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

Sample

source_name

Ewing sarcoma cell line (TC71)

cell line

TC71

cell type

Ewing sarcoma cell line

genotype

SA2 KO

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

19967954

Reads aligned (%)

98.2

Duplicates removed (%)

27.0

Number of peaks

51417 (qval < 1E-05)

hg19

Number of total reads

19967954

Reads aligned (%)

97.6

Duplicates removed (%)

27.7

Number of peaks

50917 (qval < 1E-05)