Antigen

Antigen Class

Input control

Antigen

Input control

Cell type

Cell type Class

Blood

Cell type

Th17 Cells

MeSH Description

A subset of helper-effector T-lymphocytes which synthesize and secrete INTERLEUKINS IL-17; IL-17F; and IL-22. These cytokines are involved in host defenses and tissue inflammation in autoimmune diseases.

Sample

source_name

mouse primary CD4+ T cells

cell type

Th17

culture condition

9 day in vitro culture for Th17 cells, growth protocol1

chip antibody

input whole cell lysate

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 following the manufacturer's protocols.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

36948440

Reads aligned (%)

99.1

Duplicates removed (%)

24.6

Number of peaks

550 (qval < 1E-05)

mm9

Number of total reads

36948440

Reads aligned (%)

98.9

Duplicates removed (%)

24.7

Number of peaks

588 (qval < 1E-05)