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Sample GSM4453428 Query DataSets for GSM4453428
Status Public on Apr 04, 2020
Title 0195FLAG1sta_WCE
Sample type SRA
 
Source name archaeal cells
Organism Halobacterium salinarum
Characteristics strain: AKS113
genotype: [delta]ura3 cdrL::FLAG
growth phase: stationary
epitope tag: FLAG
antibody: none
Treatment protocol Cells were crosslinked and immunopreciptated with FLAG antibody as described in Wilbanks et al., 2012 (doi: 10.1093/nar/gks063) with the following exceptions: cultures were crosslinked and immuniprecipitated as described (Wilbanks et al., 2012) with the following exceptions: cultures were crosslinked with 1% formaldehyde for 30 minutes at room temperature; immuoprecipitations were conducted using Dynabead magnetic beads (Thermo-Fisher product 10002D) conjugated with anti-FLAG (Abcam ab1162) anti-rabbit monoclonal antibody at 1:250 dilution. DNA concentration was determined by Nanodrop (Thermo Scientific).
Growth protocol Triplicate cultures of strains AKS113 (CdrL tagged at the C-terminus with the FLAG epitope, Supplementary Table 4) and ∆ura3 control strain were grown until stationary phase and subcultured in rich media supplemented with 50 µg/ml uracil. At mid-log phase (OD600 ~0.15) and early stationary phase (OD600 ~1.8), cultures were crosslinked and immunoprecipitated.
Extracted molecule genomic DNA
Extraction protocol Libraries were constructed using the KAPA Hyper Prep kit and Illumina TruSeq adapters according to manufactuer's instructions. DNA library quality was assessed by Bioanalyzer using a High Sensitivity DNA chip (Agilent). Samples were pooled and run in a single lane on an Illumina HiSeq 4000 (Duke Sequencing and Genomics Technologies core).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Description input control DNA (matched sample with 0195FLAG1sta_IP)
HBT-cdrL1-stat-pks.bed
Data processing 50 bp single reads were assessed for quality using FastQC (www.bioinformatics.babraham.ac.uk)
adapter sequences trimmed using Trim Galore (www.bioinformatics.babraham.ac.uk) and Cutadapt
Resultant sequences were aligned to H. salinarum NRC-1 genome (RefSeq: NC_002607.1, NC_002608.1, NC_001869.1) using Bowtie2
Peaks were called using MOSAiCS with arguments: fragment length 200, bin size 200, read capping 0, analysis type IO, background estimate rMOM, signal model 2S, FDR 0.01.
Genome_build: GCF_000006805.1_ASM680v1
Supplementary_files_format_and_content: wig files were generated using the "generateWig()" command in the R MOSAiCs package; bed files were generated from peak calling with MOSAiCs
 
Submission date Apr 03, 2020
Last update date Apr 05, 2020
Contact name Amy K Schmid
E-mail(s) [email protected]
Organization name Duke University
Department Biology
Lab Schmid
Street address 125 Science Dr.
City Durham
State/province NC
ZIP/Postal code 27707
Country USA
 
Platform ID GPL28343
Series (1)
GSE148065 CdrL ChIP-seq data for the paper "CdrS is required for cell division site placement but not elongation in hypersaline-adapted archaea"
Relations
BioSample SAMN14534539
SRA SRX8053622

Supplementary file Size Download File type/resource
GSM4453428_0195FLAG1sta_WCE.wig.gz 7.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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