characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-03-30T17:02:25Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-02-28T15:31:59Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA101359918
characteristics.characteristic: External Id
characteristics.text: Linkoping University Dept. Clinical and Experimental Medicine Center for Social and Affective Neuroscience
characteristics.characteristic: INSDC center name
characteristics.text: 2017-03-30T17:02:25Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-02-28T15:31:59Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1573261
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5503:ChIP
characteristics.characteristic: Submitter Id
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: Brains from eighteen adult C57BL/6J(JAX) male mice (13-14 weeks old) were frozen in -80oC isopentane after cervical dislocation. 1.0 mm micro-punches were taken from the ventrolateral and dorsolateral striatum, excluding the lateral septal nucleus, but included nuclueus accumbens and most of caudate putamen; main area containing d1/2 dopamine receptors in striatum (http://www.brain-map.org/). ChIP protocols have been described elsewhere but here we applied it to individual animals; Feng J., Wilkinson M., Liu X., et al. (2014) Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biology 15, and Dias C., Feng J., Sun H et al. (2014) β-catenin mediates behavioral resilience through Dicer1/microRNA regulation. Nature 516. Frozen punches were crosslinked in with a protease inhibitor (pi) in PBS and 1% formaldehyde buffer, and after 12 min quenched with 0.125 M glycine. After washes in ice cold pi-PBS, punches were homogenized in pi-SDS lysis buffer (1%) by aspirating the punches 15 times through a syringe needle (22 gauge). An ice chilled Bioruptor standard (Diagenode) cycled 9x5 min (30 s on 30 s off; high power) was used to fragment the chromatin. Immunoprecipitation (IP) was done at 4oC overnight using the Egr-1 Antibody (C-19) X (Santa Cruz Biotechnology) bound to Dynabeads M-280 Sheep anti-Rabbit IgG (Life technologies) in diluted pi-SDS/Triton X-100 buffer. IP samples were washed in ice-cold Hepes/LiCl RIPA buffer on a magnetic rack, with a final wash in salty 1xTE buffer (with 50mM NaCl), before elution in SDS buffer. Release and decrosslinking was performed adding RNase A (1h, 37oC) and Proteinase K (2h, 55oC), followed by QiaQuick (Qiagen) clean up. IP and Input samples were treated identically but Input did not went through overnight immunoprecipitation and was pooled prior to library preparation. NEBNext Ultra™ DNA Library Prep Kit (New England Biolabs) with NEBNext Multiplex Oligos (New England Biolabs) for Illumina was used for library preparation according to manufacturer’s recommendations. Concentrations and fragment sizes were verified using High sensitivity DNA BioAnalyzer chips (Agilent). Barcoded libraries were calibrated to same concentrations, pooled, agaros gel size selected (mean fragment length of 350+/-150bp) and cleaned using QiaQuick (Qiagen).
characteristics.characteristic: description
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: amygdala
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0001876
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: C57BL6J
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000606
characteristics.characteristic: strain
characteristics.text: ChIP
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0002692
characteristics.characteristic: title