characteristics.text: 2013-01-29T17:02:23Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T16:04:07Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA1695655
characteristics.characteristic: External Id
characteristics.text: French National League Against Cancer - Research Dept - CIT Group
characteristics.characteristic: INSDC center name
characteristics.text: 2013-01-29T17:02:23Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T16:04:07Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: 13 month
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UO_0000035
characteristics.characteristic: MetastasisFreeSurvivalDelay
characteristics.text: 1
characteristics.characteristic: MetastasisFreeSurvivalEvent
characteristics.text: ERS183245
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-1328:VADS_BW_HS_0511
characteristics.characteristic: Submitter Id
characteristics.text: 61 year
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UO_0000036
characteristics.characteristic: age
characteristics.text: frozen_sample
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/OBI_0000922
characteristics.characteristic: bio source type
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: miRNA-Seq libraries are performed from at least 1ug of extracted total RNA with a RIN greater than 7. Before starting, total RNAs are purified with miRNeasy kit wich allows the selection of the small RNA fraction less than 100b. From these samples enriched in small RNAs, libraries are performed according to the protocol published by Francois Vigneault : Curr Protoc Hum Genet. 2012 Apr;Chapter 11:Unit 11.12.1-10. High-throughput multiplex sequencing of miRNA; Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, C Christodoulou D, Seidman JG, Eisenberg E, M Church G. Extraction with Qiacube-miRNeasy 96 Mini (Qiagen) kits; 1 to 10 ug per sample, concentration in range 70-500 ng/uL, volume range 15 to 50 uL, BioAnalyzer profile RIN > 7; Ligation, amplification , quantification and purification according to manufacturer's instructions, with the following details: First, a 3 prime adenylated DNA adaptor is ligated to the enriched sample in the absence of ATP preventing the self-ligation of miRNAs.Then a 5 prime RNA adaptor is ligated in the presence of ATP at the other end of the miRNAs.The RT primer complementary of the 3 prime adaptor is added at this stage with which it will form a duplex thereby reducing the ligation between adaptors. A reverse transcription is therefore perfomed from the RT primer and finally these captured miRNAs are amplified by PCR with primers complementary to the 3 prime and 5 prime adaptors. During this PCR a specific barcode is incorporated allowing individualisation of each library.Each PCR is loaded on the Fragment Analyzer (AATI) for a precise quantification of each miRNA peak of interest.Based on these results a equimolar pool of about ten of different samples are performed. Finally the pooled PCR product is loaded on PAGE in order to excise the band of miRNA that is extracted and purified on a Qiagen MinElute column. Pool Concentration between 0.97 and 4.84 nM per uL; purification quantity is 3500 ng
characteristics.characteristic: description
characteristics.text: head and neck squamous cell carcinoma
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000181
characteristics.characteristic: disease
characteristics.text: oropharynx
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0001729
characteristics.characteristic: disease location
characteristics.text: 4
characteristics.characteristic: disease staging
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: oropharynx
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0001729
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.text: VADS_BW_HS_0511
characteristics.characteristic: title