characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-12-12T17:02:53Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-03-10T19:17:47Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA103909695
characteristics.characteristic: External Id
characteristics.text: Projet Carte dâ€™Identite des Tumeurs LIGUE NATIONALE CONTRE LE CANCER
characteristics.characteristic: INSDC center name
characteristics.text: 2017-12-12T17:02:53Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-03-10T19:17:47Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: 0.17
characteristics.characteristic: ProportionMurineRNA
characteristics.text: ERS1598863
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5039:PDAC015T
characteristics.characteristic: Submitter Id
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: two tumor sampling methods from patients with PDAC: 1- surgery for patients with tumor size < 2cm, and 2- Biopsy followed by Endoscopic Ultrasound-Guided Fine-Needle Aspiration (EUS-FNA) for patients with tumor size > 2cm. this information is given by the \Resectable\ variable. For operated patients (with surgery), tumor cells were xenografted directly. however, for biopsy cells, they were grown in culture for 1 or 2 days, before transplanted to the nude mouse. The final xenografted cells will be collected when the tumor reach a size of 1 cm. Finally, the \Differentiation\, \Fibrosis\, \Inflammation\ information are estimated on the collected xenograft tissues. Total RNA was extracted using Manual-miRneasy Mini (Qiagen) Libraries were prepared using Illumina’s guidelines for the TruSeq Stranded mRNA LT sample prep kit. Fragmentation was done using the alternative fragmentation protocol in order to produce RNA-seq libraries that are compatible with sequencing on a paired-end 100 base pair flow cell (PE-100bp FC). The steps in library prep included o Capture of mRNA on oligo-dT-beads, Concomitant fragmentation and primer annealing, First strand synthesis, Second strand synthesis, 3’ enzymatic steps resulting in end repair, 3’ adenylation, and adapter ligation and Library amplification (PCR) . The strand specificity of the kit is achieved by the presence of dUTP instead of dTTP during the second strand synthesis step. Since the polymerase used in the downstream library amplification step does not incorporate past dUTP, the incorporation of this nucleotide in second strand synthesis effectively quenches the second strand during amplification. Libraries were QC’ed with respect to concentration and size profile: The size profile of the libraries was evaluated by QC of 8 of the samples on an Agilent DNA 1000 or high sensitivity chip. The libraries contain approximately 120 nucleotides of adapter sequence and the remaining size of the library is derived from the input RNA. The library concentration was determined using the KAPA qPCR kit (KK4835) and triplicate reactions using three independent 106-fold dilutions of the libraries.
characteristics.characteristic: description
characteristics.text: pancreatic ductal adenocarcinoma
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0002517
characteristics.characteristic: disease
characteristics.text: PDAC015
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: dead
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0001422
characteristics.characteristic: organism status
characteristics.text: true
characteristics.characteristic: resectable
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000384
characteristics.characteristic: sex
characteristics.text: 9
characteristics.unit: month
characteristics.characteristic: survival time
characteristics.text: PDAC015T
characteristics.characteristic: title
characteristics.text: pancreatic cancer cells grown in nude mouse
characteristics.characteristic: xenograft
characteristics.text: true
characteristics.characteristic: xenograft CIMPclass
characteristics.text: classical
characteristics.characteristic: xenograft MultiOmicsClassification
characteristics.text: non-mucinous
characteristics.characteristic: xenograft differentiation
characteristics.text: false
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009639
characteristics.characteristic: xenograft fibrosis
characteristics.text: false
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009639
characteristics.characteristic: xenograft inflammation