Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
U-251 MG
Primary Tissue
Brain
Tissue Diagnosis
Astrocytoma

Attributes by original data submitter

Sample

source_name
U251
cell type
U251 glioblastoma cell
cell line
U251
genotype/variation
HA-SOX4 overexpression
time
3 days post virus infection
antibody
input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
In brief, after HASOX4 overexpression, approximately total ~12×10e6 U251 cells (4 X 10cm plates) were crosslinked with methanol-free formaldehyde (Thermo Scientific, 28908). Then quench the crosslinking with glycine solution. After lysis and centrifugation, chromatin was sheared into 100-500 nucleotides length by Bioruptor Machine (Diagenode, B01010002). 10 µg chromatin solution was used for input. 150 µg of chromatin solution was applied for immunoprecipitation by 5 µg HA (Abcam; ab99110). Subsequently, 100 µl Magnetic Protein G Dynabeads (Life Technologies, 10003D) were resuspended in immunoprecipitation samples incubate for 2 hours at 4°C with gentle rotation to poll down primary antibody affinity chromatin fragments. After subsequently treated with RNase, Proteinase K and high concentration of NaCl solution (5M), Input and IP Chromatin was purified with a QIAquick PCR purification kit (Qiagen, 28104) according to kit manual. The chromatin concentration was determined by Qubit fluorometer and Qubit dsDNA HS assay kit (Life Technologies, Q32850) according to kit manual. For statistic, every groups were triplicated. Libraries were synthesized from 10 ng purified input chromatin and 10 ng purified immunoprecipitated chromatin using a NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs, E6240S) with NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7335S). Replicate libraries were prepared from independent immunoprecipitations. ChIP-seq: single end 50-base length sequencing reads were generated on an Illumina HiSeq 2500 System.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
33865346
Reads aligned (%)
98.2
Duplicates removed (%)
3.2
Number of peaks
719 (qval < 1E-05)

hg19

Number of total reads
33865346
Reads aligned (%)
97.7
Duplicates removed (%)
3.6
Number of peaks
820 (qval < 1E-05)

Base call quality data from DBCLS SRA