characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2020-10-01T04:07:57Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2019-10-10T11:19:52Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA6062617
characteristics.characteristic: External Id
characteristics.text: UNIVERSITY OF MANCHESTER
characteristics.characteristic: INSDC center name
characteristics.text: 2020-10-01T04:07:57Z
characteristics.characteristic: INSDC first public
characteristics.text: 2019-10-10T11:19:52Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS3863742
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-8413:HaloReverba_ChIP-seq_ZT8_HOM_rep1
characteristics.characteristic: Submitter Id
characteristics.text: 9 to 13
characteristics.unit: week
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Liver tissue was collected from wildtype (n=2) and homozygous (n=3) HaloReverbα mice at ZT8 and from homozygous (n=2) HaloReverbα mice at ZT20, then flash-frozen in liquid nitrogen. A dual-crosslinking strategy was employed to capture tethered protein-protein-DNA interactions in addition to protein-DNA interactions. Frozen tissue was first homogenised in 2mM disuccinimidyl glutarate (DSG) (Thermo Fisher Scientific) using a handheld TissueRuptor (Qiagen) and rotated at room temperature for 15 minutes. After being spun down, the cell pellet was resuspended in 1% formaldehyde-PBS, rotated for a further 15 minutes, before glycine quenching with Stop Solution (Active Motif ChIP-IT High Sensitivity kit 53040). The cell pellet was washed and dounce-homogenised as per the standard Active Motif ChIP-IT kit instructions. It was then resuspended in 650μl of Mammalian Cell Lysis Buffer (Promega HaloChIP kit) supplemented with Protease Inhibitor Cocktail (Promega) and incubated on ice for 15 minutes before sonication at 20% amplitude for 8 cycles (30s on, 30s off, with 2 minutes of 'on' time per cycle), using the Active Motif EpiShear Probe Sonicator. Chromatin concentration was quantified with the Qubit BR dsDNA assay (Q32850, Thermo Fisher Scientific) and shearing efficacy checked with TapeStation electrophoresis (Agilent Technologies). For the pull-down step, 100μg chromatin, in a volume of 650μl Mammalian Cell Lysis Buffer, was rotated at room temperature with prepared HaloLink Resin (Promega) as per the Promega HaloChIP kit protocol. Wash and elution steps were also carried out as per the same manufacturer’s protocol, incorporating the recommended LiCl buffer wash step. ChIP DNA was cleaned up with the MinElute PCR Purification Kit (Qiagen) and quantified with the Qubit HS dsDNA assay (Thermo Fisher Scientific). Samples were not pooled; each biological replicate was taken forward individually to library preparation. Illumina TruSeq ChIP Library Preparation Kit, according to the manufacturer’s protocol
characteristics.characteristic: description
characteristics.text: adult
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001272
characteristics.characteristic: developmental stage
characteristics.text: HaloReverb homozygous
characteristics.characteristic: genotype
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: organism
characteristics.text: liver
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0002107
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000384
characteristics.characteristic: sex
characteristics.text: C57BL/6
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0004472
characteristics.characteristic: strain
characteristics.text: HaloReverba_ChIP-seq_ZT8_HOM_rep1
characteristics.characteristic: title