Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryo
Cell type
Embryonic brains
NA
NA

Attributes by original data submitter

Sample

source_name
Neurons
strain
C57BL/6
cell type
neurons from E16.5 cortex
protocol
cultured for 7 days
genotype
WT
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For cultured neurons, cells were fixed on plate with 1% formaldehyde, nuclei were isolated and then sonicated by bath ultrasonicator (Bioruptor). Lysates were clarified and DNA-histone complexes were isolated by either anti-H3K4me3 (Active motif 39159) or H3K27ac (Active motif 39133) immobilized by protein A dynabeads (Life). Purified DNA was prepared for sequencing with the TruSeq ChIP sample Prep Kit (Illumina) as per manufacturer's instructions. Libraries were sequenced on either HiSeq2000 (Illumina) with 50bp single reads or NextSeq500 with 75bp single reads.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
55612545
Reads aligned (%)
95.7
Duplicates removed (%)
0.5
Number of peaks
303 (qval < 1E-05)

mm9

Number of total reads
55612545
Reads aligned (%)
95.4
Duplicates removed (%)
0.3
Number of peaks
327 (qval < 1E-05)

Base call quality data from DBCLS SRA