Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Cortical neuron
NA
NA

Attributes by original data submitter

Sample

source_name
Primary culutured mouse cortical neurons (DIV 8)
antibody
none
treatment
Non-stimulated control
strain
C57BL/6J

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIPs for H3K9me3S10ph and Atrx were performed with approximately 2x107 neurons per sample in biological triplicates/group. Primary cortical neurons +/- isotonic KCl stimulation (5 hr) were crosslinked with 1% paraformaldehyde (PFA) for 12 min at room temperature and then quenched for five min with 0.125 M glycine. Pelleted cells were washed 5X with 1X PBS containing protease inhibitors before being subjected to lysis, sonication, IP (7.5 μg antibody per sample was used) and DNA purification, as previously described. Following DNA purification, ChIP-seq libraries were prepared according to the Illumina protocol and sequenced with the HiSeq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
41829496
Reads aligned (%)
74.7
Duplicates removed (%)
65.5
Number of peaks
445 (qval < 1E-05)

mm9

Number of total reads
41829496
Reads aligned (%)
74.6
Duplicates removed (%)
65.6
Number of peaks
468 (qval < 1E-05)

Base call quality data from DBCLS SRA