ChIP-Atlas: SRX6428311

Antigen

Cell type Class: Neural
Cell type: Medulloblastoma
MeSH Description: A malignant neoplasm that may be classified either as a glioma or as a primitive neuroectodermal tumor of childhood (see NEUROECTODERMAL TUMOR, PRIMITIVE). The tumor occurs most frequently in the first decade of life with the most typical location being the cerebellar vermis. Histologic features include a high degree of cellularity, frequent mitotic figures, and a tendency for the cells to organize into sheets or form rosettes. Medulloblastoma have a high propensity to spread throughout the craniospinal intradural axis. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, pp2060-1)

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: Lysates were clarified from sonicated nuclei and proteine-DNA complexes were isolated with antibody. Dissociated tissues were fixed for 15 min at room temperature with 1% formaldehyde-containing medium. Nuclei were isolated and sonicated in sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA and protease inhibitor cocktail). Sonicated chromatin (~300 µg) was used for immunoprecipitation by incubation with appropriate antibodies (4 mg) overnight at 4°C. Ten percent of chromatin used for each ChIP reaction was kept as input DNA. Pre-rinsed magnetic protein A/G beads (50 ml) were added to each ChIP reaction and reactions were incubated for 1 hr at 4°C.The beads were then incubated in 200 ml elution buffer at 65°C for 20 min to elute immunoprecipitated materials. The ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB catalogue number E6240L) and then run on the Illumina sequencer HiSeq 2500.