Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Dendritic Cells
MeSH Description
ANTIGEN-PRESENTING CELLS of dendritic cell morphology found in the LYMPH NODES and other lymphoid tissues.

Attributes by original data submitter

Sample

source_name
Dendritic cells
strain
C57BL/6
genotype
Mbd2 -/-
chip antibody
none (input)
tissue
bone marrow
cell type
dendritic

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Bone Marrow Dendritic Cells (BMDCs) cells were crosslinked with 1% formaldehyde at room temperature for 10 min, followed by 5 min incubation with 125mM glycine. Chromatin was sheared by sonication and protein-DNA complexes were immunoprecipitated with an anti_H3K9,K14ac antibody (Milipore) and the DNA was subsequently extracted. ChIP DNA was end repaired by incubation at 20°C for 30 min with 3 U of T4 DNA Polymerase (NEB), 10 U of Polynucleotide Kinase (NEB), 2 U DNA Polymerase I Large (Klenow) fragment (NEB), 1x T4 DNA ligase reaction buffer (NEB) and 400 nM dNTPs. The enzymes were then heat inactivated at 75ºC for 20 min, after which the DNA was ethanol precipitated. A tail of 'A' bases was added to the 3’ ends of the DNA by incubation with 5 U Klenow Fragment (3’-5’ exo-; NEB), 200nM dATP and 1x buffer 2 (NEB) at 37°C for 30 min. The enzymes were heat inactivated and cleaned up as before .Barcoded Ilumina paired end adaptors were then ligated to the processed ChIP DNA by incubation with 300 U of T4 DNA ligase (NEB), 1x T4 DNA ligase buffer (NEB), 7.5% PEG-6000 and 2 pmol of annealed Illumina adaptors for 3 hr at room temperature. Ligated DNA was purified using MinElute PCR columns (Qiagen) and eluted in 10 μl water. Ligated DNA was amplified by 16-18 cycles of PCR with primers complementary to the adaptor sequences and Phusion 2x premix (Finnzymes). The DNA was purified using QIAquick PCR Purification columns (Qiagen).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
128660112
Reads aligned (%)
86.9
Duplicates removed (%)
13.1
Number of peaks
681 (qval < 1E-05)

mm9

Number of total reads
128660112
Reads aligned (%)
86.8
Duplicates removed (%)
13.2
Number of peaks
655 (qval < 1E-05)

Base call quality data from DBCLS SRA