Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Bone
Cell type
TC-71
Primary Tissue
Bone
Tissue Diagnosis
Sarcoma Ewings

Attributes by original data submitter

Sample

source_name
Ewing sarcoma cell line (TC71)
cell line
TC71
cell type
Ewing sarcoma cell line
genotype
WT
antibody
CTCF (provided in iDeal ChIP-seq kit Diagenode)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChiP were performed following manufacturer instructions using iDeal ChIP-seq kit for transcription factors and for histones (Diagenode). For this, Ewing cell lines were fixed for 10 minutes with 1% of methanol-free formaldehyde (28908, Thermo-Scientific). Chromatin was sonicated (Bioruptor, Diagenode) for 20 cycles (30-sec on, 30-sec off) set at position “high” to generate DNA fragments with an average size around 150-300pb. The library were constructed using TruSeq ChIP library preparation kit (Illumina) according to manufacturer recommendations

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
24644271
Reads aligned (%)
98.0
Duplicates removed (%)
27.9
Number of peaks
51248 (qval < 1E-05)

hg19

Number of total reads
24644271
Reads aligned (%)
97.3
Duplicates removed (%)
28.9
Number of peaks
50563 (qval < 1E-05)

Base call quality data from DBCLS SRA