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Sample GSM4838872 Query DataSets for GSM4838872
Status Public on Mar 11, 2021
Title 621H::goxR-strep_ChAP
Sample type SRA
Source name 621H::goxR-strep_ChAP
Organism Gluconobacter oxydans
Characteristics strain: 621H
genotype: 621H::goxR-strep
Treatment protocol Afterwards, the cell pellet was resuspended in 20 ml PBS with 1% (v/v) formaldehyde incubated for 20 min at room temperature to crosslink the Strep-tagged GoxR protein to DNA. To stop the crosslinking, glycine was added to a final concentration of 125 mM followed by incubation for 5 min at room temperature. Afterwards, cells were washed twice with 40 ml buffer A (100 mM Tris-HCl, pH 8.0, 1 mM EDTA) and pellets were stored overnight at -80°C.
Growth protocol For preparation of ChAP-Seq samples, the strain G. oxydans 621H::goxR-strep was used. A preculture was inoculated in 15 ml mannitol medium and incubated for 8 h at 30°C. Subsequently, 1 ml of the first preculture was transferred into 50 ml mannitol medium. After cultivation overnight, this second preculture was used to inoculate the main culture (1 l in a 5 l baffled Erlenmeyer flask) to an OD600 of 0.5. The culture was incubated at 30°C and 130 rpm. In the late exponential phase (OD600 ca. 2.8), cells were harvested by centrifugation and washed once in 40 ml PBS (137 mM NaCl, 2.7 mM KCl, 1.5 mM KH2PO4, 8 mM Na2HPO4, pH 7.4).
Extracted molecule genomic DNA
Extraction protocol Cell disruption, sonication of the DNA, purification of DNA bound to Strep-tagged GoxR, and the final DNA purification after digestion of protein was performed as described (PMID: 32453397).
The obtained DNA fragments were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer´s protocol for DNA fragments without size selection. Adapter-ligated DNA was amplified by using 15 PCR cycles. Quantification of the resulting libraries was performed with the KAPA library quantification kit and sequenced on a MiSeq (Illumina) using paired-end sequencing with a read-length of 2 × 150 bases.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
Data processing Library strategy: ChAP-seq
Read processing and quality trimming was performed with the CLC Genomics Workbench (Qiagen Aarhus A/S). For the mapping to the G. oxydans 621H reference genome (NC_006672.1-NC_006677.1) one mismatch per read was allowed.
The expected peak width was estimated via the following procedure: (i) all the peaks higher than 3-fold mean coverage were detected. (ii) Points at which their coverage dropped below 1/2  of the maximal peak height were found and the distance between them was considered as a peak width.
Peak intensity is the highest read coverage for a peak normalized to the average coverage of non-peak genomic area.
Genome_build: NC_006672.1-NC_006677.1
Supplementary_files_format_and_content: Peak tsv file
Submission date Oct 21, 2020
Last update date Mar 12, 2021
Contact name Angela Kranz
Organization name Forschungszentrum Jülich GmbH
Department IBG-1: Biotechnology
Street address Wilhelm-Johnen-Strasse
City Jülich
State/province NRW
ZIP/Postal code 52425
Country Germany
Platform ID GPL28332
Series (1)
GSE159734 ChAP-seq analysis to identify GoxR binding sites
BioSample SAMN16493311
SRA SRX9322405

Supplementary file Size Download File type/resource
GSM4838872_ChAPseq_result_matrix.tsv.tsv.gz 3.9 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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