characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-07-19T17:02:02Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-09-22T09:51:54Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104313294
characteristics.characteristic: External Id
characteristics.text: NSERM UMR1163, Laboratory of Normal and Pathological Homeostasis of the Immune System, Paris, France
characteristics.characteristic: INSDC center name
characteristics.text: 2018-07-19T17:02:02Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-09-22T09:51:54Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1938272
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5940:H3K27ac_C2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: B cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000236
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Original B-lymphobast cells come from peripheral blood mononuclear cells (PBMC). These cells are obtained from blood samples after ficoll separation. PBMC from controls and patients were transduced with the Epstein Barr Virus (EBV) to generate the B-lymphobast cells lines. Cells were expanded and frozen. The B-lymphobast are cultured in medium composed of RPMI, Glutamine, Fetal bovin serum and penicillin-streptomycin. B-lymphoblastoid cell lines transformed with EBV of 3 controls (C1 to C3) and 3 TTC7A deficient patients (P3_E71K, P4_E71K, P*/L478P) were cultured in RPMI medium 1640+Glutamax (Gibco, ref 61870-010) supplemented with 10% (vol/vol) Fetal Bovine Serum (Gibco), sodium pyruvate (1 mM, LifeTechnologies) and penicillin and streptomycin (100U/ml each, LifeTechnologies). Cells with blocked in early G1/S phase with thymidine double blockage (2mM, 18 h first treatment, 9 h release and 15 h second treatment). The antibodies used for ChIP were: H3K27ac (catalogue number: 39685, active motif), H3K27me3 (catalogue number: 39155, active motif) Immunoprecipitated DNA (ChIP) and whole cell extracts DNA (input) were treated with RNaseA and proteinase K then purified by using Qiaquick PCR purification kit (Qiagen, 28106). TruSeq ChIP kit from Illumina was used to perform library preparation according to the manufacturer's recommendations. Briefly, IP and input DNA were first size selected using SPRIselect beads (Agencourt) in order to have fragments between 100 and 500bp after BioAnalyzer profiling. 1 to 10ng of DNA were used in a first step of end-repair followed by the adenylation of 3’-end allowing further ligation of specific Illumina adaptors required for sequencing. These adaptors contain specific indexes (barcodes) different for each sample so that library from different samples can be mixed together before sequencing. After PCR amplification (12-15 cycles), quality assessment of DNA libraries was achieved using BioAnalyzer profiling and Qubit quantification. After equimolar pooling of libraries, the final dilution was accurately quantified using Kapa library quantification kit.
characteristics.characteristic: description
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
characteristics.text: 2
characteristics.characteristic: individual
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: blood
characteristics.characteristic: organism part
characteristics.text: normal
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000461
characteristics.characteristic: phenotype
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: H3K27ac_C2
characteristics.characteristic: title