Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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)

Attributes by original data submitter

Sample

source_name
G3-medulloblastoma
generation of cells
spheres from tumor cells
antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde at 37°C for 10min. Cells were lysed and after centrifugation nuclei were re-suspended in RIPA buffer. DNA was sonicated with a Branson sonifier to obtain DNA fragments at nucleosomal size. Chromatin bound to target proteins (Miz1, c-Myc, NMyc) was precipitated by incubation with Protein A- and Protein G-dynabeads beads for 6 hrs or overnight. After several washings chromatin was eluted with 1 % SDS and crosslinking was reverted overnight. DNA was purified by Phenol/Chloroform extraction and enrichments were checked by qPCR. Libraries for ChIP-seq samples were contructed following manufactor's intructions using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240). Briefly, ChIP DNA was end repaired, A-tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of a agarose gel and extracted with a Qiagen PCR purification column. Size-selected DNA was amplified with 18 PCR cycles.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
8567057
Reads aligned (%)
93.5
Duplicates removed (%)
36.0
Number of peaks
507 (qval < 1E-05)

mm9

Number of total reads
8567057
Reads aligned (%)
93.2
Duplicates removed (%)
36.4
Number of peaks
580 (qval < 1E-05)

Base call quality data from DBCLS SRA