Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Runx3

Cell type

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

Attributes by original data submitter

Sample

source_name
Splenic CD8+ T cells
cell type
Splenic CD8+ T cells
passages
Collected from 18 mice. Cells were freshly isolated, fixed and frozen at -80°C.
strain
ICR
chip antibody
Runx3 poly clonal home made

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 48ul of anti-Runx3 Ab, anti-H3K4me1 or NIS were added to 12 mL of diluted, fragmented chromatin. DNA was purified using QIAquick spin columns (QIAGEN). For ChIP-seq analysis, ChIP-seq libraries were prepared using the ChIP-Seq sample preparation kit (IP-102-1001, illumina) according to the manufactures instructions. Illumina sequencing was performed using Illumina genome analyzer IIx according to the manufactures instructions by loading 15 pM of denatured library template onto separate lanes of a flow cell. Sequencing short reads (40-42 bp) were aligned to the mouse genome (mmp9) using the ELAND program (Illumina).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
7809314
Reads aligned (%)
92.9
Duplicates removed (%)
39.0
Number of peaks
111 (qval < 1E-05)

mm9

Number of total reads
7809314
Reads aligned (%)
92.5
Duplicates removed (%)
39.3
Number of peaks
145 (qval < 1E-05)

Base call quality data from DBCLS SRA