|
| Status |
Public on Oct 30, 2018 |
| Title |
IP_3548-LB |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Escherichia coli |
| Characteristics |
strains: DLT3548
parsf location: E.coli xylE::parSF
iptg induction (um): 100 uM
parbf allele: ParBF-mVenus
antibody: anti ParBF
|
| 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 : 16 608 073 ; average fragment size : 223
DLT3548_SopC_nosopB_pJYB294.fasta
|
| 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, DLT2075_converted.fasta, DLT3548_SopC_nosopB_pJYB294.fasta, DLT3567_Rox.fasta/DLT2075_converted.fasta DLT3548_SopC_nosopB_pJYB294.fasta DLT3567_Rox.fastahome_net/labourd/projets/ChipSeq_Roxanne/Geo_deposit/labour_addsamples/labour_aaddsamples_ref
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 |
Oct 29, 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 |
SAMN10342010 |
| SRA |
SRX4950938 |
