|
| Status |
Public on Sep 14, 2015 |
| Title |
RctB binding DNA (Cy5) vs total DNA (input, Cy3) in wildtype_replicate 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Genomic DNA precipitated by using RctB antibody
|
| Organism |
Vibrio cholerae O1 biovar El Tor str. N16961 |
| Characteristics |
strain: CVC209
genotype/variation: wildtype
chip antibody: RctB
|
| Treatment protocol |
Exponential cells were cross-linked with 1% formaldehyde (roome temperature, 30 min).
|
| Growth protocol |
Cells of V. cholerae WT (CVC209) and MCH1 (CVC2099) were cultivated in L broth at 37°C to exponential phase.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After cell lysis (2.5 mg/ml lysozyme, 37°C, 30 min) and sonication (5x20 sec), ParB2-DNA or RctB-DNA complexes were precipitated with antibody against ParB2 or RctB using Dynabeads-Protein G magnetic beads (Invitrogen) following manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Amplified DNA was labelled with either Cy3 or Cy5 as described by Venkova-Canoca et al. [Venkova-Canoca et al., PLoS Genet 9: e1003579 (2013)]
|
| |
|
| Channel 2 |
| Source name |
total, input
|
| Organism |
Vibrio cholerae O1 biovar El Tor str. N16961 |
| Characteristics |
strain: CVC209
genotype/variation: wildtype
chip antibody: none
|
| Treatment protocol |
Exponential cells were cross-linked with 1% formaldehyde (roome temperature, 30 min).
|
| Growth protocol |
Cells of V. cholerae WT (CVC209) and MCH1 (CVC2099) were cultivated in L broth at 37°C to exponential phase.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After cell lysis (2.5 mg/ml lysozyme, 37°C, 30 min) and sonication (5x20 sec), ParB2-DNA or RctB-DNA complexes were precipitated with antibody against ParB2 or RctB using Dynabeads-Protein G magnetic beads (Invitrogen) following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Amplified DNA was labelled with either Cy3 or Cy5 as described by Venkova-Canoca et al. [Venkova-Canoca et al., PLoS Genet 9: e1003579 (2013)]
|
| |
|
| |
| Hybridization protocol |
After adding hybridization buffer (Agilent), samples were applied to microarrays and incubated at 60°C for 17 hr following manufacturer's instructions.
|
| Scan protocol |
After washing, scanning was done using Agilent scanner and Agilent Feature Extraction Software following manufacturer's instructions as described by Venkova-Canoca et al. [Venkova-Canoca et al., PLoS Genet 9: e1003579 (2013)] .
|
| Description |
RctB WT Rep2
biological replicate 2 of 3
Vibrio cholerae N16961 (CVC209)
|
| Data processing |
Agilent Feature Extraction Software was used for background subtraction and normalization.
|
| |
|
| Submission date |
Sep 14, 2015 |
| Last update date |
Sep 14, 2015 |
| Contact name |
Jonghwan Baek |
| Organization name |
NIH
|
| Department |
NCI
|
| Lab |
Laboratory of Biochemistry and Molecular Biology
|
| Street address |
37 Convent Dr
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL20909 |
| Series (1) |
| GSE72978 |
Genome-wide ParB2-DNA and RctB-DNA interaction analyses in Vibrio cholerae |
|
