|
| Status |
Public on Jun 27, 2021 |
| Title |
E. coli WT vs hdeD 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT 1
|
| Organism |
Escherichia coli BW25113 |
| Characteristics |
strain: BW25113
genotype: Wild type
|
| Growth protocol |
E. coli strains were grown at 37°C in M9-Glycerol medium containing 0.2% casamino until a mid-log phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by a hot phenol method. Water-saturated phenol and ethanol precipitation were used, following the digestion with RNase-free DNase I (Takara Bio). Total RNA was dissolved in RNase-free water.
|
| Label |
Cy3
|
| Label protocol |
5 µg of total RNA were used for labeled cDNA preparation using FairPlay III Microarray Labeling kit (Agilent).
|
| |
|
| Channel 2 |
| Source name |
hdeD-1
|
| Organism |
Escherichia coli BW25113 |
| Characteristics |
strain: JW3479
genotype: hdeD-deficient
|
| Growth protocol |
E. coli strains were grown at 37°C in M9-Glycerol medium containing 0.2% casamino until a mid-log phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by a hot phenol method. Water-saturated phenol and ethanol precipitation were used, following the digestion with RNase-free DNase I (Takara Bio). Total RNA was dissolved in RNase-free water.
|
| Label |
Cy5
|
| Label protocol |
5 µg of total RNA were used for labeled cDNA preparation using FairPlay III Microarray Labeling kit (Agilent).
|
| |
|
| |
| Hybridization protocol |
Each 300 ng of Cy3- and Cy5-labeled cDNA were mixed and added to 1X Blocking Buffer (Agilent) and 1X HI-RPM GE Hybridization Buffer (Agilent). After precipitation of impurities, 40 µl of the labelled-cDNA mixture was applied to theDNA chip, and the hybridization was carried out at 65°C for 17 hr. The DNA chip was washed at room temperature with Agilent Gene Expression Wash Buffer 1 (Agilent) and at 37°C with Agilent Gene Expression Wash Buffer 2 (Agilent).
|
| Scan protocol |
Scanned on an Agilent G2565CA scanner.
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (version 8.1).
Agilent Feature Extraction Software (v 8.1) was used for background subtraction.
|
| |
|
| Submission date |
Jun 26, 2021 |
| Last update date |
Jun 27, 2021 |
| Contact name |
Kaneyoshi Yamamoto |
| E-mail(s) |
kanyamam@hosei.ac.jp
|
| Organization name |
Hosei University
|
| Department |
Frontier Bioscience
|
| Street address |
3-7-2 Kajinocho
|
| City |
Koganei |
| State/province |
Tokyo |
| ZIP/Postal code |
1848584 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13359 |
| Series (1) |
| GSE178954 |
The transcriptome of gadE, hdeA, or hdeD null strains compared to wild-type of E. coli under minimum medium conditions |
|
