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Status |
Public on Jun 23, 2022 |
Title |
ScpB ChIP DNA of strain BSG5146 (WT ParB) repeat 2 |
Sample type |
SRA |
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Source name |
BSG5146
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Organism |
Bacillus subtilis |
Characteristics |
strain: BSG5146 genotype: 1A700, parB(WT)::kanR, trpC2 chip antibody: Eurogentec SK5045 anti-ScpB
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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
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
FD4IPWT APR ChIP2.txt APR ChIP/WT2.txt
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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)
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Submission date |
Jun 20, 2022 |
Last update date |
Jun 23, 2022 |
Contact name |
Hon-Wing Liu |
E-mail(s) |
hon-wing.liu@unil.ch
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Phone |
0766963933
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Organization name |
Université de Lausanne
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Street address |
Le Biophore, CH-1015 Lausanne
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City |
Ecublens VD |
ZIP/Postal code |
1025 |
Country |
Switzerland |
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Platform ID |
GPL30886 |
Series (1) |
GSE206446 |
The ParB clamp docks onto Smc for DNA loading via a joint-ParB interface [ChIP-seq] |
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Relations |
BioSample |
SAMN29207138 |
SRA |
SRX15797444 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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