Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BCL6

Cell type

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

Attributes by original data submitter

Sample

source_name
Primary CXCR5hi CD4 T cells isolated from human tonsils
tissue
tonsil
cell type
CXCR5hi PD1hi CD45RO+ CD4+ T cells, CD19-
antibody
BCL6 (Santa Cruz, sc-858)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Tfh cell sorts were initially gated on CD4+CD19-, then CD45RO+, then as CXCR5hi (GC Tfh). The following anti-human Abs were used: CD45RO (clone UCHL1), CD19 (clone HIB19), CD4 (clone RPA-T4) (eBioscience, San Diego, CA); CXCR5 (clone RF8B2). GC Tfh (CXCR5hi PD1hi CD45RO+ CD4+ T cells, CD19‑) were isolated from human tonsils, fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Chromatin immunoprecipitation was performed by incubation of the chromatin with antibodies against BCL6 (Santa Cruz, sc-858), H3K4me3(Abcam, ab8580), H4K4me1(Abcam, ab8895) and H3K27ac (Abcam, ab4729). Immunocomplexes were pulled down using protein A beads and after increasing stringency washes 10ng of ChIP DNA was recovered and used to generate a BCL6 ChIP-seq library according to Illumina ChIP-seq Library preparation Kit. A negative control library was prepared in parallel using 10ng of input chromatin DNA. Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Both libraries were sequenced using HiSeq 2000 for 50 cycles.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
183197598
Reads aligned (%)
30.7
Duplicates removed (%)
65.5
Number of peaks
10920 (qval < 1E-05)

hg38

Number of total reads
183197598
Reads aligned (%)
32.1
Duplicates removed (%)
64.3
Number of peaks
11607 (qval < 1E-05)

Base call quality data from DBCLS SRA