Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Neurons
MeSH Description
The basic cellular units of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the NERVOUS SYSTEM.

Attributes by original data submitter

Sample

source_name
Neuronal nuclei from 10 month old APP/PS1-21 SAHA-treated animals
cellular population
neuronal
strain
Tg(Thy1-APPSw,Thy1-PSEN1*L166P)21Jckr
chip antibody
none
age
10 months
genotype
APP/Ps1-21 transgenic
drug treatment
SAHA: (18g cyclodextrin + 0.67g SAHA)/L water

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were fixed, extracted in RIPA buffer, and sonicated to achieve an average fragment size of ~300bp. For ChIP 0.5µg of antibody were used with 500ng of chromatin Libraries were constructed according to standard Illumina protocols using NEB's kits Ultra DNA Library Prep Kit (Ref: E7370L) and Multiplex Oligos for Illumina Index Primer Set (E7335L)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
75744679
Reads aligned (%)
93.8
Duplicates removed (%)
14.8
Number of peaks
525 (qval < 1E-05)

mm9

Number of total reads
75744679
Reads aligned (%)
93.6
Duplicates removed (%)
14.7
Number of peaks
638 (qval < 1E-05)

Base call quality data from DBCLS SRA