Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZNF341

Cell type

Cell type Class
Blood
Cell type
T cells
NA
NA

Attributes by original data submitter

Sample

source_name
T cells (Patient 4) with T-Cell Receptor stimulation (anti-CD3 + anti-CD28)
patient diagnosis
hyper-IgE syndrome (HIES)
cell type
T cells
antibodies
Anti-ZNF341 (8B3.1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-Seq, total RNA extracted using the RNeasy Mini Kit (Qiagen). Poly(A)+ RNA was selected twice from total RNA using Dynal oligo magnetic beads (Invitrogen). Double-stranded cDNA was synthesized using SuperScript (Invitrogen) and fragmented using Bioraptor (Diagenode). Adaptors (Illumina) were ligated to the dsDNA using T4 DNA ligase (New England Biolabs) after end-repair using End-It kit (Epicentre) and dA addition. Libraries were size-selected for 250-400 bp fragments, purified using 2% E-Gel (Invitrogen), and amplified for 18 cycles by PCR with PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix. For ChIP-Seq, chromatin was isolated from 10 million cells, after cross-linking with 1% methanol-free formaldehyde (Thermo Fisher Scientific). Chromatin was fragmented by sonication and subjected to immunoprecipitation with 10 µg of either mouse IgG (Santa Cruz Biotechnology, Dallas TX) or mouse monoclonal anti-ZNF341 (8B3.1) antibodies prebound to Magna ChIPTM Protein A+G Magnetic Beads (Millipore, Billerica MA). The immunoprecipitate was washed and cross-linked, and ChIP-Seq DNA libraries were then prepared with the fragmented DNA and the KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
74991804
Reads aligned (%)
69.2
Duplicates removed (%)
29.1
Number of peaks
1816 (qval < 1E-05)

hg38

Number of total reads
74991804
Reads aligned (%)
71.7
Duplicates removed (%)
27.2
Number of peaks
1545 (qval < 1E-05)

Base call quality data from DBCLS SRA