Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryo
Cell type
Embryonic heart
NA
NA

Attributes by original data submitter

Sample

source_name
embryonic heart
developmental stage
E12.5
strain
Black-Swiss
genotype
Wild-type
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
E12.5 mouse hearts were dissected and cross-linked in 1.5% of formaldehyde methanol-free for 10 minutes at room temperature. Samples were quenched by incubation with 2.5M glycine for 5 minutes. Hearts were ressuspended in lysis buffer (50 mM HEPES-KOH pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP40; 0.25% Triton X-100) and dounce homogenized for nuclei isolation. The cross-linked chromatin was sonicated in Shearing buffer (1mM EDTA; 10mM Tris-HCl pH 7.6; 0.1% SDS) using a Covaris S2 (2% Duty cycle, 3 Intensity; 200 cycles per burst; for 8 minutes) to an average size of 200 bp. Precleared chromatin extract was incubated overnight at 4°C with 4μg of rabbit anti-HIF-1α antibody (Novus) and immunoprecipitated with protein A–Sepharose beads. 10 ng of ChIP DNA was used to generate a standard Illumina sequencing library. libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina MiSeq

mm10

Number of total reads
31068764
Reads aligned (%)
97.4
Duplicates removed (%)
10.9
Number of peaks
663 (qval < 1E-05)

mm9

Number of total reads
31068764
Reads aligned (%)
97.2
Duplicates removed (%)
10.9
Number of peaks
758 (qval < 1E-05)

Base call quality data from DBCLS SRA