Rhodobacter sphaeroides

Data table header descriptions
ID_REF
VALUE log2 LOESS normalized ratio (Cy3/Cy5)

Data table
ID_REF VALUE
1 -0.480307833
2 -0.480307833
3 -0.14563078
4 0.148108548
5 0.148108548
6 -0.428595872
7 0.18273371
8 0.18273371
9 -0.0841246
10 -0.0841246
11 -0.292868517
12 -0.690108451
13 -0.770481249
14 -0.724029479
15 -0.320614568
16 -0.842751531
17 -0.886398197
18 -0.192092675
19 -0.239171529
20 -0.426883636

Total number of rows: 15208

Table truncated, full table size 262 Kbytes.




Supplementary file Size Download File type/resource
GSM1953715_2_lag20_vs_exp_low_.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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