title: birA_Rep1
organism: Mus musculus
description: Protocols: For ChIP assay,cells were cross-linked at room temperature for 2.5 min with 1% formaldehyde. Chromatin was prepared and sonicated on ice for 8 min using a Covaris S220 Focused-ultrasonicator. Samples were immunoprecipitated with antibodies (5-6μg) overnight at 4οC followed by incubation for 3 h with protein G Sepharose beads (Millipore) and washed sequentially. Primary MEFs were isolated from E13.5 animals and cultured in standard medium containing Dulbecco's modified Eagle medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 50μg/ml streptomycin, 50 U/ml penicillin (Sigma) and 2mM L glutamine (Gibco). : Cells were rinsed with PBS, exposed to tRA (10 μM) (Sigma-Aldrich) and cultured at 37oC for 16h, or to UVC irradiation (10 J/m2) and cultured at 37oC for 2h prior to fixation (2.5 min with 1% formaldehyde, at R.T.). The complexes were eluted and the crosslinking was heat reversed. Purified DNA fragments were analyzed by sequencing. Libraries were prepared by using the Illumina TruSeq DNA nano sample preparation Kit . After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified to create the final libraries. After validation (Agilent 2200 TapeStation) all libraries were individually quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-05-25T04:05:11Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-07-19T14:26:32Z
attributes.tag: External Id
attributes.value: SAMEA5799936
attributes.tag: INSDC center name
attributes.value: IMBB-FORTH
attributes.tag: INSDC first public
attributes.value: 2020-05-25T04:05:11Z
attributes.tag: INSDC last update
attributes.value: 2019-07-19T14:26:32Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8154:birA_Rep1
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: mouse embryonic fibroblast cell
attributes.tag: cell type
attributes.value: fibroblast
attributes.tag: common name
attributes.value: house mouse
attributes.tag: developmental stage
attributes.value: E13.5
attributes.tag: genotype
attributes.value: B6
attributes.tag: organism part
attributes.value: embryo
attributes.tag: sample name
attributes.value: E-MTAB-8154:birA_Rep1
attributes.tag: scientific_name
attributes.value: Mus musculus