|
| Status |
Public on Jul 30, 2012 |
| Title |
KP_exp_glucose_1 |
| Sample type |
RNA |
| |
|
| Source name |
K. pneumoniae Expression M9 glucose 1
|
| Organism |
Klebsiella pneumoniae subsp. pneumoniae MGH 78578 |
| Characteristics |
strain: MGH78578
|
| Treatment protocol |
The cell culture was treated with the RNAprotect reagent (Qiagen).
|
| Growth protocol |
K. pneumoniae MGH78678 was grown to mid-log phase (O.D.600nm 0.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
KP_exp_glucose_1_aligned_norm_RMA.pair
|
| 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 NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Feb 13, 2012 |
| Last update date |
Jul 30, 2012 |
| Contact name |
Donghyuk Kim |
| E-mail(s) |
dkim@unist.ac.kr
|
| Organization name |
UNIST
|
| Department |
Department of Chemical Engineering
|
| Lab |
Systems Biology Lab
|
| Street address |
50 UNIST-gil, Eonyang-eup, Ulju-gun
|
| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL15223 |
| Series (2) |
| GSE35746 |
Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [tiling arrays] |
| GSE35822 |
Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling |
|
