Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Tfap4

Cell type

Cell type Class
Blood
Cell type
Germinal Center
MeSH Description
The activated center of a lymphoid follicle in secondary lymphoid tissue where B-LYMPHOCYTES are stimulated by antigens and helper T cells (T-LYMPHOCYTES, HELPER-INDUCER) are stimulated to generate memory cells.

Attributes by original data submitter

Sample

source_name
Germinal center light zone cells
strain
C57BL/6
chip antibody
anti-AP4 (in house)
tissue
lymph node
cell type
Germinal center light zone cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cells were fixed with 1% paraformaldehyde for 10 minutes at room temperature. Soluble chromatin was prepared as described by Ciofani et al (Cell,2012, PubMed ID: 23021777), and immunoprecipitated with antibodies. Immunoprecipitated DNA and input DNA were used for library preparation according to the Illumina ChIP-seq protocol. After end-repair and indexed adapter ligation, fragments were size-selected using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) prior to amplification. The size-selected and amplified fragment libraries were verified on a 2100 Bioanalyzer (Agilent) prior to being pooled and sequenced.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
21705549
Reads aligned (%)
91.4
Duplicates removed (%)
50.8
Number of peaks
9876 (qval < 1E-05)

mm9

Number of total reads
21705549
Reads aligned (%)
91.2
Duplicates removed (%)
51.0
Number of peaks
9864 (qval < 1E-05)

Base call quality data from DBCLS SRA