{"database":"biostudies-arrayexpress","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":10,"searchCount":0},"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Catherine Ory"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["DNA-seq"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-10931"],"description":["We searched for genetic alterations and polymorphisms specifically associated with the exposure to ionizing radiations in thyroid tumoral and non tumoral samples of Ukrainian patients exposed or not to radioactive iodines."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - After normalisation and quality control, exome enriched libraries have been sequenced on a HiSeq 4000 from Illumina (Illumina Inc., CA, USA) as paired-end 150 bp reads. Libraries have been pooled by 6 on each lane in order to reach an average sequencing depth of at least 100X for good quality sample DNA. Sequence quality parameters have been assessed throughout the sequencing run and standard bioinformatics analysis of sequencing data was based on the Illumina pipeline to generate FASTQ file for each sample.","Nucleic Acid Extraction - DNA quantity and quality was assessed by spectophotometry (260/280 and 260/230 ratio) using NanoDrop and by fluorometry using Qbit DNA HS assay (ThermoFisher scientific, France). Genomic DNA quality was verified on a Bioanalyzer 2100 (Agilent Technologies, USA).","Sample Collection - The Chernobyl Tissue Bank (CTB) provided the post-Chernobyl series of thyroid tumors and non tumoral tissues adjacent to the tumors, as Genomic DNA samples. All informations used for samples annotation were provided by the CTB. The confirmation of diagnosis was performed by the International Pathology Panel of the CTB, which is supported by NCI grant number U24CA082102:  Dr A Abrosimov, Pr T Bogdanova, Pr G Fadda, Professor J Hunt, Pr M Ito, Pr V LiVolsi,  Pr J Rosai, Pr ED Williams. Tumors and adjacent non tumoral tissues were considered as radiation-induced and exposed, respectively, when the patients were under 15 years old (period of high thyroid radiation sensitivity), and lived in oblasts of Ukraine highly contaminated at the time of the Chernobyl accident. The series also included Ukrainian patients, born in the same oblasts than radiation-induced cases after March 1987 and therefore considered at as non-exposed (sporadic PTC) due to radioactive iodines short decay.","Library Construction - Whole Exome Sequencing (WES) has been performed by the Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Evry, FRANCE. Once quality controlled by the DNA and Cell Bank laboratory, genomic DNA (200 ng) has be captured using in-solution enrichment methodology (Human All Exon v6 – 60 Mb, Agilent Technologies, CA, USA). Library preparation and exome enrichment protocol (~20.000 targeted genes) have been performed automatically on NGSx (Perkin Elmer Inc, MA, USA) and Bravo (Agilent Technologies, CA, USA) respectively, according to manufacturer’s instructions (SureSelect, Agilent Technologies CA, USA)."],"pubmed_authors":["Nicolas Ugolin","Catherine Ory"],"view_count":["10"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Exome analysis of thyroid tumors and adjacent non tumoral tissues of Ukrainien patients exposed or not to Chernobyl radioiodines","description":"We searched for genetic alterations and polymorphisms specifically associated with the exposure to ionizing radiations in thyroid tumoral and non tumoral samples of Ukrainian patients exposed or not to radioactive iodines.","dates":{},"accession":"E-MTAB-10931","cross_references":{"ENA":["ERP131852"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0004184"]}}