characteristics.text: 2024-01-01
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec, Canada.  Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, Canada. 3 Cancer Research Centre, Laval University, Quebec, Canada.
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS18296917
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13818:ChIP_C8Dox0-RPI_Rep1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: Clone8
characteristics.characteristic: cell_line
characteristics.text: mouse embryonic fibroblast cell
characteristics.characteristic: cell_type
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 or 100 base single-end or paired-end sequencing on an Illumina HiSeq 4000 or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre).
characteristics.characteristic: description
characteristics.text: embryonic stage 14
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.characteristic: disease
characteristics.text: TTF1-/-//Neo+Tre3G-3FLAGmTTF1
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: ≥ 7 days DMEM 10%FBS
characteristics.characteristic: growth condition
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: embryonic structure
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: ChIP_C8Dox0-RPI_Rep1
characteristics.characteristic: title