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Sample GSM6254213 Query DataSets for GSM6254213
Status Public on Jun 23, 2022
Title ScpB ChIP DNA of strain BSG5146 (WT ParB) repeat 2
Sample type SRA
 
Source name BSG5146
Organism Bacillus subtilis
Characteristics strain: BSG5146
genotype: 1A700, parB(WT)::kanR, trpC2
chip antibody: Eurogentec SK5045 anti-ScpB
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde for 30 minutes. After quenching and cell lysis, chromatin was sonicated using a Bandelin Sonopuls HD2070.
DNA libraries were prepared by Genomic Facility at CIG, UNIL, Lausanne. Briefly, the DNA was fragmented by sonication (Covaris S2) to fragment sizes ranging from 220–250 bp. DNA libraries were prepared using the Ovation Ultralow Library Systems V2 Kit (NuGEN) including 15 cycles of PCR amplification. 20-30 million sequence reads were obtained on a NovaSeq 6000 system with 150-bp read length
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description FD4IPWT
APR ChIP2.txt
APR ChIP/WT2.txt
Data processing Raw ChIP-seq data pairs (L1/L2) were merged,
ChIP-seq data was trimmed using Trimmomatic-0.39 (SE -phred33, ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Mapped with bowtie2, sorted with samtools
Binning at 1kb.
Obtained .bam files were further imported to SeqMonk for Read Count Quantitation.
Assembly: NC_000964 (1A700)
Supplementary files format and content: Read Count Quantitation and generation of Probe Report in .txt format with SeqMonk (used All Reads, Correct for total read count, Correcct for Milion Reads)
 
Submission date Jun 20, 2022
Last update date Jun 23, 2022
Contact name Hon-Wing Liu
E-mail(s) hon-wing.liu@unil.ch
Phone 0766963933
Organization name Université de Lausanne
Street address Le Biophore, CH-1015 Lausanne
City Ecublens VD
ZIP/Postal code 1025
Country Switzerland
 
Platform ID GPL30886
Series (1)
GSE206446 The ParB clamp docks onto Smc for DNA loading via a joint-ParB interface [ChIP-seq]
Relations
BioSample SAMN29207138
SRA SRX15797444

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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