ChIP-Atlas: SRX490418

Antigen

Cell type Class: Neural
Cell type: Ependymoma
MeSH Description: Glioma derived from EPENDYMOGLIAL CELLS that tend to present as malignant intracranial tumors in children and as benign intraspinal neoplasms in adults. It may arise from any level of the ventricular system or central canal of the spinal cord. Intracranial ependymomas most frequently originate in the FOURTH VENTRICLE and histologically are densely cellular tumors which may contain ependymal tubules and perivascular pseudorosettes. Spinal ependymomas are usually benign papillary or myxopapillary tumors. (From DeVita et al., Principles and Practice of Oncology, 5th ed, p2018; Escourolle et al., Manual of Basic Neuropathology, 2nd ed, pp28-9)

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: 10-20mg of fresh frozen primary tumour samples were homogenized in 1% Formaldehyde and allowed to incubate at room temperature for 6 – 10 min. Cross-linking was stopped with the addition of 125mM of Glycine, and samples were washed twice with ice-cold PBS containing (1% BSA and 10% FBS). Samples were then sonicated to ~200 bp fragments using a Biorupter (Diagenode). The chromatin immunoprecipitation was then performed using 5 mg of H3K27me3 antibody (C15410069-Diagenode) overnight at 4C as described previously (Lupien et al., Cell 2008). Following chromatin immunoprecipitation, DNA was quantified using picogreen, and libraries were prepared and barcoded according to NEB NEXT ChIP seq library preparation protocol performed using Agencourt bead purification. This protocol was followed according to NEB instructions.