Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Macrophages
MeSH Description
The relatively long-lived phagocytic cell of mammalian tissues that are derived from blood MONOCYTES. Main types are PERITONEAL MACROPHAGES; ALVEOLAR MACROPHAGES; HISTIOCYTES; KUPFFER CELLS of the liver; and OSTEOCLASTS. They may further differentiate within chronic inflammatory lesions to EPITHELIOID CELLS or may fuse to form FOREIGN BODY GIANT CELLS or LANGHANS GIANT CELLS. (from The Dictionary of Cell Biology, Lackie and Dow, 3rd ed.)

Attributes by original data submitter

Sample

source_name
Bone marrow derived macrophage- stimulated 60'
cell type
Bone marrow derived macrophage
small molecule inhibitor treatement
-
strain
C57BL/6
chip antibody
input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslinking ChIP was performed as described in (Lee et al. 2006)1 with slight modifications. Chromatin shearing was performed with a Covaris S2 focused-ultrasonicator using settings (time 20 min, duty cycle 5%, intensity 4, cycles per burst 200, temperature 4C, power mode frequency sweeping, degassing mode continuous). Immunoprecipitation was performed using 15 ug of antibody bound to 100 uL of Dynabead Protein A magnetic beads. DNA purification after immunoprecipitation and decrosslinking was perfomed using the QIAGEN Qiaquick PCR purification kit. RNA was isolated from 1x106 or more BMDM cells using the RNeasy Mini Kit (Qiagen, Gaithersburg, MD) and then samples were prepared as instructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA). H3S28p antibody: MABE13 (Millipore); H3K27ac antibody: Active Motif (39133). Eluted DNA was used to construct sequencing libraries using the Illumina TruSeq ChIP Sample Prep Kit. 50 cycle, single-end read sequencing was performed with the Illumina HiSeq 2000. Illumina adapters # 5,8,12,16 were used to 4-plex all samples into groups of 4/sequencing lane.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
58171064
Reads aligned (%)
94.7
Duplicates removed (%)
14.5
Number of peaks
646 (qval < 1E-05)

mm9

Number of total reads
58171064
Reads aligned (%)
94.4
Duplicates removed (%)
14.4
Number of peaks
714 (qval < 1E-05)

Base call quality data from DBCLS SRA