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Cut&Run of Aldh18a1 using 46C mouse ES cells

ABSTRACT: Cut&Run of Aldh18a1 using 46C mouse ES cells

PROVIDER: PRJEB51482 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR9130870_1.fastq.gz	Fastqsanger.gz
	ERR9130870_2.fastq.gz	Fastqsanger.gz
	ERR9130871_1.fastq.gz	Fastqsanger.gz
	ERR9130871_2.fastq.gz	Fastqsanger.gz
	ERR9130872_1.fastq.gz	Fastqsanger.gz

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Cut&Run of Aldh18a1 using 46C mouse ES cells

Project description:Using a proteomic approach we identified Aldh18a1 as a protein co-localized with RNA polymerase II. We then carried out Aldh18a1 Cut&Run assays to confirm its co-localization with RNA polymerase II (E-MTAB-11510). As a result, we observed Aldh18a1 is co-localized with RNA polymerase II primarily on transcription start sites.

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Project description:We designed a benchmarking method to evaluate peak calling procedures for CUT&RUN data and the effects of varying preprocessing approaches, such as fragment length filtering and spike-in calibration. To support this work, we generated new CUT&RUN datasets with distinct experimental characteristics alongside publicly available datasets. In particular, we produced libraries with an average read length of approximately 133 bp—longer than typical CUT&RUN read lengths—which provide higher sequencing coverage and improved read mappability. These datasets provide complementary data for evaluating how experimental characteristics influence preprocessing strategies and peak-calling performance in CUT&RUN.

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