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Status |
Public on Sep 25, 2014 |
Title |
Agrobacterium tumefaciens C58_in_AB5.5_with_HeatShock_rep2 |
Sample type |
RNA |
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|
Source name |
Agrobacterium tumefaciens C58 AB5.5 low pH and Heat Shock
|
Organism |
Agrobacterium fabrum str. C58 |
Characteristics |
strain: C58 treatment: Low pH & Heat Shock
|
Growth protocol |
Agrobacterium tumefaciens C58 low pH and Heat Shock was grown at 40°C for 11 hour then grown untill reach to quarter of O.D.600nm of Standard sample at 28°C in AB5.5 media.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA concentration was measured by SpectorPhotometer(NonoDrop). cDNA were synthesized from the reverse transcription of Total RNA using the Life Technologies SuperScript II Double-Strand Synthesis Kit
|
Label |
Cy3
|
Label protocol |
Labeling was performed by NimbleGen Labelling kit following their standard operating protocol. See www.nimblegen.com.
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Hybridization protocol |
Hybridization was performed using the NimbleGen Hybridization kit and 4-Chip Workstation following their standard operating protocol. See www.nimblegen.com.
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Scan protocol |
Scanning was performed by GenePix 4100A, following their standard operating protocol. See http://www.moleculardevices.com/systems/microarray-scanners/genepix-4100a-microarray-scanner.
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Description |
This sample is the second one which is grown under low pH condition and expose to heat shock at the same time
|
Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleGen Deva software, version 1.2 (Roche NimbleGen, Inc.).
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Submission date |
Sep 24, 2014 |
Last update date |
Sep 25, 2014 |
Contact name |
Hui-Hsien Chou |
E-mail(s) |
hhchou@iastate.edu
|
Phone |
515-294-9242
|
Organization name |
Iowa State University
|
Department |
Genetics, Development and Cell Biology
|
Lab |
Complex Computation Lab
|
Street address |
503 Science II
|
City |
Ames |
State/province |
IA |
ZIP/Postal code |
50011 |
Country |
USA |
|
|
Platform ID |
GPL19222 |
Series (2) |
GSE61737 |
Agrobacterium tumefaciens C58 whole-genome tiling microarray design and validation |
GSE61738 |
Prokaryote whole-genome tiling microarray design and validation |
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