Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

Cell type Class

Blood

Cell type

GM12878

Tissue

blood

Lineage

mesoderm

Description

B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

Sample

source_name

GM12878 cells

cell line

GM12878 cells

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

Cells were sorted by FACS and 5e4 cells were pelleted and resuspended in 50ul of ATAC RSB with 0.1% NP40, 0.1% Tween-20, and 0.01%. After three minutes, 1ml of ATAC RSB with 0.1% Tween-20 was added, tubes were inverted, and nuclei were centrifuged at 500 rcf for 10 min. Supernatant was carefully removed and nuclei were resuspended in 50ul transposition mix (25ul TD buffer, 2.5ul transposase, 16.5ul PBS, 0.5ul 0.1% digitonin, 0.5ul 10% Tween-20, and 5ul water). Transposition was performed for 30 minutes at 37 C with shaking in a thermomixer at 1000 RPM. Reactions were purified with a Zymo DNA Clean & Concentrator 5 kit and library generation was performed as described.

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

23161072

Reads aligned (%)

39.7

Duplicates removed (%)

26.0

Number of peaks

23368 (qval < 1E-05)

hg19

Number of total reads

23161072

Reads aligned (%)

39.5

Duplicates removed (%)

26.1

Number of peaks

23955 (qval < 1E-05)