|
| Status |
Public on Dec 26, 2018 |
| Title |
Citrobacter rodentium ΔnlpE grown in DMEM to OD600 of 0.5-0.6, biological replicate 2 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
NlpE
|
| Organism |
Citrobacter rodentium |
| Characteristics |
genotype/variation: NlpE
strain: DBS100
growth protocol: DMEM broth, 37°C shaking
|
| Treatment protocol |
No treatment
|
| Growth protocol |
DMEM to exponential phase (OD600 = 0.5-0.6).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA: TRIzol reagent (Invitrogen), reverse-transcribed into cDNA. Genomic DNA: QIAamp kit (QIAgen).
|
| Label |
Alexa Fluor 647
|
| Label protocol |
RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 647.
|
| |
|
| Channel 2 |
| Source name |
genomic DNA, reference channel
|
| Organism |
Citrobacter rodentium |
| Characteristics |
genotype: WT
strain: DBS100
growth protocol: LB broth, 37°C shaking
|
| Treatment protocol |
No treatment
|
| Growth protocol |
DMEM to exponential phase (OD600 = 0.5-0.6).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA: TRIzol reagent (Invitrogen), reverse-transcribed into cDNA. Genomic DNA: QIAamp kit (QIAgen).
|
| Label |
Alexa Fluor 546
|
| Label protocol |
RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 647.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).
|
| Scan protocol |
Scanning and image acquisition was performed on a InnoScan 710 using the mapix software. Spot intensity an local background was measured.
|
| Description |
ΔnlpE
|
| Data processing |
Data were processed with the mapix software. Values from each channel were background substracted and the % contribution of each sopts to the total fluorsecence in each channel was calculated. Then the ratio Ch1/Ch2 was calculated. We used gDNA for data normalization accross slides.
|
| |
|
| Submission date |
May 21, 2018 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Sebastien Faucher |
| E-mail(s) |
sebastien.faucher@gmail.com
|
| Phone |
514-398-7886
|
| Organization name |
McGill University
|
| Department |
Natural Resource Sciences
|
| Lab |
Faucher
|
| Street address |
21,111 Lakeshore
|
| City |
St-Anne-de-Bellevue |
| State/province |
QC |
| ZIP/Postal code |
H9X 3V9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL25012 |
| Series (1) |
| GSE114699 |
The Virulence Effect of CpxRA in Citrobacter rodentium Is Independent of the Auxiliary Proteins NlpE and CpxP |
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