Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
CD8+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
In vitro effector CD8+ T cells
cell type
Day 3 in vitro activated effector CD8+ T cells
mouse strain
P14 TCR transgenic C57Bl/6
chip antibody
Normal Rabbit IgG (Life Technologies, 10500C, Lot 939223A)
nebnext index for illumina barcode
NEBNext Index 2 (CGATGT)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
In vitro effector CD8+ T cells were fixed with 1% formaldehyde and flash frozen at -80°C. The fixed cells were lysed and the chromatin was sheared using a Covaris E210 Ultrasonicator. Transcription factor-DNA and histone-DNA complexes were immunoprecipitated and then eluted from magnetic beads. The formaldehyde crosslinks were reversed, and the ChIP DNA fragments were purified. ChIP DNA was prepared for high-throughput Illumina sequencing using the NEBNext ChIP-Seq Library Master Mix Set for Illumina kit and the NEBNext Multiplex Oligos for Illumina kit according to a modified manufacturer's protocol. For each ChIP or input sample, 10-50 ng of DNA was used to prepare a sequencing library. The DNA fragments were end-repaired, dA-tailed, and ligated to illumina adaptors according th the kit instructions. DNA fragments of 150-600 bp in length were then selected using Pippin Prep 2% Agarose Gel Cassettes and the Pippin Prep DNA Size Selection System. The ChIP DNA was then amplified with 12 PCR cycles using the NEBNext Multiplex Oligos. Amplifed DNA was purfied using a 1:1 ratio of DNA to Agencort AMPure XP beads.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
34606332
Reads aligned (%)
96.0
Duplicates removed (%)
16.1
Number of peaks
551 (qval < 1E-05)

mm9

Number of total reads
34606332
Reads aligned (%)
95.8
Duplicates removed (%)
16.0
Number of peaks
609 (qval < 1E-05)

Base call quality data from DBCLS SRA