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
Lymph nodes and spleen
cell type
Naive T Lymphocytes
genotype
CD4-Cre/ATF7ipfl/fl
strain
C57BL/6
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer ChIP-Seq and subsequent data analysis was performed by Active Motif. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500 (75 nt reads, single end).

Sequencing Platform

instrument_model
Illumina Genome Analyzer

mm10

Number of total reads
39845811
Reads aligned (%)
98.0
Duplicates removed (%)
8.0
Number of peaks
563 (qval < 1E-05)

mm9

Number of total reads
39845811
Reads aligned (%)
97.9
Duplicates removed (%)
8.1
Number of peaks
532 (qval < 1E-05)

Base call quality data from DBCLS SRA