|
| Status |
Public on Apr 16, 2023 |
| Title |
IL1403_vs_IL1530_R1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
cells from batch culture
|
| Organism |
Lactococcus lactis |
| Characteristics |
strain: IL1403
carbon source: cellobiose
growth phase: mid-exponential
|
| Treatment protocol |
N/A
|
| Growth protocol |
Bacteria cells were grown in an M17 medium supplemented with cellobiose. Cells were harvested at mid-exponential growth phase at OD600 0.6-0.7.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using GeneMATRIX Universal RNA Purification Kit (EURx, Poland), according to the manufacturer protocol.
|
| Label |
Cy3,Cy5
|
| Label protocol |
Samples of total RNA (100ng) were labeled with Low Input QuickAmp Labeling Kit, Two-Color (Agilent) with Cy3- and Cy5-UTP according to the manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
cells from batch culture
|
| Organism |
Lactococcus lactis |
| Characteristics |
strain: IL1530
carbon source: cellobiose
growth phase: mid-exponential
|
| Treatment protocol |
N/A
|
| Growth protocol |
Bacteria cells were grown in an M17 medium supplemented with cellobiose. Cells were harvested at mid-exponential growth phase at OD600 0.6-0.7.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using GeneMATRIX Universal RNA Purification Kit (EURx, Poland), according to the manufacturer protocol.
|
| Label |
Cy5,Cy3
|
| Label protocol |
Samples of total RNA (100ng) were labeled with Low Input QuickAmp Labeling Kit, Two-Color (Agilent) with Cy3- and Cy5-UTP according to the manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
Labeled probes were hybridized to custom designed microarrays in 8x15k format, made by Agilent (Design ID: 084868) using Gene Expression Hybridization Kit, Hybridization Chamber and Hybridization oven (all from Agilent) for 17 hours at 65°C.
|
| Scan protocol |
After washing using Gene Expression Wash Buffer Set (Agilent) the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5μm and 100% laser power. PMT gain was set to around 600 and 750 for 532 nm and 635 nm excitation respectively with minor adjustments to normalize images. Feature extraction was done using GenePix Pro 6.1 (Molecular Devices, USA).
|
| Data processing |
GPR files were analyzed further with Acuity 4.0 software starting with lowess normalization. Normalized Log2 Ratio data from biological and technical replicates were averaged.
|
| |
|
| Submission date |
Apr 11, 2023 |
| Last update date |
Apr 17, 2023 |
| Contact name |
Marek Skoneczny |
| E-mail(s) |
kicia@ibb.waw.pl, mrksknc@gmail.com
|
| Organization name |
Institute of Biochemistry and Biophysics PAS
|
| Street address |
Pawińskiego 5A
|
| City |
Warszawa |
| ZIP/Postal code |
02-106 |
| Country |
Poland |
| |
|
| Platform ID |
GPL32506 |
| Series (1) |
| GSE229414 |
Control of bacterial phenotype and chromosomal gene expression by single plasmids of Lactococcus lactis IL594 |
|
