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Sample GSM3020710 Query DataSets for GSM3020710
Status Public on May 01, 2018
Title Hfq_stationary_Rif A
Sample type SRA
 
Source name Bacterial cells grown to OD 2.0
Organism Pseudomonas aeruginosa PAO1
Characteristics optical density: OD 2.0
genotype: Hfq-VSVG FRT
treatment protocol: sample taken 30 minutes after treatment with 150 ug/mL rifampicin
chip antibody: Agarose-immobilized anti-VSVG antibody (Sigma-Aldrich, catalog number A1970, monoclonal antibody clone P5D4)
Growth protocol Bacterial cultures were started from single colonies, grown overnight, and back-diluted in LB media
Extracted molecule genomic DNA
Extraction protocol DNA associated with proteins of interest were immunoprecipitated from lysates with anti-VSVG monocolonal antibody
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following manufacturer’s instructions, bead-based size selection of DNA fragments was used in a subset of samples, see SAMPLES section
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_stat_Rif_AllPeaks.bed
R1 raw file checksum: 9a44a73c0adb1ef52a6c220dee0b0ddb
R2 raw file checksum: 37e04d13b8c40ccde6b3f9ff9ec5f32e
Data processing Paired ChIP-Seq reads corresponding to fragment sizes of either 200 or 400 bp (see SAMPLES section) were aligned to the PAO1 genome using bowtie2 (version 2.3.1) allowing 1 mismatch in a 28 bp seed region with no discordant or unpaired alignments.
The program samtools (version 1.3.1) was used to extract read 1 from each mapped read pair.
For Hfq experiments (samples 1-4): Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from stationary-phase wild-type cells (sample 5) with the following settings: KDE = 50, seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2
For Crc experiments (samples 6 and 7): Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from log-phase wild-type cells (sample 8) with the following settings: KDE = 30, seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2; only peaks with greater than 3x enrichment were considered.
Bed files for each experimental replicate were created by QuEST and the final processed bed files were generated by identifying the largest overlapping peak region which statisfy the following conditions: (1) peak regions must have a positive peak shift, (2) peak regions must have a positive strand correlation, (3) peak regions must have a q-value of less than 0.01, and (4) peak regions must be shared by two or more experimental replicates.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: wig files were generated using QuEST; Scores represent normalized smoothed read density
Supplementary_files_format_and_content: bed intervals reflect regions with significant (as defined above) enrichment of reads in the experimental condition in comparision to the mock control condition.
 
Submission date Feb 23, 2018
Last update date May 01, 2018
Contact name Simon L Dove
E-mail(s) [email protected]
Organization name Boston Children's Hospital and Harvard Medical School
Department Division of Infectious Diseases
Lab Dove Laboratory
Street address 300 Longwood Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL18782
Series (1)
GSE111037 Co-transcriptional association of Hfq and Crc with the Pseudomonas aeruginosa PAO1 genome
Relations
BioSample SAMN08284316
SRA SRX3528049
BioSample SAMN08583740

Supplementary file Size Download File type/resource
GSM3020710_Hfq_stat_Rif_A_normalized.profile.wig.gz 21.2 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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