Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Muscle
Cell type
Rh-4
NA
NA

Attributes by original data submitter

Sample

source_name
RMS cell line, PAX3-FOXO1
cell line
RH4
cell type
rhabdomyosarcoma
antibody
CTCF, EMD Millipore (cat07-729 lot2628833 pAb)
enrichment target
CTCF
target function
Domain Insulator

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol. DNase DNA purification was performed by column (MiniElute PCR purification kit, Qiagen). Standard Illumina barcodes were introduced during library preparation

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
24892850
Reads aligned (%)
73.6
Duplicates removed (%)
24.2
Number of peaks
45175 (qval < 1E-05)

hg38

Number of total reads
24892850
Reads aligned (%)
74.2
Duplicates removed (%)
23.8
Number of peaks
45364 (qval < 1E-05)

Base call quality data from DBCLS SRA