Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Neural
Cell type
Prefrontal Cortex
MeSH Description
The rostral part of the frontal lobe, bounded by the inferior precentral fissure in humans, which receives projection fibers from the MEDIODORSAL NUCLEUS OF THE THALAMUS. The prefrontal cortex receives afferent fibers from numerous structures of the DIENCEPHALON; MESENCEPHALON; and LIMBIC SYSTEM as well as cortical afferents of visual, auditory, and somatic origin.

Attributes by original data submitter

Sample

source_name
wild-type mice
strain
C57BL/6
tissue
prefrontal cortex
age
5-6 months old

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
PFC slices were punched from two wild-type mice, two FAD mice and two BIX01294-treated FAD mice, and cross-linked with 1% formaldehyde for 12 min at room temperature. Glycine was used to quench the cross-link. After washing, the tissues were homogenized and sonicated to get sheared chromatin. The library preparations were sequenced on an Illumina Hiseq platform and 50 bp single-end reads or 150 bp paired-end reads were generated.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
16463293
Reads aligned (%)
83.6
Duplicates removed (%)
20.5
Number of peaks
290 (qval < 1E-05)

mm9

Number of total reads
16463293
Reads aligned (%)
83.5
Duplicates removed (%)
20.5
Number of peaks
243 (qval < 1E-05)

Base call quality data from DBCLS SRA