|
| Status |
Public on Jul 01, 2024 |
| Title |
ParBF, S.typhi LT2 gyrB, F, IP2 |
| Sample type |
SRA |
| |
|
| Source name |
plasmid
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 |
| Characteristics |
strain name: BLC16
tissue: plasmid
plasmid f: F1-10B
genotype: LT2 gyrB652ts
dna topology: CCC
chip antibody: anti ParBF
|
| Treatment protocol |
Cells were treated with formalhedyde (1 %)
|
| Growth protocol |
Samples were prepared from exponential growing phase cultures in LB media (OD600 ~0.5) at 37°C or 30°C for E. coli or S. Thy LT2, respectively.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated cell and protein-DNA complexes were isolated with anti ParBF antibody
A maximum of 2 ng of ChIP DNA was used to synthetize the library as described in manufacturer’s instructions (Ion ChIP-Seq Library Preparation on the Ion Proton™ System - revision B - Step10). The last size selection was modified by a double size selection (0.55X/0.25X) of binding to AMPure® XP beads followed by a step of wash and elution. Then, qualification and quantification were made with the Bioanalyzer - Agilent, Santa Clara, CA
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent S5 |
| |
|
| Description |
Mapped reads: 1489543; average fragment size: 187
|
| Data processing |
Basecalls and alignment performed using Torrent_Suite 5.12.1
ChIP-seq reads were aligned to the corresponding genomes of reference, including the plasmids content.
The F plasmid reads were counted in the centre of DNA fragment according to each average librairy size.
The F plasmid reads, substracted from background, were binned with a window and a step of 40 and 20, respectively.
Assembly: Escherichia coli str. K-12 substr. MG1655ASM584v2
Supplementary files format and content: The counting of reads over the genomic sequences was performed using bedtools 2.26.0 with the tool genomecov and the options -d, -s, -strand and -ibam
|
| |
|
| Submission date |
Feb 22, 2024 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Jean-Yves Bouet |
| E-mail(s) |
jean-yves.bouet@univ-tlse3.fr
|
| Phone |
(+33) 561 33 59 06
|
| Organization name |
CNRS
|
| Lab |
Universite Toulouse III - Paul Sabatier, Centre de Biologie Integrative, CBI-LMGM
|
| Street address |
169 avenue Marianne Grunberg-Manago
|
| City |
Toulouse |
| ZIP/Postal code |
31062 |
| Country |
France |
| |
|
| Platform ID |
GPL34219 |
| Series (1) |
| GSE256357 |
ParBF DNA binding profiles over various supercoiling level and on linear DNA |
|
| Relations |
| BioSample |
SAMN40037782 |
| SRA |
SRX23702264 |
