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Sample GSM918879 Query DataSets for GSM918879
Status Public on Apr 20, 2012
Title control wild-type strain vs ΔphaEC strain replicate 6
Sample type RNA
 
Channel 1
Source name wild-type strain
Organism Haloferax mediterranei
Characteristics Stage: late exponential
strain: wild-type
Treatment protocol The wild-type strain and ΔphaEC strain were harvested at the late exponential stage.
Growth protocol The wild-type strain and ΔphaEC strain were were cultivated at 37°C to late exponential growth phase in MG medium containing 10 g/L glucose as carbon source.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol (invitrogen) following manufacturer's instructions
Label cy3
Label protocol Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.
 
Channel 2
Source name ΔphaEC strain
Organism Haloferax mediterranei
Characteristics Stage: late exponential
strain: ΔphaEC
Treatment protocol The wild-type strain and ΔphaEC strain were harvested at the late exponential stage.
Growth protocol The wild-type strain and ΔphaEC strain were were cultivated at 37°C to late exponential growth phase in MG medium containing 10 g/L glucose as carbon source.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol (invitrogen) following manufacturer's instructions
Label cy5
Label protocol Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.
 
 
Hybridization protocol standard CapitalBio Methods
Scan protocol Luxscan 10K (CapitalBio)
Description compare gene expression profiles of wild-type strain with ΔphaEC strain
Data processing After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated. SAM (significance Analysis of Microarrays, version 2.23b) software was used to normalize data.
 
Submission date Apr 19, 2012
Last update date Apr 20, 2012
Contact name Jing Han
E-mail(s) hanjing@im.ac.cn
Organization name Institute of Microbiology, Chinese Academy of Sciences
Street address NO.1 West Beichen Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL15465
Series (1)
GSE37421 Genes differentially expressed Haloferax mediterranei strains: control wild-type strain vs ΔphaEC strain

Data table header descriptions
ID_REF
VALUE the geometric mean of lowess normalized log2 ratio (test/control)

Data table
ID_REF VALUE
1 0.9458
2 1.0060
3 4.0226
4 1.5159
5 0.7212
6 0.6517
7 4.7845
8 -2.0487
9 -0.3923
10 -1.1357
11 -1.4624
12 -0.8399
13 -0.5660
14 0.4267
15 0.6754
16 -1.3835
17 -1.9379
18 -1.1999
19 1.2849
20 -1.4200

Total number of rows: 15744

Table truncated, full table size 196 Kbytes.




Supplementary file Size Download File type/resource
GSM918879_091204_09519C_N6_Cy3+09519C_M6_Cy5_003-7.lsr.gz 723.6 Kb (ftp)(http) LSR
Processed data included within Sample table

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