GSM2319580: human BJ fibroblast ChIP Input rep2; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Input control
Antigen
Input control
Cell type
Cell type Class
Epidermis
Cell type
BJ
Primary Tissue
Skin
Tissue Diagnosis
Normal
Attributes by original data submitter
Sample
source_name
BJ foreskin fibroblasts
antibody
none
sonication of purified dna prior to library prep
none
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
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.