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Sample GSM2175006 Query DataSets for GSM2175006
Status Public on Jul 21, 2016
Title PV-4 wild type 3
Sample type RNA
 
Source name Shewanella loihica PV-4 wild type
Organism Shewanella loihica PV-4
Characteristics genotype: Wild-type
phenotype: normal
Treatment protocol No treatment, we compare the wild type cell (non ppix accumulating) versus the PPIX accumulating deltahemH1 strain
Growth protocol both strains were revived from frozen stock and subsequently transferred into 50ml of LB medium, 200 rpm, 30 degree celsius.
Extracted molecule total RNA
Extraction protocol genomic DNA is extracted using the GenElute bacterial gDNA extraction kit from Sigma; RNA is extracted using trizol reagent, followed by column collection and washing using the Nucleospin RNA kit from Macherey-Nagel.
Label Cy5
Label protocol DNA labeling is done with Cy-3 using random primers and Klenow fragment of DNA polymerase I. RNA is labeled with Cy5 using random primers and Reverse transcriptase II.
 
Hybridization protocol Hybridization was done in Maui hybridization system at 42 degree C for 16 hours, followed by washing with wash buffer I, II, and III, breifly spinned before scanning
Scan protocol Scanning was done using the Nimblegen MS200 microarray scanner
Data processing Data was extracted from scanned image using the NimbleScan software, the raw data is processed using the pure culture microarray data analysis pipeline developed in our lab
The scanned images were gridded using the void gridding files. The local background signal for each probe was calculated as the mean signal intensity of the four neighbouring void spots. When all of the four neighbouring void spots were not valid, the set of eight void spots surrounding its closest neighbours was used.
 
Submission date May 23, 2016
Last update date Jul 21, 2016
Contact name Ming Xie
E-mail(s) [email protected]
Organization name Institute for Environmental Genomics
Department Microbiology and plant biology
Lab 2230
Street address 101 L DAVID BOREN BLVD
City Norman
State/province Oklahoma
ZIP/Postal code 73019
Country USA
 
Platform ID GPL21934
Series (1)
GSE81743 Differential regulation of the two ferrochelatase paralogues in Shewanella loihica PV-4 in response to environmental stresses

Data table header descriptions
ID_REF
VALUE mean signal intensity

Data table
ID_REF VALUE
162139869 7791.527633
162139868 21632.2939
162139867 8611.325778
127514794 16830.98323
127514793 3914.375833
127514792 16162.33583
127514791 27871.39018
127514790 6567.711478
127514789 5606.095644
127514788 2754.527867
127514787 6295.244256
127514786 1521.216389
127514785 2812.304356
127514784 5781.64
127514783 1279.125833
127514782 5657.908144
127514781 5910.061756
127514780 8158.4076
127514779 13748.05686
127514778 9192.813889

Total number of rows: 3849

Table truncated, full table size 81 Kbytes.




Supplementary file Size Download File type/resource
GSM2175006_WT_3.txt.gz 385.9 Kb (ftp)(http) TXT
Processed data included within Sample table

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