ChIP-Atlas: SRX1177315

Antigen

Cell type Class: Neural
Cell type: Glioblastoma
MeSH Description: A malignant form of astrocytoma histologically characterized by pleomorphism of cells, nuclear atypia, microhemorrhage, and necrosis. They may arise in any region of the central nervous system, with a predilection for the cerebral hemispheres, basal ganglia, and commissural pathways. Clinical presentation most frequently occurs in the fifth or sixth decade of life with focal neurologic signs or seizures.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: Chromatin immunoprecipitation (ChIP) was performed as previously described (Heintzman et al., 2007). Briefly, 10-20 million of cultured cells and ~0.2 g of frozen tissue samples were cross-linked in 1% formaldehyde at room temperature for 10 and 25 minutes, respectively. Cross-linked samples were sonicated until chromatin fragments were of 200-600 bp in length. Chromatin immunoprecipitation was carried out using 3-5 µg of antibody and 200 µg of chromatin preparation in RIPA buffer at 4 degree overnight. After five washes in RIPA and one wash with 1xTE buffer, chromatins were eluted and reverse cross-linked at 65 oC overnight. DNA was purified after phenol extraction. Libraries were prepared according to Illumina's instructions, using TruSeq DNA Sample Preparation Kits v2, Set A (Cat# FC-121-2001). 4-12 library preps were mixed for multiplexed single-read sequencing using Illumina Hi-seq 2000 (Illumina).