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
Embryonic cerebral cortex
developmental time
E15.5
tissue
Whole cortex lysate
genotype
Prdm16 flox/flox
chip-seq antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
PRDM16 ChIP-seq was carried out using dual chromatin crosslinking with PFA and EGS, followed by sonication and antibody precipitation. H3K27ac and H3K4me ChIP-seq were carried out using native chromatin digestion with microccocal nuclease, followed by antibody precipitation of DNA-histone complexes. For library preparation, genomic DNA was purified, end repaired, ligated with barcoded adaptors, amplified for 11 PCR cycles and purified using the Ovation Ultralow System V2 (NuGEN). Library fragments in the range of 100-800 bp were size-selected using agarose gel electrophoresis followed by DNA gel extraction and purification.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
60458240
Reads aligned (%)
98.6
Duplicates removed (%)
13.1
Number of peaks
644 (qval < 1E-05)

mm9

Number of total reads
60458240
Reads aligned (%)
98.3
Duplicates removed (%)
13.0
Number of peaks
697 (qval < 1E-05)

Base call quality data from DBCLS SRA