|
| Status |
Public on Nov 30, 2023 |
| Title |
C. difficile strain R20291_pMTL84151 transconjugant Replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Clostridioides difficile strain R20291_pMTL84151 transconjugant
|
| Organism |
Clostridioides difficile R20291 |
| Characteristics |
strain: R20291
cell type: bacterial cells
treatment: conjugated with pMTL84151 vector plasmid
|
| Growth protocol |
C. difficile transconjugants were cultured on BHIS agar plates containing 300 ug/mL of D-cycloserine and 15 ug/mL of thiamphenicol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA of C. difficile strains was extracted using RNeasy minikit (QIAGEN) according to the manufacturer’s instructions
|
| Label |
Cy3
|
| Label protocol |
0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.
|
| |
|
| Hybridization protocol |
Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint Microarray (Agilent Technologies, USA) at 65°C for 17 h.
|
| Scan protocol |
After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
Biological replicate 1 of 3. Clostridioides difficile strain R20291_pMTL84151 transconjugant, control.
|
| Data processing |
Scanned images are analyzed by Feature extraction10.7.3.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.
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| |
|
| Submission date |
Nov 30, 2022 |
| Last update date |
Nov 30, 2023 |
| Contact name |
JunJia Gong |
| Organization name |
National Cheng Kung University
|
| Department |
Institute of Basic Medical Sciences
|
| Street address |
University Rd, No. 1
|
| City |
Tainan |
| ZIP/Postal code |
70101 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL32901 |
| Series (1) |
| GSE219066 |
Clostridioides difficile: R20291_pMTL84151 transconjugant (C) vs. R20291_pMTL84151-03890 (T1) |
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