Illumina HiSeq 2000 paired end sequencing; ChIP-seq analyses of CTCF ... - SRA

Links from BioSample

ERX3374718: Illumina HiSeq 2000 paired end sequencing; ChIP-seq analyses of CTCF binding in liver samples from CAST/EiJ and SPRET/EiJ (Mus spretus) mice, and of the cohesin subunit RAD21 in C57BL/6J mouse liver
1 ILLUMINA (Illumina HiSeq 2000) run: 35.3M spots, 7.1G bases, 3.9Gb downloads

Design: ChIP-seq analyses of CTCF binding in liver samples from CAST/EiJ and SPRET/EiJ (Mus spretus) mice, and of the cohesin subunit RAD21 in C57BL/6J mouse liver

Submitted by: EMBL-EBI

Study: ChIP-seq analyses of CTCF binding in liver samples from CAST/EiJ and SPRET/EiJ (Mus spretus) mice, and of the cohesin subunit RAD21 in C57BL/6J mouse liver

PRJEB32870 • ERP115602 • All experiments • All runs

show Abstracthide Abstract

We explored the relationship between the evolutionary dynamics of CTCF binding and the functional stability of higher order genome structures, by performing ChIP-seq experiments in closely related Mus species or strains and intersecting with Hi-C-derived topologically associating domains (TADs) and expression data. All experiments were performed in adult male liver samples in 3 biological replicates and with an input control set. We also generated RAD21 (cohesin subunit) ChIP-seq from a replicate of adult male mouse (C57BL/6J) liver to determine localization of cohesin with respect to CTCF.

Sample: do3181

SAMEA5684701 • ERS3488687 • All experiments • All runs

Organism: Mus spretus

Library:

Name: do3181_p

Instrument: Illumina HiSeq 2000

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: PAIRED

Construction protocol: Liver samples were collected from three Mus m. castaneus and three M. spretus individuals Liver tissue from three male individuals from the Mus species was crosslinked, dounced and lysed as described in Schmidt et al. 2009 (PMID: 19275939). The chromatin was sonicated using a Misonix sonicator 3000 homogenizer with 12 cycles of 30s ON and 60s OFF at a power-output 30 Watt. CTCF was immunoprecipitated using the Merck-Millipore antibody (cat# 07-729). NGS libraries prepared according to Schmidt et al. 2009 (PMID: 19275939) ligating Illuminas low-plex TruSeq adapters.

Experiment attributes:

Experimental Factor: immunoprecipitate: CTCF

Experimental Factor: organism: Mus spretus

Runs: 1 run, 35.3M spots, 7.1G bases, 3.9Gb

Run	# of Spots	# of Bases	Size	Published
ERR3350211	35,295,293	7.1G	3.9Gb	2019-11-21

ID:: 9448268

SRA

Sequence Read Archive

Result Filters

Send to:

Links from BioSample

Supplemental Content

Related information

Recent activity