|
Status |
Public on Oct 30, 2018 |
Title |
input_3586 |
Sample type |
SRA |
|
|
Source name |
bacteria
|
Organism |
Escherichia coli |
Characteristics |
strain: DLT3586 parsf location: F1-10B iptg induction (µm): na parbf allele: wild type antibody: input
|
Treatment protocol |
Cells were treated with formalhedyde (1 %)
|
Growth protocol |
Samples were prepared from exponential growing phase cultures at 37°C in LB media (OD = 0.5) in the presence of IPTG (where indicated)
|
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 |
Total reads : 7 798 374 ; average fragment size : 219
|
Data processing |
Basecalls and alignment performed using Torrent_Suite 5.0.4 ChIP-seq reads were aligned to the N16961 genome Genome_build: Escherichia coli str. K-12 substr. MG1655 ASM584v2 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 option –d and –fs
|
|
|
Submission date |
Jun 04, 2018 |
Last update date |
Oct 30, 2018 |
Contact name |
Delphine Labourdette |
E-mail(s) |
labourd@insa-toulouse.fr
|
Organization name |
INSA
|
Department |
LISBP
|
Lab |
Plateforme Biopuces
|
Street address |
Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil
|
City |
Toulouse |
ZIP/Postal code |
31140 |
Country |
France |
|
|
Platform ID |
GPL25140 |
Series (1) |
GSE115274 |
Genome-wide maps of ParBF (SopB) binding on plasmid F or E.coli chromosome carrying parSF |
|
Relations |
BioSample |
SAMN09303691 |
SRA |
SRX4157936 |