Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
Non-neuronal nuclei from 10 month old vehicle-treated WT littermates of APP/PS1-21 animals
cellular population
non-neuronal
strain
Tg(Thy1-APPSw,Thy1-PSEN1*L166P)21Jckr
chip antibody
none
age
10 months
genotype
WT
drug treatment
Vehicle: 18g cyclodextrin/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
33603067
Reads aligned (%)
96.2
Duplicates removed (%)
16.1
Number of peaks
449 (qval < 1E-05)

mm9

Number of total reads
33603067
Reads aligned (%)
96.0
Duplicates removed (%)
16.1
Number of peaks
498 (qval < 1E-05)

Base call quality data from DBCLS SRA