GSM8095998: ParBF, S.typhi LT2, F, IP1; Salmonella enterica subsp. en... - SRA

SRX23702266: GSM8095998: ParBF, S.typhi LT2, F, IP1; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; ChIP-Seq
1 ION_TORRENT (Ion Torrent S5) run: 9.8M spots, 1.9G bases, 1.3Gb downloads

External Id: GSM8095998_r1

Submitted by: Universite Toulouse III - Paul Sabatier, Centre de Biologie Integrative, CBI-LMGM, CNRS

Study: ParBF DNA binding profiles over various supercoiling level and on linear DNA

PRJNA1079266 • SRP491033 • All experiments • All runs

show Abstracthide Abstract

We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) of the DNA binding pattern of ParBF (SopB) of plasmid F. This study, performed in E. coli and Salmonella typhimurium, investigates the impact of DNA supercoiling on ParBF DNA binding profiles in vivo. We found that variation in DNA supercoiling does not significantly affect the ParB DNA binding profiles even on linear DNA. Overall design: Chromatin immunoprecipitation DNA-sequencing for ParB of plasmid F (ParBF) in bacterial strains exhibiting various DNA supercoiling level, and on linearized plasmid F at several positions relative to the centromere parSF. Biological replicates are labelled IP1 and IP2. Anti ParBF antibody is affinity purified before used.

Sample: ParBF, S.typhi LT2, F, IP1

SAMN40037780 • SRS20533417 • All experiments • All runs

Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Library:

Name: GSM8095998

Instrument: Ion Torrent S5

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: SINGLE

Construction protocol: Lysates were clarified from sonicated cell and protein-DNA complexes were isolated with anti ParBF antibody A maximum of 2 ng of ChIP DNA was used to synthetize the library as described in manufacturer's instructions (Ion ChIP-Seq Library Preparation on the Ion Proton™ System - revision B - Step10). The last size selection was modified by a double size selection (0.55X/0.25X) of binding to AMPure® XP beads followed by a step of wash and elution. Then, qualification and quantification were made with the Bioanalyzer - Agilent, Santa Clara, CA

Runs: 1 run, 9.8M spots, 1.9G bases, 1.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR28052510	9,809,234	1.9G	1.3Gb	2024-07-01

ID:: 31986890

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