The hollow, muscular organ that maintains the circulation of the blood.
Attributes by original data submitter
Sample
source_name
heart extract
strain
CD-1
chip antibody
none
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Ventricles from three P15 mouse hearts were used as biological triplicates for the ChIP-seq experiments. Tissue samples were ground to powder and crosslinked with 2% formaldehyde in PBS for 30 min and quenched with 0.125 M glycine for 10 min at room temperature. Crosslinked samples were then washed with cold PBS and further homogenized with a Dounce tissue grinder. Samples were collected by a brief spin, and treated with 10 mM Tris-HCl (pH 8.0), 10mM NaCl and 0.2% NP-40 for 30 min to collect nuclei. After nuclear extraction, chromatin was sheared on a Bioruptor Pico (Diagenode) for 20 cycles (30 sec on/ 30 sec off for each cycle) at 4°C in sonication buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.25% sarkosyl, 1 mM DTT, 1x cOmplete Protease Inhibitor Cocktail (Roche), and 200 µM PMSF, pH 8.0). After sonication, 1% of the sonicated chromatin from each sample was taken out as “input” samples. The remaining sonicated chromatin was evenly split for Meis1 or Hoxb13 ChIP. Sonication buffer was added to make the final volume to 1 mL. NaCl was then added to a final concentration of 300 mM for each sample. Antibody (anti-Meis1 Santa Cruz, sc-10599X, 1:200 or anti-Hoxb13 GeneTex, GTX129245, 1:100) was added to each sample and incubated at 4°C overnight with gentle rotation. The next day, 30 µL of pre-washed Dynabeads Protein G (Invitrogen, 10004D) was added to each sample for a two-hour incubation. After that, the beads were washed twice with 1 mL RIPA 0 buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, pH 8.0), twice with 1 mL RIPA 0.3 buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 300 mM NaCl, pH 8.0), twice with 1 mL LiCl wash buffer (250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0), and finally twice with 1 mL TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). For each ChIP sample or input sample, 100 uL of SDS elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0) was added and incubation was done at 65°C overnight on a ThermoMixer (Eppendorf) at 1000 rpm. The next day, supernatant was collected and further treated with 0.5 µg RNaseA (Sigma, 11119915001) for 30 min at 37°C, followed by 20 µg Proteinase K (NEB, P8107S) treatment at 37°C for 2h. DNA was recovered using MinElute PCR Purification Kit (QIAGEN, 28004) according to manufacturer's protocol. ChIP-Seq libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) according to manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 9-15 cycles. Final ChIP-Seq libraries were pooled and sequenced on an Illumina Nextseq 500 system using the 75bp high output sequencing kit for single-end sequencing