Antigen

Antigen Class

Histone

Antigen

H3K27ac

Cell type

Cell type Class

Blood

Cell type

CD4+ T cells

NA

NA

Sample

source_name

Pre-activated CD4+ T cells

strain

C57BL/6

tissue

Spleen

cell type

Pre-activated CD4+ T cells

treated with

none (untreated)

chip antibody

H3K27ac

chip antibody vendor

Abcam

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin from 2 × 107 cells was sonicated for 20 cycles of 12 sec on/48 sec off, into 200-500 bp fragments, DNA ends were repaired using polynucleotide kinase and Klenow enzyme, and treated with Taq polymerase to generate a protruding 3’ “A” nucleotide. DNA fragments of ~250-450 bp were purified from agarose gels and used for cluster generation and sequencing. Various Antibodies against STAT3, IRF4, H3K4me1, H3K4me3, H3K27me3, H3K27ac were used. PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform or on Illumina Genome Analyzer II.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

40216859

Reads aligned (%)

98.7

Duplicates removed (%)

32.4

Number of peaks

34133 (qval < 1E-05)

mm9

Number of total reads

40216859

Reads aligned (%)

98.6

Duplicates removed (%)

32.5

Number of peaks

34145 (qval < 1E-05)