title: PDAC011T
organism: Homo sapiens
description: 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.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2017-12-12T17:02:53Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2017-03-10T19:17:47Z
attributes.tag: External Id
attributes.value: SAMEA103909691
attributes.tag: INSDC center name
attributes.value: Projet Carte dâ€™Identite des Tumeurs LIGUE NATIONALE CONTRE LE CANCER
attributes.tag: INSDC first public
attributes.value: 2017-12-12T17:02:53Z
attributes.tag: INSDC last update
attributes.value: 2017-03-10T19:17:47Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: ProportionMurineRNA
attributes.value: 0.18
attributes.tag: Submitter Id
attributes.value: E-MTAB-5039:PDAC011T
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: human
attributes.tag: disease
attributes.value: pancreatic ductal adenocarcinoma
attributes.tag: individual
attributes.value: PDAC011
attributes.tag: organism status
attributes.value: dead
attributes.tag: resectable
attributes.value: true
attributes.tag: sample name
attributes.value: E-MTAB-5039:PDAC011T
attributes.tag: scientific_name
attributes.value: Homo sapiens
attributes.tag: sex
attributes.value: female
attributes.tag: survival time
attributes.value: 29
attributes.tag: xenograft
attributes.value: pancreatic cancer cells grown in nude mouse
attributes.tag: xenograft CIMPclass
attributes.value: false
attributes.tag: xenograft MultiOmicsClassification
attributes.value: classical
attributes.tag: xenograft differentiation
attributes.value: mucinous
attributes.tag: xenograft fibrosis
attributes.value: false
attributes.tag: xenograft inflammation
attributes.value: false