|
| Status |
Public on Apr 06, 2010 |
| Title |
EGD-e8 |
| Sample type |
genomic |
| |
|
| Source name |
Genomic DNA from Listeria monocytogenes EGD-e
|
| Organism |
Listeria monocytogenes EGD-e |
| Characteristics |
strain: EGD-e
|
| Growth protocol |
overnight BHI culture
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MasterPureTM Gram Positive DNA Purification kit protocol(http://www.epibio.com/item.asp?id=429)
|
| Label |
cy3, cy5
|
| Label protocol |
NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)
|
| |
|
| Hybridization protocol |
NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)
|
| Scan protocol |
NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)
|
| Description |
CGH reference
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 385K CGH data extraction
binsignal.txt - Binary presence/absence representation of mqlsignal table after intensity cutoffs have been applied.
cutoffs.txt - Cutoff values used for each sample to generate the binsiganl.txt file.
genepf.txt - Positive fraction (PF) values for annotated Listeria monocytogenes genes with probe coverage >90%. Positive fraction is computed as the fraction of probes mapping to that gene that have an intensity exceeding the cutoff.
|
| |
|
| Submission date |
Feb 17, 2010 |
| Last update date |
Apr 06, 2010 |
| Contact name |
Xiangyu Deng |
| E-mail(s) |
xdeng7@iit.edu
|
| Organization name |
Illinois Insititute of Technology
|
| Department |
National Center for Food Safety and Technology
|
| Street address |
6502 S. Archer Rd.
|
| City |
Summit-Argo |
| State/province |
IL |
| ZIP/Postal code |
60502 |
| Country |
USA |
| |
|
| Platform ID |
GPL8942 |
| Series (1) |
| GSE20367 |
Probing the pan genome of a foodborne bacterial pathogen Listeria monocytogenes |
|
