|
Status |
Public on Jul 01, 2024 |
Title |
ParBF, E.coli topA, F, IP2 |
Sample type |
SRA |
|
|
Source name |
plasmid
|
Organism |
Escherichia coli |
Characteristics |
strain name: DLT4106 tissue: plasmid plasmid f: F1-10B genotype: W3110 rpsL topA31::miniTn10 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
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Ion Torrent S5 |
|
|
Description |
Mapped reads: 20939631; 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
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|
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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 |
GPL25140 |
Series (1) |
GSE256357 |
ParBF DNA binding profiles over various supercoiling level and on linear DNA |
|
Relations |
BioSample |
SAMN40037785 |
SRA |
SRX23702261 |