Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Notch1

Cell type

Cell type Class
Blood
Cell type
RAW 264.7
Primary Tissue
Blood
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

source_name
Raw 264.7_mtDNA
cell line
RAW 264.7 (ATCC TIB-71)
cell type
macrophage-like; Abelson leukemia virus transformed
molecule subtype
mitochondrial DNA (mtDNA)
chip antibody
Anti-Notch1 antibody - ChIP Grade
chip antibody vendor
Abcam

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
LPS-treaetd M1 cells are firstly fixed in 1% final concentration of formaldehyde for 10 minutes. For mtDNA ChIP-seq, mitochondria are purified from the formaldehyde fixed cells. In both case, ChIP-isolated DNA fragments are carried out using the ChIP Assay Kit (Millipore # 17-295). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired and blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hi-Seq following the manufacturer's protocols.sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
31960811
Reads aligned (%)
3.8
Duplicates removed (%)
46.1
Number of peaks
8289 (qval < 1E-05)

mm9

Number of total reads
31960811
Reads aligned (%)
3.8
Duplicates removed (%)
46.9
Number of peaks
8245 (qval < 1E-05)

Base call quality data from DBCLS SRA