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Elucidating DNA-binding protein dynamics in Salmonella Typhimurium within macrophages using a breakthrough low-input ChIP-exo workflow [RNA-seq]

ABSTRACT: Elucidating DNA-binding protein dynamics in Salmonella Typhimurium within macrophages using a breakthrough low-input ChIP-exo workflow [RNA-seq]

PROVIDER: PRJNA1124932 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29441511_1.fastq.gz	Fastqsanger.gz
	SRR29441511_2.fastq.gz	Fastqsanger.gz
	SRR29441512_1.fastq.gz	Fastqsanger.gz
	SRR29441512_2.fastq.gz	Fastqsanger.gz
	SRR29441513_1.fastq.gz	Fastqsanger.gz

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Elucidating DNA-binding protein dynamics in Salmonella Typhimurium within macrophages using a breakthrough low-input ChIP-exo workflow [RNA-seq]

Project description:We present genome-wide transcript expression profiles of Salmonella Typhimurium 14028s under both macrophage in vitro and in vivo conditions. These transcriptome data were integrated with ChIP-mini datasets to elucidate the transcriptional roles of H-NS and RpoD under macrophage in vivo conditions.

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Elucidating transcription factor binding dynamics in Salmonella Typhimurium under macrophages in vivo conditions using a low-Input ChIP-exo approach [ChIP-mini]

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Project description:Input Strategy for Improving Analysis of ChIP-exo Data and Beyond

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Project description:Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.

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