Antigen

Antigen Class

TFs and others

Antigen

CTCF

Cell type

Cell type Class

Pluripotent stem cell

Cell type

hESC derived neural cells

NA

NA

Sample

source_name

KOLF2.1J

cell line

KOLF2.1J

cell type

Neurons

chip antibody

CTCF (ActiveMotif, Cat:61311)

Sequenced DNA Library

library_name

GSM7114652

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the Diagenode Bioruptor Pico. Libraries were prepared by blunting and ligating ChIP DNA fragments to sequencing adapters for amplification with barcoded primers (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 15 cycles; 5 min at 72°C). Libraries were quantified with Qubit dsDNA HS Assay kit and visualized with Standard Sensitivity NGS Fragment Analysis Kit (Advanced Analytical DNF-473) and Fragment Analyzer 5200 (Agilent).

Sequencing Platform

instrument_model

Illumina NovaSeq 6000

hg38

Number of total reads

31290761

Reads aligned (%)

69.9

Duplicates removed (%)

12.7

Number of peaks

34298 (qval < 1E-05)

hg19

Number of total reads

31290761

Reads aligned (%)

69.2

Duplicates removed (%)

13.4

Number of peaks

33957 (qval < 1E-05)