Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZNF341

Cell type

Cell type Class
Blood
Cell type
PBMC
Tissue
blood
Lineage
mesoderm
Description
peripheral blood mononuclear cells

Attributes by original data submitter

Sample

source_name
EBV (Patient 4)_ZNF341 isoform 1
patient diagnosis
hyper-IgE syndrome (HIES)
cell type
EBV-B
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
79331678
Reads aligned (%)
70.5
Duplicates removed (%)
27.5
Number of peaks
4349 (qval < 1E-05)

hg38

Number of total reads
79331678
Reads aligned (%)
72.9
Duplicates removed (%)
26.1
Number of peaks
4586 (qval < 1E-05)

Base call quality data from DBCLS SRA