GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2690551 Query DataSets for GSM2690551
Status Public on Sep 13, 2018
Title Rif treated GapR-3xFLAG ChIP-seq
Sample type SRA
Source name Caulobacter crescentus NA1000
Organism Caulobacter vibrioides NA1000
Characteristics growth stage: exponential phase
genotype: gapR::gapR-3xFLAG
media: PYE
growth treatment: 25 µg/mL of rifampicin was added for 20 min prior to fixation
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 MiSeq
Description gDNA
Cells were fixed with 1% formaldehyde and quenched with glycine. Cells were lysed with lysozyme and sonication, and cell debris cleared by centrifugation. Supernatants were diluted to use 500 μg of protein was used for ChIP and pre-cleared with 50 μL of Protein-A Dynabeads (Life Technologies) pre-blocked in ChIP buffer + 0.01% SDS and 100 μg ultrapure BSA (Ambion). Beads were pelleted and 90 μL of the supernatant was removed as input DNA. Remaining pre-cleared supernatant was incubated with 1 µL of FLAG antibody (Sigma), and immune complexes were captured with pre-blocked Protein-A Dynabeads. Beads were then washed and complexes eluted. Crosslinking was reversed at 65 °C in the presence of RNase A, and treated with Proteinase K (NEB). gDNA was recovered by phenol:chloroform:isoamyl alcohol extraction and precipitation.
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
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 GPL20784
Series (1)
GSE100657 A bacterial chromosome structuring protein binds overtwisted DNA to stimulate type II topoisomerases and enable DNA replication
BioSample SAMN07299076
SRA SRX2969616

Supplementary file Size Download File type/resource
GSM2690551_GapR_chip-rif.wig.gz 13.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap