Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Embryo
Cell type
Metanephros
NA
NA

Attributes by original data submitter

Sample

source_name
E13.5 metanephros
genotype
HoxD inv(11-12)d13lacZ/inv(11-12)d13lacZ
strain
B6CBAF1
embryonic age
E13.5
antibody
anti-H3K4me3 (17-614, Millipore)
tissue
metanephros

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP were produced from E13.5 metanephros. Pairs of metanephros were individually fixed in 1% Formaldehyde for 20 minutes at room temperature and stored at -80°C. Genotyping was done on tail biopsies. Shearing was performed on a Bioruptor (Diagenod) in 1% SDS. ChIP was done by over-night incubation of protA/protG magnetic beads conjugated with the desired antibody in 1.2ml dilution buffer, rotating at 30 rpm 4°C. Washes were performed in 1ml of washing buffers, incubated at 4°C for 2 minutes: 2x RIPA/2x RIPA-500mM NaCl/2x LiCl/2x TE. Beads were eluted and chromatin fixation was reversed during an over-night incubation at 65°C in presence of proteinase K. The eluate was treated with RNase A, PCI purified and precipitated. 5-10 ng of purified DNA were used to built libraries according to the manufacturer's protocol (Illumina). The material was sequenced with 100 bp single-end reads on the Illumina HiSeq according to the manufacturer's specifications.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
29384564
Reads aligned (%)
93.2
Duplicates removed (%)
41.2
Number of peaks
20435 (qval < 1E-05)

mm9

Number of total reads
29384564
Reads aligned (%)
93.2
Duplicates removed (%)
41.3
Number of peaks
20426 (qval < 1E-05)

Base call quality data from DBCLS SRA