|
| Status |
Public on Sep 04, 2015 |
| Title |
IP_F |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Escherichia coli |
| Characteristics |
strains: DLT1215
plasmids: pOX38B
antibody: affinity purified anti-SopB
|
| 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)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated cell and protein-DNA complexes were isolated with anti SopB antibody
Library of precipitated DNA from ChIP preparation were constructed by adding 130-bp DNA adapters and sequenced with Illumina 50 cycles Truseq SBS kit v3 (FC-401-3002, Illumina); Library of precipitated DNA from ChIP preparation were constructed by adding 130-bp DNA adapters and sequenced with Illumina Library of precipitated DNA from ChIP preparation were constructed by adding 130-bp DNA adapters and sequenced with Illumina technology
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Total reads (PF): 50,921,857
|
| Data processing |
Base-calling software : RTA-1.17.20.0
Data filtering steps : None (automatic Illumina quality filtering)
Read alignment : BWA-0.6.2
Additional processing software : Samtools and home-made script to generate density files.
Genome_build: ASM584v2 ; AP001918
Supplementary_files_format_and_content: All processed data files are in text format and represent the density tags for each DNA strand (F: forward; R:reverse)
|
| |
|
| Submission date |
Apr 14, 2015 |
| Last update date |
May 15, 2019 |
| 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 |
GPL20045 |
| Series (1) |
| GSE67869 |
Genome-wide maps of ParBF (SopB) binding along DNA in E. coli |
|
| Relations |
| BioSample |
SAMN03486361 |
| SRA |
SRX996333 |
