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Status |
Public on Jul 21, 2016 |
Title |
PV-4 wild type 3 |
Sample type |
RNA |
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|
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.
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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
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Scan protocol |
Scanning was done using the Nimblegen MS200 microarray scanner
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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.
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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 |
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