|
| Status |
Public on Jul 27, 2022 |
| Title |
IL1403_vs_IL594_Gal_M |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
cells from batch culture
|
| Organism |
Lactococcus lactis |
| Characteristics |
strain: IL1403
carbon source: galactose
growth phase: mid-exponential [M]
|
| Treatment protocol |
N/A
|
| Growth protocol |
IL594 and IL1403 cells were grown in an M17 medium supplemented with desired sugar: cellobiose, galactose, or glucose. Cells were harvested at four distinct growth phases: early exponential [E] at OD600 0.1-0.2, mid-exponential [M] at OD600 0.6-0.7, transition [phase between the exponential and stationary growth; T] at OD600 0.8-0.9, and stationary [S] after further 12 h of incubation.
|
| 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 (5μg) were labeled with 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: IL594
carbon source: galactose
growth phase: mid-exponential [M]
|
| Treatment protocol |
N/A
|
| Growth protocol |
IL594 and IL1403 cells were grown in an M17 medium supplemented with desired sugar: cellobiose, galactose, or glucose. Cells were harvested at four distinct growth phases: early exponential [E] at OD600 0.1-0.2, mid-exponential [M] at OD600 0.6-0.7, transition [phase between the exponential and stationary growth; T] at OD600 0.8-0.9, and stationary [S] after further 12 h of incubation.
|
| 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 (5μg) were labeled with 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 technical replicates (dye swap) were averaged.
|
| |
|
| Submission date |
Jul 26, 2022 |
| Last update date |
Jul 27, 2022 |
| 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) |
| GSE209756 |
The presence of plasmids in L. lactis IL594 determines changes in host phenotype and expression of chromosomal genes |
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