|
| Status |
Public on Jan 12, 2015 |
| Title |
OSU12-hisD, histidine depleted, 10 min, rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
OSU12-hisD, histidine depleted, 10 min
|
| Organism |
Escherichia coli |
| Characteristics |
strain: DH1 ΔhisD::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5
condition: histidine depleted
|
| Treatment protocol |
The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 16,000 × g for 5 min at 4°C, and the pelleted cells were stored at –80°C prior to use.
|
| Growth protocol |
Cells were grown in the minimal media, modified M63. The final cell concentrations were controlled ~ 10^8 cells/mL within the exponential growth phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 3 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
|
| Data processing |
Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009). The log10 mRNA concentration (pM) data are provided as a supplementary file on the SERIES record.
|
| |
|
| Submission date |
Mar 10, 2014 |
| Last update date |
Jan 13, 2015 |
| Contact name |
Bei-Wen Ying |
| E-mail(s) |
ying.beiwen.gf@u.tsukuba.ac.jp
|
| Phone |
81 29 853 6633
|
| Organization name |
University of Tsukuba
|
| Street address |
1-1-1 Tennoudai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8572 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13336 |
| Series (1) |
| GSE55719 |
Transcriptome reorganization of gene-rewired Escherichia coli cells in response to histidine depletion |
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