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Cell Lines for Oesophageal and Pancreatic Cancer

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The human distal oesophageal adenocarcinoma cell lines, FLO-1 and KYAE-1, were purchased from European Collection of Cell Cultures (Salisbury, UK). The human pancreatic cancer cell line AsPc-1 was purchased from the American Type Culture Collection (Manassas, VA, USA). AsPc-1shTAK1 cells stably expressing small hairpin RNA sequences to knockdown the expression of TAK1 has been previously described in Melisi et al (2011) (link). Distal oesophageal adenocarcinoma and pancreatic cancer cell lines were maintained in RPMI 1640 and Dulbecco's modified Eagle's media (LONZA, Basel, Switzerland), respectively, supplemented with 10% heat-inactivated FBS, 20 mmol l−1 HEPES (pH 7.4), penicillin (100 UI ml−1), streptomycin (100 mg ml−1), and 4 mmol l−1 glutamine (ICN Biomedicals Ltd., Irvine, CA, USA) in a humidified atmosphere of 95% air and 5% CO2 at 37 °C. The TAK1 kinase activity was targeted using (5Z)-7-oxozeaenol TAK1 kinase selective inhibitor (TOCRIS bioscience, Bristol, UK). For in vitro assays, (5Z)-7-oxozeaenol was dissolved in 100% dimethyl sulfoxide (DMSO) at a stock concentration of 10 mM. Cell irradiation was performed using a GammaCell 40 irradiator (Best Theratronics Ltd., Ottawa, Canada) as previously described in Melisi et al, 2009 (link).
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Cell Line Authentication and Characterization

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EAC cell lines OE19, OACM5.1C, ESO26, KYAE-1, and FLO-1 were purchased from the European Collection of cell cultures and authenticated by SNP arrays (2012). OE33 cells were purchased from Sigma (St. Louis, MO) and MKN7 cells from the Broad Institute and characterized within the Cancer Cell Line Encyclopedia project. Only low-passage cell aliquots of original stocks were used for experiments.
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Oesophageal Adenocarcinoma Cohort Characterization

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Batch P (numbered 3108–3323) were the 22 discovery cohort oesophageal adenocarcinomas with matched normal squamous epithelium or blood as described [22 (link)]. Batch B1 (7394–7442) were a further 21 tumours all with matched blood (Additional file 5). Briefly, the tumours reflected the known clinico-demographic features of the disease: male predominance (6:1), mean age 68 years (53 to 82), and mostly advanced disease (33/43 > stage I). The study was approved by the East of England-Cambridge South National Research and Ethics Service Committee (Research Ethics Committee Numbers 10/H0305/1 approved 17/02/2010 and 07/H0305/52 approved 28/08/2007), and all patients gave individual informed consent. Sample collection and DNA extraction were as described [22 (link)]. Authenticated Oesophageal adenocarcinoma cell lines [41 (link)] OE33, JH-EsoAd1 and FLO-1 were obtained from the originators or European Collection of Cell Cultures (ECACC) (OE33), and identity checked by short tandem repeat (STR) analysis.
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Culturing Esophageal Adenocarcinoma Cell Lines

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Five EGJ adenocarcinoma cell lines, OACM5.1C, OE19, OE33, SK-GT-4 and FLO-1, were purchased from the European Collection of Cell Cultures (ECACC; Salisbury, UK). FLO-1 was cultured in DMEM (Sigma-Aldrich, St Louis, MO, USA) containing 10% fetal bovine serum (FBS) in a 5% CO2 air-humidified atmosphere at 37°C. The other cell lines (OACM5.1C, OE19, OE33 and SK-GT-4) were cultured in RPMI-1640 (Life Technologies, Carlsbad, CA, USA) under the same conditions, according to the manufacturer's recommendations.
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Cell Line Culture Conditions

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OE33 (EAC), FLO-1 (EAC), SK-GT-4 (EAC) and KYSE-410 (ESCC) cell lines were purchased from the European Collection of Cell Cultures (ECACC, UK). All cells lines were cultured in RPMI 1640 with 10% FCS and 1 mM L-Glutamine and Penicillin/Streptomycin at 37°C and 5% CO2.
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