|
| Status |
Public on Sep 01, 2022 |
| Title |
UVevolved_1R172_expression |
| Sample type |
RNA |
| |
|
| Source name |
lineage-1, 172 rounds (688 days)
|
| Organism |
Escherichia coli |
| Characteristics |
strain: K-12 substr. MDS42
day: 688
|
| Treatment protocol |
Then, aliquots of the cells were immediately added to the same volume of ice-cold ethanol with 10% (w/v) phenol.
|
| Growth protocol |
The cells were cultured for 16–19 h and then sampled at the time of the logarithmic growth phase (OD600 values were 0.072–0.135).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using an RNeasy mini kit with on-column DNase digestion (Qiagen), following the manufacturer’s protocols. The purified RNA was quality-controlled using an Agilent 2100 Bioanalyzer and an RNA 6000 Nano kit (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
A microarray experiment was performed using an Agilent 8× 60 K array, which was designed for the E. coli W3110 strain so that 12 probes were contained for each gene. Purified total RNA (100 ng) was labelled with Cyanine3 (Cy3) using a Low Input Quick Amp WT labelling kit (One-color; Agilent Technologies). The Cy3-labelled cRNA was checked its amount (> 5 µg) and specific activity (> 25 pmol/µg) using NanoDrop ND-2000.
|
| |
|
| Hybridization protocol |
Then the cRNA of 600 ng was fragmented and hybridised to a microarray for 17 h at 65°C, rotating at 10 rpm in a hybridisation oven (Agilent Technologies).
|
| Scan protocol |
Then, the microarray was washed and scanned according to the manufacturer’s instructions.
|
| Description |
Gene expression after 688 days of evolution under UV irradiation, lineage-1
|
| Data processing |
Microarray image analysis was performed using Feature Extraction version 10.7.3.1 (Agilent Technologies).
|
| |
|
| Submission date |
Nov 17, 2021 |
| Last update date |
Sep 04, 2022 |
| Contact name |
Atsushi Shibai |
| E-mail(s) |
atsushi.shibai@riken.jp
|
| Phone |
+81-6-7710-9060
|
| Organization name |
RIKEN
|
| Department |
Center for Biosystems Dynamics Research
|
| Lab |
Laboratory for Multiscale Biosystem Dynamics
|
| Street address |
6-2-3 Furuedai
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0874 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18948 |
| Series (1) |
| GSE189008 |
Purifying selection acting on the sequence of highly expressed proteins in the microevolution |
|
