Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryo
Cell type
Embryonic limb
NA
NA

Attributes by original data submitter

Sample

source_name
limb bud, hearts, branchial arches
developmental stage
E10.5
strain
NMRI
genotype/variation
wild type
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fore- and hindlimb buds, hearts and branchial arches of approximately 150 Hand2-3xFLAG embryos and 150 wild-type control embryos at E10.5 were collected in ice-cold PBS. Single nuclei suspensions were cross-linked for 5min with 1% formaldehyde and processed as described (Visel et al., 2009). The ChIP procedure was performed using established protocols with minor modifications (Kim et al. 2007, Lopez-Rios et al. 2012) Library was constructed using the DNA library Prep Kit (New England Biolabs). Following end repair and adaptor ligation, DNA fragments were size selected (200-250bp) by agarose gel electrophoresis and PCR amplified (18 cycles) using Illumina primers. After purification, samples were loaded on an Illumina flow cell for solid-phase amplification. SR50 sequencing of libraries was carried out on a HiSeq 2000 system (Illumina)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
240227388
Reads aligned (%)
87.3
Duplicates removed (%)
87.1
Number of peaks
57127 (qval < 1E-05)

mm9

Number of total reads
240227388
Reads aligned (%)
87.0
Duplicates removed (%)
87.2
Number of peaks
68658 (qval < 1E-05)

Base call quality data from DBCLS SRA