Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Embryo
Cell type
Embryonic limb
NA
NA

Attributes by original data submitter

Sample

source_name
Embryonic limb bud
tissue
Embryonic limb bud
genotype
WT
embryonic stage
E12.5
background
G4 ESC

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the respective antibody. We sheared chromatin using Bioruptor until reaching a fragment size of 200-500bp. 10-15μg of chromatin was then used for each replicate H3K27ac ChIP and 30μg for CTCF ChIP. Antibodies: H3K27ac (Diagenode, C15410174) and CTCF (Active motif: 613111) was then performed as in Ibrahim et al. 2013. Libraries were prepared using the Nextera adaptors and sequenced

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
30962103
Reads aligned (%)
98.5
Duplicates removed (%)
18.0
Number of peaks
15200 (qval < 1E-05)

mm9

Number of total reads
30962103
Reads aligned (%)
98.2
Duplicates removed (%)
18.0
Number of peaks
15189 (qval < 1E-05)

Base call quality data from DBCLS SRA