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Sample GSM2690566 Query DataSets for GSM2690566
Status Public on Sep 13, 2018
Title GapR_2hr_g20
Sample type SRA
 
Source name Caulobacter crescentus NA1000
Organism Caulobacter vibrioides NA1000
Characteristics growth stage: exponential phase
genotype: delta-gapR Pxyl-gapR
media: PYE + 0.2% glucose
growth treatment: grown 2hr in 0.2% glucose, 20 mins post synchrony in 0.2% glucose
Growth protocol Caulobacter crescentus was grown to OD 0.2-0.4 before treatment or harvest
Extracted molecule genomic DNA
Extraction protocol Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with either Phusion (NEB) or Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 250-600 bp.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description gDNA
Cells were lysed with lysozyme and SDS, and proteins were removed by Proteinase K. CTAB was added and DNAs were extracted by phenol:chloroform:isoamyl alcohol and precipitated. DNA was sheared to 300-800 bp fragments using a Bioruptor Plus sonicator (Diagenode). RNase A (Qiagen) was added and the fragments were electrophoresed, and 300-600 bp fragments were size selected, purified with Gel Extraction Kit (Qiagen), and resuspended in 50 µL EB. Sequencing reads were aligned to NC_011916.1 offset by 1 MB.
Data processing Reads were aligned to Caulobacter NC_011916.1 (NA1000) with bowtie (single-end reads) or bowtie2 (paired end reads) allowing for 1 mismatch
Bowtie alignments were converted to wiggle files by mapping the center of each read.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: wig files were generated using custom python scripts, tab delimited files, first column represents genome position, second column represents value of position
 
Submission date Jun 29, 2017
Last update date May 15, 2019
Contact name Monica S Guo
E-mail(s) msguo@uw.edu
Organization name University of Washington
Department Microbiology
Lab Guo
Street address 750 Republican St
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL18276
Series (1)
GSE100657 A bacterial chromosome structuring protein binds overtwisted DNA to stimulate type II topoisomerases and enable DNA replication
Relations
BioSample SAMN07299082
SRA SRX2969634

Supplementary file Size Download File type/resource
GSM2690566_1MB_GapR_2hr_g20.wig.gz 10.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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