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Sample GSM4029399 Query DataSets for GSM4029399
Status Public on May 21, 2020
Title YF11[Flag-DndC]-2-mock
Sample type SRA
 
Source name bacteria
Organism Salmonella enterica
Characteristics serovar: Cerro 87
chip antibody: none
genotype: YF11[pFlag-DndC]
role: No antibody control
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 SAMN12566527
SRA SRX6708231

Supplementary file Size Download File type/resource
GSM4029399_JG-0928_FC-DndC-YF11-MOCK-2.sorted.bam.tdf 2.1 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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