|
| Status |
Public on Aug 21, 2013 |
| Title |
no_O2_Y_intermedia_ATCC29909_Oxygenstudy_28C_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Yersinia intermedia ATCC29909
|
| Organism |
Yersinia intermedia ATCC 29909 |
| Characteristics |
genotype: Wild Type
treatment: anaerobic
|
| Treatment protocol |
Yersinia intermedia ATCC29909 was grown to mid log phase at 28 °C in minimal medium with glucose in the presence or in the absence of oxygen
|
| Growth protocol |
Yersinia intermedia ATCC29909 was grown to mid log phase at 28 °C in minimal medium with glucose in the presence or in the absence of oxygen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the hot-phenol method (Bernstein et al 2004) followed by two DNAse digestion steps. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed following Nimblegens standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA) following Nimblegen's standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA) following Nimblegen's standard operating protocol.
|
| Description |
This sample is of Y. intermedia ATCC 29909 grown in minimal medium with glucose at 28 C in the absence of oxygen. It is the 2nd of three biological replicates used in this experiment, each from separate cultures.
|
| 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), without background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Aug 20, 2013 |
| Last update date |
Aug 21, 2013 |
| Contact name |
Lavanya Babujee |
| E-mail(s) |
babujee@wisc.edu
|
| Phone |
608-770-5803
|
| Organization name |
UW-Madison
|
| Department |
Genetics
|
| Street address |
425 Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL17599 |
| Series (1) |
| GSE50043 |
Expression analysis of Yersinia intermedia strain ATCC 29909 at 28 C in minimal medium with glucose under aerobic and anaerobic conditions |
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