Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CHD4

Cell type

Cell type Class
Others
Cell type
SCC-9
Primary Tissue
Tongue
Tissue Diagnosis
Carcinoma Squamous Cell

Attributes by original data submitter

Sample

source_name
Squamous cell carcinoma cell line SCC9, -DOC1, CHD4 ChIP
cell line
SCC9
cell type
Squamous cell carcinoma cell line
doc1 status
-DOC1
chip antibody
anti-CHD4

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Elution buffer (1% SDS, 100 mM NaHCO3) followed by PCR purification kit/columns. Samples were prepared for ChIP sequencing according to the NEXTflex ChIP-Seq kit (Bioo Scientific). Briefly, 10 ng of chromatin was end repaired and enriched for the 300-400 bp fraction using Ampure XP beads (Agencourt). The repaired DNA library was 3’ end adenylated and barcoded Illumina adaptors were ligated followed by bead purification. The adaptor modified library was enriched by PCR for 18 cycles. The ChIP libraries were sequenced according to the Illumina TruSeq Rapid v2 protocol on the HiSeq2500 for a single read 50bp in length and a 7bp index read.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
27758660
Reads aligned (%)
61.2
Duplicates removed (%)
36.2
Number of peaks
1916 (qval < 1E-05)

hg38

Number of total reads
27758660
Reads aligned (%)
63.0
Duplicates removed (%)
35.0
Number of peaks
1903 (qval < 1E-05)

Base call quality data from DBCLS SRA