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Pipeline publication

[…] ue Microarray (TMA) containing 65 tumors and 8 adenomas as well as their resection margins, previously characterized [, ]. Paraffin-embedded sections were rehydrated and antigen exposure was performed by boiling in citric acid. OCT-embedded sections were fixed in 4% PFA and processed as before . Cells were seeded on cover slips and cultured 48 h in serum-free medium. Cells were fixed in 4% PFA and permeabilized in 0.1% Triton. Tissues and cells were blocked in PBS containing 5% Blotto and incubated with antibodies following the manufacturer’s instructions. Detection was performed on a Leica MPS60 for paraffin sections and on a Leica DM RXA for OCT sections. Acquisitions were performed using Metamorph (Molecular Devices) software. Deconvoluted 3D pictures were obtained from Autoquant X3 (MediaCybernetics) and Imaris (Bitplan) softwares., The colorectal cancer cell lines HT29, HCT116 and SW480 were originally obtained from the ATCC and used from frozen stocks at low passages. Caco-2/15, a stable clone of Caco-2 cells, has been previously described . The cells were cultured as described previously [, ]., Protein extractions and Western blotting were performed as described previously . Briefly, cell extracts were loaded on 12% SDS-PAGE gels under denaturing conditions before being transferred onto nitrocellulose membranes., Cells were lysed with RiboZol (Amresco). RNA extraction, reverse transcription-PCR and real-time PCR amplification were performed as previously described in an Mx3000 P qPCR syst […]

Pipeline specifications

Software tools MetaMorph, AutoQuant, Imaris