organism: Mus
description: Protocols: All mice were housed in the same husbandry conditions within the Biological Resources Unit in the Cancer Research UK-Cambridge Institute under a Home Office Licence. C57BL/6J and CAST/EiJ mouse strains were used in experiments as parental strains (F0) as well as for breeding of reciprocal crosses of F1 mice. All mice used in the experiments were males between eight and 12 weeks of age, and harvested at the same time of day (between 8 and 11am). Liver perfusion was performed on mice post mortem, prior to tissue dissection. Harvested tissues were formaldehyde cross-linked for ChIP-seq experiments. Before cross-linking, dissected tissue was immediately chopped post mortem and added to a cross-linking solution containing 1% formaldehyde. Tissue was incubated for 20 min prior to quenching with 1/20th volume of 2.5 M glycine. Samples were incubated for a further 10 min before washing with PBS and flash-freezing and storage at -80oC. The ChIP-seq protocol was as described by Schmidt et al. (2009). Protein-bound DNA was immunoprecipitated with 10g of an antibody against CEBPA (Santa Cruz, sc-9314), HNF4A (ARP 31946_P050), FOXA1 (ab5089, Abcam), H3K27ac (ab4729, Abcam), or H3K4me3 (Millipore 05-1339). Immunoprecipitated DNA was end-repaired, A-tailed, and Illumina sequencing adapters ligated before 16 cycles of PCR amplification.
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism
attributes.value: Mus
attributes.tag: development stage
attributes.value: 8 - 12 weeks
attributes.tag: genetic modification
attributes.value: none
attributes.tag: genotype
attributes.value: C57BL/6J
attributes.tag: individual
attributes.value: mm10BL6100279
attributes.tag: organism part
attributes.value: liver
attributes.tag: sex
attributes.value: male
attributes.tag: strain
attributes.value: mus musculus