Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Neural
Cell type
C6
Tissue
Brain
Cell Type
Glial Cell
Disease
Glioma

Attributes by original data submitter

Sample

source_name
C6 rat glioma cells_ChIP DNA
cell type
C6 glioma cells
chip antibody
anti-H3K4me3 antibody (Millipore, catalog# 07-473, lot# JBC1888194)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-chip experiments, 5 x 107 C6 glioma cells were cultured to 90% confluence. Cells were treated with 1% formaldehyde, and the cross-linked chromatin was sonicated (average size, 300 bp). Immunoprecipitation were performed with components of the ChIP IT kit according to the manufacturer’s instructions (Active Motif, Carlsbad, CA). Each sample was immunoprecipitated with 1 µg of anti-H3K4me3 antibody (Millipore). The amount and quality of immunoprecipitated DNA were determined by capillary electrophoresis with a Bioanalyzer 2100 and a High Sensitivity DNA LabChip kit from Agilent Technologies (Santa Clara, CA). Samples were amplified using the ChIP-Seq DNA sample prep kit from Illumina, following the manufacturer's instructions, and sequenced using the Ilumina HiSeq 2000 (University of Uppsala Genomic). Center).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

rn6

Number of total reads
13470983
Reads aligned (%)
90.3
Duplicates removed (%)
1.5
Number of peaks
18059 (qval < 1E-05)

Base call quality data from DBCLS SRA