Antigen

Antigen Class

TFs and others

Antigen

AFF1

Cell type

Cell type Class

Neural

Cell type

SH-EP

NA

NA

Sample

source_name

SHEP MYCN-ER

cell line

SHEP MYCN-ER

treatment

DMSO

antibody

AFF1

Sequenced DNA Library

library_name

GSM5963923

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

For ChIP-seq, DNA fragments was immunoprecipitated with indicated antibodies and Protein A/G beads. For ChIP-seq, SHEP MYCN-ER cells were crosslinked with 1% paraformaldehyde for 10 minutes and were quenched with glycine for 5 minutes. After cell lysis, fixed chromatin was fragmented to 200-600 bp DNA size using a Diagenode Bruptor Plus. DNA fragments was immunoprecipitated with indicated antibodies and Protein A/G beads. Specific antibodies against MYCN, MAX, AFF1 and AFF4, were generated by immunization in rabbits with recombinant antigens. 1-10 ng of immunoprecipitated DNA was used for DNA library preparation.

Sequencing Platform

instrument_model

Illumina NovaSeq 6000

hg38

Number of total reads

21312791

Reads aligned (%)

25.9

Duplicates removed (%)

28.1

Number of peaks

376 (qval < 1E-05)

hg19

Number of total reads

21312791

Reads aligned (%)

25.8

Duplicates removed (%)

28.2

Number of peaks

349 (qval < 1E-05)