Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9me3

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/ATF7ip+/fl
strain
C57BL/6
chip antibody
H3K9me3 (Active Motif, cat# 39161, Lot# 2)

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
43860566
Reads aligned (%)
96.1
Duplicates removed (%)
15.3
Number of peaks
4867 (qval < 1E-05)

mm9

Number of total reads
43860566
Reads aligned (%)
95.8
Duplicates removed (%)
15.4
Number of peaks
4696 (qval < 1E-05)

Base call quality data from DBCLS SRA