|
Status |
Public on May 21, 2020 |
Title |
YF11[Flag-DndC]-3 |
Sample type |
SRA |
|
|
Source name |
bacteria
|
Organism |
Salmonella enterica |
Characteristics |
serovar: Cerro 87 chip antibody: Anti Flag : Monoclonal ANTI-FLAG® M2 antibody produced in mouse F1804– Sigma Aldrich genotype: YF11[pFlag-DndC] role: ChIP
|
Treatment protocol |
Briefly, bacteria were fixed with formaldehyde (1%) for 30 min, stopped crosslink with glycine (250 mM) for 15 min and sheared through Covaris sonication to an average DNA size of 200 bp. About 10ul anti-Flag antibody (Sigma) was added to each cell lysate following by overnight incubation at 4° C. Protein G agarose (Thermo Fisher) was used for further pull-down.
|
Growth protocol |
S. enterica 87 expressing Salmonella DndBCDE strains were grown in Luria-Bertani (LB) broth at 37 °C.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Samples were then reversed cross-linking with Proteinase K at 65°C, and protein binding DNA was purified by DNA purification kit (Qiagen). NEB NEBNext® UltraTM II DNA Library Prep Kit for Illumina was used for library preparation.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Reads were then removed adapter by cutadapt Clean reads were aligned to the corresponding genome using Bowtie 2 with the default option Peak calling was performed using CisGenome with parameters “window statistic >=5 and p-value <= e-6” using two-sample analysis mode Bam files were converted to a .tdf format for visualization separately at forward and reverse strand in the GenomeView Genome_build: CP008925.1 Supplementary_files_format_and_content: TDF file from BAM using igvtools count. By default includes duplicates
|
|
|
Submission date |
Aug 13, 2019 |
Last update date |
May 21, 2020 |
Contact name |
Xiaolin Wu |
E-mail(s) |
xiaolinwu@whu.edu.cn
|
Organization name |
Singapore-MIT Alliance for Research and Technology (SMART)
|
Street address |
1 CREATE Way
|
City |
Singapore |
State/province |
Singapore |
ZIP/Postal code |
138602 |
Country |
Singapore |
|
|
Platform ID |
GPL27048 |
Series (2) |
GSE135768 |
ChIP-seq study on Dnd proteins |
GSE135949 |
Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria |
|
Relations |
BioSample |
SAMN12566526 |
SRA |
SRX6708232 |