Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Naive T cells
NA
NA

Attributes by original data submitter

Sample

source_name
Naive T cells from spleen and nodes
strain
C57/Bl6j
age
7 weeks
genotype/variation
Wild-type
cell type
CD4 T cells
chip antibody
anti-Ig (Dako, catalog# X0936, lot# 73343)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslinking, extraction and shearing of chromatin was performed by using the Truchip chromatin shearing reagent kit from 300,000 Th2 cells by following manufacturer protocol. Then, sheared chromatin was immunoprecipitated with different antibodies by using the Active Motif's ChIP IT Kit by following manufacturer's instructions Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina. After library validation on a fragment analyzer, the purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina MiSeq

mm10

Number of total reads
1057390
Reads aligned (%)
86.3
Duplicates removed (%)
25.1
Number of peaks
49 (qval < 1E-05)

mm9

Number of total reads
1057390
Reads aligned (%)
85.9
Duplicates removed (%)
26.9
Number of peaks
35 (qval < 1E-05)

Base call quality data from DBCLS SRA