characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-05-16T17:02:07Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-05-16T18:32:04Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104057715
characteristics.characteristic: External Id
characteristics.text: unspecified
characteristics.characteristic: INSDC center name
characteristics.text: 2017-05-16T17:02:07Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-05-16T18:32:04Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1721608
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5678:SCC_13
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: Skin lesions and healthy skin tissue samples were collected from patients at the Dermatology department in Princess Alexandra hospital. The study was approved by Metro South Human Research Ethics Committee and The University of Queensland Human Research Ethics Committee (HREC-11-QPAH-236, HREC-11-QPAH-477, HREC-12-QPAH-217, and HREC-12-QPAH-25). Written, informed consent was obtained from all patients prior to participation. Following biopsy, tissues were immersed in RNA later (Life Technologies, Carlsbad, CA) and stored at -80°C until required. All samples were sectioned and processed according to routine protocol in the Department of Anatomical Pathology located in Princess Alexandra Hospital. RNA isolation was performed using the Qiagen RNeasy Plus Mini kit (Qiagen GmbH, Hilden, Germany). Briefly, tissue samples were cut into small pieces, and transferred into 1.5mL tube containing lysing matrix D (MP Biomedicals, Santa Ana, CA, USA) and 600uL buffer RLT containing 1% beta-mercaptoethanol and homogenised using a Fast Prep benchtop homogeniser (MP Biomedicals, Santa Ana, CA, USA). Samples were spun 5 times using setting 6.5 for 30 seconds each, and chilled on ice between spins. Lysate was removed and transferred to a fresh tube. For unfixed BCC samples embedded in OCT, 20 x 10 micron sections were cut and placed into 600 µL buffer RLT, and homogenised using a 18.5 gauge blunt needle attached to an RNAse free syringe and resuspended 5 times. The remaining RNA extraction steps were performed as above. RNA concentration was measured using the Qubit fluorometer (Life Technologies, Carlsbad, CA) and RNA integrity determined using the 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA) on RNA Pico chips. The minimum acceptable quality for RNA for analysis by qPCR was RIN >6. Complementary DNA (cDNA) was synthesised from 200 ng total RNA using the Sensifast cDNA kit (Bioline, London, UK) as per the manufacturer’s instructions. RNA sequencing libraries of poly (A) RNA from 500ng total RNA obtained from AK, IEC and SCC and SK samples, were generated using the TruSeq unstranded mRNA library prep KIT for Illumina multiplexed sequencing (Illumina, San Diego, CA, USA). TruSeq stranded mRNA library prep kit was used to generate poly (A) RNA libraries for RNA obtained from normal health skin samples (Illumina, San Diego, CA, USA). Libraries were sequenced (100 bp, paired-end) on the Illumina 2000 platform and FASTQ files were analysed.
characteristics.characteristic: description
characteristics.text: squamous cell carcinoma
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000707
characteristics.characteristic: disease
characteristics.text: 8
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: skin
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: SCC_13
characteristics.characteristic: title