characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-05-15T17:01:33Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-03-08T15:32:14Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA103898516
characteristics.characteristic: External Id
characteristics.text: Laboratory for Translational Genetics VIB Center for Cancer Biology (CCB) Department of Human Genetics, KULeuven
characteristics.characteristic: INSDC center name
characteristics.text: 2017-05-15T17:01:33Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-03-08T15:32:14Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1587684
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5562:BT1137
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: ESC derived cell line
characteristics.characteristic: cell line
characteristics.text: epiblast-like cells
characteristics.characteristic: cell type
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: WT cells were collected from a B6 incipient congenic (N5; >95% B6) blastocyst-derived embryonic stem cell line (wt) converted in vitro to epiblast-like cells. homozygous cells for Tet1 gene trap GT(RRG140) were collected from B6 incipient congenic (N5; >95% B6) blastocyst-derived embryonic stem cell line (KO) converted in vitro to epiblast-like cells. Cells were trypsinized and fixed in freshly prepared 1% para-formaldehyde at room temperature for 10 min and quenched with 1.25M glycine. Nuclei were isolated and chromatin was sheared to 200-500bp using Bioruptor sonicator for 20 cycles (30s ON, 30s OFF). Sheared chromatin was immunoprecipated using appropriate antibody and incubated overnight with Dyna beads Protein G (10004D). Immunocomplexes were washed for 5 minutes each with the following buffers: 1X low salt buffer (20mM Tris pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), 1X high salt buffer (20mM Tris pH 8.1, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), 1X LiCl buffer (10mM Tris pH 8.1, 250mM LiCl,1mM EDTA, 1% deoxycholate, 1% NP-40) and 2X TE buffer (+ 50mM NaCl). Chromain was eluted with elution buffer (50 mM Tris-Hcl, pH 8.0, 10 mM EDTA and 1% SDS) and reverse cross-linked by incubation at 65 °C in 5M NaCl buffer over night. DNA was purified using Zymo ChIP DNA Clean & Concentrator Kit (D5205) for library preparation. Library was prepared using NEBNext Ultra DNA Library Prep Kit and sequenced on an Illumina HiSeq 2500
characteristics.characteristic: description
characteristics.text: pPyCAGIP empty vector
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: 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.characteristic: strain
characteristics.text: BT1137
characteristics.characteristic: title