GSM1438429: Input DMSO 24h, rep1; 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
SF8628
NA
NA
Attributes by original data submitter
Sample
source_name
Pediatric, K27M mutated DIPG cells treated with DMSO for 24h, input
cell line
SF8628
age
year 3
tissue
pons
gender
female
treatment
DMSO
treatment duration
24h
chip antibody
none
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, 1×10^6 cells, treated with vehicle or 6 μM GSKJ4 for 24 and 72 hours, were harvested, washed with PBS and fixed with 1% formaldehyde for 5 minutes at room temperature. Cells were then quenched with 125 mM glycine for 5 minutes. After wash, cell extracts were prepared using lysis buffer (50 mM HEPES/KOH at pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton-X100, 0.1% Na-deoxycholate, 1 mM PMSF, 1 mM Pefoblock, 1 mM benzamidine, 1 mg/ml bacitracin) on ice for 10 minutes. Chromatin was sheared by sonication (bioruptor, High power, 15 × 2 cycles), to average lengths of 500 bp, then immunoprecipitated using an antibody against histone H3K27me3 (#9733, Cell Signaling). After repeated washings, the DNA was recovered from the beads by incubating the beads in elution buffer (10 mM Tris at pH 8.0, 10 mM EDTA at pH 8.0, 1% SDS, 150 mM NaCl, 5 mM DTT) at 65 oC. Both input DNA and eluted DNA were subsequently purified using Qiagen Mini Elute PCR purification kit. ChIP DNA libraries were prepared with the Ovation Ultralow DR Multiplex system (NuGEN).