Computational protocol: Real-imaging cDNA-AFLP transcript profiling of pancreatic cancer patients: Egr-1 as a potential key regulator of muscle cachexia

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Protocol publication

[…] The cDNA fragments of interest were excised from dried gel, followed by elution in 100 μl TE for 10 min at 95°C. 5 μl were re-amplified with TaqI-Ø and MseI-Ø primers. Specific fragments were verified by visualizing 5 μl PCR product on a 1.5% agarose gel. The amplified fragments were directly sequenced with the primers TaqI-ØIRD700 and MseI-ØIRD800 using the SequiTherm EXCEL II DNA sequencing kit (Epicentre) on the automated infrared sequencer DNAIR 4200 (Li-COR).Sequencing data were aligned against BlastX and BlastN in the publicly available databases and clustered according to gene ontology using the nodes of the DNASpace software package (DNASIS MAX 2.6, Miraibio). […]

Pipeline specifications

Software tools BLASTX, BLASTN, DNASIS Max
Application Nucleotide sequence alignment
Organisms Homo sapiens
Diseases Muscular Diseases, Neoplasms, Pancreatic Neoplasms, Wasting Syndrome