Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Th1 Cells
MeSH Description
A subset of helper-inducer T-lymphocytes which synthesize and secrete INTERLEUKIN-2; INTERFERON-GAMMA; and INTERLEUKIN-12. Due to their ability to kill antigen-presenting cells and their lymphokine-mediated effector activity, Th1 cells are associated with vigorous delayed-type hypersensitivity reactions.

Attributes by original data submitter

Sample

source_name
Five-day cultured Th1 cells generated from primary splenic CD4_T cells
strain
C57BL/6
cell type
Th1 cell
chip antibody
Mouse IgG1 Isotype Control Ab (Southern Biotech, catalog# 0102-01, lot# JC044-V877)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. IP and input sample libraries were prepared using ChIP-Seq Sample Prep kit (Illumina). Adaptor-ligated DNA fragments were size fractionated by 12% acrylamide gel, and the 170- to 250-bp fraction was recovered. DNA thus obtained was amplified by 18 cycles of PCR. One nanogram of DNA was used for the sequencing reaction of the Illumina GAIIx or Illumina Hiseq 2500, according to the manufacturer’s instructions. A total of 250,000–370,000 clusters was generated per tile, and 36 cycles of the sequencing reactions were performed.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
39074441
Reads aligned (%)
71.8
Duplicates removed (%)
47.5
Number of peaks
817 (qval < 1E-05)

mm9

Number of total reads
39074441
Reads aligned (%)
71.7
Duplicates removed (%)
47.6
Number of peaks
901 (qval < 1E-05)

Base call quality data from DBCLS SRA