alias: GSM2319572
title: GSM2319572: Euchromatin_fraction_rep2; Homo sapiens; ChIP-Seq
library_construction_protocol: Crosslinked chromatin was sonicated using a Diagenode Bioruptor and sedimented on a 6-40% sucrose gradient for 3 hours at 41K rpm (see Methods of text for full details). Fraction #2 (near top of the gradient) containing highly sonicated fragments was harvested as the Euchromatin fraction, while Fractions #10-17 containing larger chromatin fragments was pooled as the Euchromatin fraction. Alternatively, chromatin was immunoprecipitated using Dynabead Protein G beads saturated with anti-H3K9me3 antibodies (abcam 8898, lot GR164997-3). H3K9me3-directed IPs were also performed using chromatin from the Euchromatin and Sonication-Resistant Heterochromatin fractions. DNA was purified by reversing crosslinks overnight, treating with RNase A and Proteinase K, and performing phenol-chloroform extraction. 50 ng of purified DNA was used to prepare libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370S). For samples containing larger DNA fragments (gradient input, Sonication-Resistant Heterochromatin fraction, and IP from the Sonication-Resistant Heterochromatin fraction), the purified DNA was sheared to 100-300bp with a Covaris sonicator prior to library preparation.
identifiers.namespace: GEO
identifiers.id: GSM2319572