GSM3003390: input SUDIPGXIII DMSO rep2; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Input control
Antigen
Input control
Cell type
Cell type Class
Neural
Cell type
SU-DIPG-XIII
NA
NA
Attributes by original data submitter
Sample
source_name
SU-DIPGXIII
treatment
DMSO treated
tissue
diffuse intrinsic pontine glioma
chip target
none (input)
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were using a hypotonic buffer (25 mM Tris (pH 8.0), 1.5 mM MgCl2, 0.2% NP40, 10 mM KCl). Isolated nuclei were washed in buffer A (0.34 M sucrose, 4 mM MgCl2, 60 mM KCl, 50 mM HEPES (pH 7.4), and digested with micrococcal nuclease I (New England Biotechnology) to obtain mono- and di-nucleosomes. Micrococcal nuclease reactions were stopped by the addition of EGTA to 10 mM, nuclei were then pelleted and chromatin was extracted in 10 mM EDTA. Buffer B (20 mM Tris (pH 8.0), 5 mM EDTA (pH 8), 500 mM NaCl, ) was added to dilute each sample to 100 ng/µl before incubating overnight at 4°C with 5 µg of the following antibodies: H3K27ac (Active Motif, #39135), H3K4me1 (Abcam, ab8895), or H3K27me3 (Millipore, 07-449). Antibody-chromatin complexes were retrieved using Protein G Magnetic Beads (EMD Millipore), followed by extensive washing and elution in a buffer containing 1% SDS, 50 mM Tris HCl (pH 7.0), and 1 mM EDTA. Libraries for sequencing were prepared using the NEBNext library preparation kit (New England Biotechnology) and sequenced on an Illumina HiSeq2500 to a length of 50 base pairs.