Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Hoxa13

Cell type

Cell type Class
Embryo
Cell type
Embryonic limb
NA
NA

Attributes by original data submitter

Sample

source_name
E11.0 autopod
strain/background
ICR
genotype/variation
WT
tissue
autopod
developmental stage
E11.0
chip antibody
Hoxa13 (home-made)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed according to a standard protocol (Cold Spring Harbor, NY) with the following modifications. Whole limb buds from E11.5 and the autopod from E11.0 wild type ICR mice were dissected in ice-cold PBS. Embryonic tissues were homogenized 13 times with a Dounce homogenizer, then fixed in 1% formaldehyde/PBS for 10minutes at 4C and quenched with 0.1 M glycine. The cross-linked material was sonicated to produce 200-1000 bp fragments with a DNA Shearing System S2 (Covaris). The immunoprecipitations were performed with 11 pairs of autopods from E11.0 embryos, whole limb buds from a litter of E11.5 embryos. PierceTM Protein A/G magnetic beads (Thermo Scientific) were conjugated to each antibody. Sonicated chromatin was incubated with the prepared protein A/G beads overnight at 4C with rotation. 10 ug of anti-Hoxa13 or 8 ug of anti-Hoxa11 were used for each experiment. E12.5 ChIP-Seq was performed as described previously (Beccari et al. 2016. Genes Dev. 30, 1172-1186). Anti-Hoxa13 antibody: Yamamoto et al. Development 125, 1325-1335 and Beccari et al. 2016. Genes Dev. 30, 1172-1186. Anti-Hoxa11 antibody: Yamamoto et al. Development 125, 1325-1335 and manuscript in preparation. The E11.0 and E11.5 libraries were prepared using NEB Next UltraTM DNA Library Prep kit for Illumina (NEB) according to the manufacturer's protocol. The E12.5 libraries were prepared as described previously (Beccari et al. 2016. Genes Dev. 30, 1172-1186).

Sequencing Platform

instrument_model
Illumina Genome Analyzer

mm10

Number of total reads
73263862
Reads aligned (%)
98.2
Duplicates removed (%)
54.4
Number of peaks
1322 (qval < 1E-05)

mm9

Number of total reads
73263862
Reads aligned (%)
98.1
Duplicates removed (%)
54.5
Number of peaks
1489 (qval < 1E-05)

Base call quality data from DBCLS SRA