Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Blood
Cell type
CD4+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
Synovial Fluid
diagnosis
JIA patient
tissue
Synovial Fluid
cell type
CD4+CD45RO+ T cells
chip antibody
anti H3K27ac (ab4729; Abcam)
in vitro activation
no

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 was purified using ChIP DNA Clean & Concentrator kit (Zymo Research), end-repair, a-tailing, and ligation of sequence adaptors was done using Truseq nano DNA sample preparation kit (Illumina). Samples were PCR amplified, checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and barcoded libraries were sequenced 75bp single-end on Illumina NextSeq500 sequencer.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
22330454
Reads aligned (%)
94.4
Duplicates removed (%)
3.3
Number of peaks
5775 (qval < 1E-05)

hg19

Number of total reads
22330454
Reads aligned (%)
93.8
Duplicates removed (%)
3.6
Number of peaks
5693 (qval < 1E-05)

Base call quality data from DBCLS SRA