|
| Status |
Public on Mar 10, 2014 |
| Title |
gsexp_iron_deficient_1 |
| Sample type |
RNA |
| |
|
| Source name |
gsexp_iron_deficient_1
|
| Organism |
Geobacter sulfurreducens PCA |
| Characteristics |
genotype: Wild Type
|
| Treatment protocol |
N/A
|
| Growth protocol |
Biological triplicates of wild type G. sulfurreducens were harvested during mid-log phase from the three following conditions: fresh water acetate fumarate media (iron sufficient condition), fresh water acetate fumarate media with NO trace iron (iron deficient condition), or ferric citrate acetate media (iron excess condition)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol reagent (Invitrogen). Residual DNA was removed by digestion with DNAse I (Qiagen) followed by purification using the RNeasy Mini kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed following the Nimblegen standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by the UCSD GeneChip Core, following the Nimblegen standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed with an Axon GenePix 4000B scanner by the UCSD GeneChip Core, following the Nimblegen standard operating protocol. See www.nimblegen.com.
|
| Description |
Gene expression of wild type G. sulfurreducens cultured in iron deficient conditions
|
| Data processing |
Probe level data was normalized with the Robust multi-array analysis (RMA) algorithm without background correction (data in the 6th column of .gff file), as implemented in NimbleScan 2.4 software
Fold changes, log2 difference values, and p-values were calculated. A gene was considered differentially expressed if the log2 difference was >1 and highly differentially expressed if the log2 difference was > 3 with a p-value < 0.05.
|
| |
|
| Submission date |
Jan 22, 2014 |
| Last update date |
Mar 10, 2014 |
| Contact name |
Mallory Embree |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, San Diego
|
| Department |
Bioengineering
|
| Street address |
PFBH/EBU3a, 9500 Gilman Drive Rm. 414
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL9112 |
| Series (2) |
| GSE54304 |
Analysis of the iron stimulon and fur regulon of Geobacter sulfurreducens [expression] |
| GSE54306 |
Analysis of the iron stimulon and fur regulon of Geobacter sulfurreducens |
|
