Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC3

Cell type

Cell type Class
Blood
Cell type
Neutrophils
MeSH Description
Immature neutrophils.

Attributes by original data submitter

Sample

source_name
Peripheral blood neutrophils
chip antibody
RRID: AB_307122; Catalog: ab9263; Lot: GR3221084-1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. DNA end repair was performed using an Epicenter End-It kit (Lucigen ER0720), according to manufacturer's instructions and column purified in a Zymo Minelute column (Zymo D4013). A-tails were added by incubating DNA in 1x NEB buffer 2 (New England Biolabs B7002S) with the addition of 200uM dATP and 7.5 units Klenow (exo-) (New England Biolabs M0212L) at 37 degrees for 45 minutes. NEB Next adaptors (New England Biolabs E7337A) were ligated using an NEB quick ligation kit (New England Biolabs M2200L) at benchtop temperature for 30 minutes followed by treatment with 2uL USER enzyme (New England Biolabs M5505L) for 15 minutes at 37°C. DNA was purified using a two-step SPRI bead protocol (from Rohland/Reich; Genome Research), resulting in purification of DNA fragments between 200-800 bp.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
35802760
Reads aligned (%)
27.3
Duplicates removed (%)
66.9
Number of peaks
10306 (qval < 1E-05)

hg38

Number of total reads
35802760
Reads aligned (%)
28.7
Duplicates removed (%)
65.5
Number of peaks
10257 (qval < 1E-05)

Base call quality data from DBCLS SRA