Illumina HiSeq 4000 sequencing; ChIP-seq of H3K27ac and H3K27me3 in HSJD-DIPG-007 cell line upon treatment with ICG-001 and JQ1
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Neural
Cell type
HSJD-DIPG-007
NA
NA
Attributes by original data submitter
Sample
ENA first public
2020-07-17
ENA last update
2020-06-02
ENA-CHECKLIST
ERC000011
External Id
SAMEA6870818
INSDC center alias
Mayo Clinic
INSDC center name
Mayo Clinic
INSDC first public
2020-07-17T04:03:21Z
INSDC last update
2020-06-02T13:59:21Z
INSDC status
public
Submitter Id
E-MTAB-9152:HSJD-DIPG-007_input_ICG_1
broker name
ArrayExpress
cell line
HSJD-DIPG-007
common name
human
developmental stage
adult
disease
diffuse intrinsic pontine glioma
organism part
brain
sample name
E-MTAB-9152:HSJD-DIPG-007_input_ICG_1
Sequenced DNA Library
library_name
HSJD-DIPG-007_input_ICG_1_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked in 1% formaldehyde followed by quenching with Glycine (Final concentration 125 mM). Samples were then lysed and sonicated for 20 cycles (30 seconds on/ 30 seconds off) (Bioruptor pico, Diagenode). Precleared chromatin was incubated with 1µg antibody for H3K27ac (196-050, Diagenode), H3K27me3 (C15410195, Diagenode), and rabbit IgG (C15410206, Diagenode). Protein A sepharose beads were used to pull down the antibody-chromatin complex and samples were then de-crosslinked and DNA was extracted. Cells were treated with 2.5 uM ICG-001 or 0.25 uM JQ1 for 48 hours before harvesting. DNA was extracted using phenol/chlorofom/Isoamylic alcohol (25:24:1). Aqueous phase was collected and DNA was precipitated using 100% ethanol followed by washing with 70% ethanol and resuspension in water. Microplex Library preparation kit v2 (diagenode) was used to prepare libraries from ChIP DNA according to manufacturer's instructions.