Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Non-neuronal cells
NA
NA

Attributes by original data submitter

Sample

source_name
Non-neuronal nuclei from 20 month old SAHA-treated animals
cellular population
non-neuronal
strain
C57B/6JRj
chip antibody
none
age
20 months
genotype
WT
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
81668236
Reads aligned (%)
97.1
Duplicates removed (%)
15.3
Number of peaks
680 (qval < 1E-05)

mm9

Number of total reads
81668236
Reads aligned (%)
96.9
Duplicates removed (%)
15.2
Number of peaks
793 (qval < 1E-05)

Base call quality data from DBCLS SRA