Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Neurospheres
NA
NA

Attributes by original data submitter

Sample

source_name
mouse neurospheres
genotype
p53-/-;p18-/-
chip antibody
Input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, 5-7 x 107 crosslinked cells were resuspended in 10 ml buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Sigma protease inhibitor) and incubated on ice for 10 minutes. Samples were pelleted at 1,350xg for 5 minutes, resuspended in 10 ml buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Sigma protease inhibitor) and incubated on ice for 10 minutes. Pelleted samples were resuspended in 2 ml Covaris sonication buffer (10 mM Tris-HCL, pH 8.0, 1 mM EDTA, 0.1% SDS, 1x Sigma protease inhibitor) and sonicated using a Covaris E220 focused ultrasonicator. Samples were diluted with 5 volumes of buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 1% Triton X-100, 1x Sigma protease inhibitor). Chromatin was subjected to ChIP using rabbit polyclonal antibodies. Libraries were prepared according to Illumina's instructions

Sequencing Platform

instrument_model
Illumina MiSeq

mm10

Number of total reads
14892010
Reads aligned (%)
98.6
Duplicates removed (%)
5.6
Number of peaks
321 (qval < 1E-05)

mm9

Number of total reads
14892010
Reads aligned (%)
98.5
Duplicates removed (%)
5.8
Number of peaks
327 (qval < 1E-05)

Base call quality data from DBCLS SRA