Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
ChIP-seq_HCT116_Homozygous_SMARCA4
cell line
HCT116
cell type
colorectal carcinoma derived cell line
genotype/variation
Homozygous ARID1A-KO
chip antibody
SMARCA4/BRG1 (Abcam, EPNCIR111A, ab110641)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Cat.# IP-202-1012)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
28629677
Reads aligned (%)
95.4
Duplicates removed (%)
3.4
Number of peaks
768 (qval < 1E-05)

hg38

Number of total reads
28629677
Reads aligned (%)
96.8
Duplicates removed (%)
2.7
Number of peaks
541 (qval < 1E-05)

Base call quality data from DBCLS SRA