Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Microglia
MeSH Description
The third type of glial cell, along with astrocytes and oligodendrocytes (which together form the macroglia). Microglia vary in appearance depending on developmental stage, functional state, and anatomical location; subtype terms include ramified, perivascular, ameboid, resting, and activated. Microglia clearly are capable of phagocytosis and play an important role in a wide spectrum of neuropathologies. They have also been suggested to act in several other roles including in secretion (e.g., of cytokines and neural growth factors), in immunological processing (e.g., antigen presentation), and in central nervous system development and remodeling.

Attributes by original data submitter

Sample

source_name
HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre_Input
strain background
C57BL/6
genotype/variation
HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre
cell type
FACS sorted microglia
chip antibody
none (input DNA)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Mice were sacrificed at an age of 6 weeks and microglia were isolated by FACS sorting of brain homogenate for CD11bhi CD45lo cells. Sequencing library preparation was performed using the KAPA Library Preparation Kit with Real-time PCR Library Amplification for Illumina Platforms Kit (Kapa Biosystems) as per the manufacturer's protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
47546150
Reads aligned (%)
97.9
Duplicates removed (%)
18.8
Number of peaks
250 (qval < 1E-05)

mm9

Number of total reads
47546150
Reads aligned (%)
97.6
Duplicates removed (%)
19.9
Number of peaks
260 (qval < 1E-05)

Base call quality data from DBCLS SRA