Faecal and salivary samples were thawed on ice, aliquoted, and genomic DNA was extracted using the Qiagen Allprep PowerFecal DNA/RNA kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany). Genomic DNA from pancreatic tumorous and non-tumoral tissue samples was extracted using the Qiagen DNeasy blood and tissue kit in a protocol modified from Del Castillo et al26 (link): cells were lysed mechanically (with 5 mm stainless steel beads at 25 Hz for 150 s), followed by lysozyme treatment (20 mg/mL) and protease and RNAse digestion (56°C for 2 h). All samples were randomly assigned to extraction batches. To account for potential bacterial contamination of extraction, polymerase chain reaction (PCR) and sequencing kits, we included negative controls (extraction blanks) with each tissue DNA extraction batch (online supplemental figure 1).
Kartal E., Schmidt T.S., Molina-Montes E., Rodríguez-Perales S., Wirbel J., Maistrenko O.M., Akanni W.A., Alashkar Alhamwe B., Alves R.J., Carrato A., Erasmus H.P., Estudillo L., Finkelmeier F., Fullam A., Glazek A.M., Gómez-Rubio P., Hercog R., Jung F., Kandels S., Kersting S., Langheinrich M., Márquez M., Molero X., Orakov A., Van Rossum T., Torres-Ruiz R., Telzerow A., Zych K., Benes V., Zeller G., Trebicka J., Real F.X., Malats N, & Bork P. (2022). A faecal microbiota signature with high specificity for pancreatic cancer. Gut, 71(7), 1359-1372.
Corresponding Organization : European Molecular Biology Laboratory
Other organizations :
European Molecular Biology Laboratory, Heidelberg University, Spanish National Cancer Research Centre, Centro de Investigación Biomédica en Red de Cáncer, Universities of Giessen and Marburg Lung Center, German Center for Lung Research, Universidad de Alcalá, Hospital Universitario Ramón y Cajal, Goethe University Frankfurt, Frankfurt Cancer Institute, Universität Greifswald, Universitätsklinikum Erlangen, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, European Foundation for the Study of Chronic Liver Failure, Pompeu Fabra University
Genomic DNA extracted from faecal, salivary, pancreatic tumorous, and non-tumoral tissue samples
control variables
Extraction batch assignments (samples were randomly assigned)
Negative controls (extraction blanks) included with each tissue DNA extraction batch
controls
Positive control: None specified
Negative control: Extraction blanks included with each tissue DNA extraction batch
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to
get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
