GSM2471875: SU-DIPG-VI panobinostat input; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Unclassified
Antigen
Unclassified
Cell type
Cell type Class
Neural
Cell type
Diffuse intrinsic pontine glioma
NA
NA
Attributes by original data submitter
Sample
source_name
patient-derived cell culture
cell type
Diffuse intrinsic pontine glioma (DIPG) cells
treated with
none
molecule subtype
precipitated DNA
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA-seq samples were pelleted and lysed in Trizol reagent then subsequently precipitated. ChIP-seq samples were fixed in 1% formaldehyde for 10 min before glycine quench and freezing at -80C. ChIP-seq pellets were lysed in LB1 Buffer before beginning ChIP protocol. After extraction from Trizol, RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Thermo AM8740 and Second Strand Synthesis. ChIP-seq libraries were prepared directly from DNA isolated following IP. Libraries for ChIP-seq and RNA-seq were end-repaired using T4 DNA Polymerase, E. coli Klenow fragment, and T4 polynucleotide kinase. DNA was then A-tailed using exo(-) Klenow fragment and ligated to adaptors from NEBNext MultiPlex Oligos or TruSeq Preindexed Adaptors using New England BioLabs Quick Ligase. Libraries were sequeced at 1x75 (RNA-seq) or 2x75 (ChIP-seq) on either Illumina HiSeq or NextSeq