Welcome to the GitLab page of the Huch lab! Here you find the repositories which contain the source code developed to support our research. This page primarily contains scripts and notebooks for data analysis, including sequencing and image analysis, which were used in our published papers. We invite researchers, students, and developers to explore, contribute, and collaborate with us as we advance our scientific objectives. Your feedback and contributions are invaluable in enhancing our research efforts!
We provide Sequencing Docker Stacks —preconfigured, containerized environments for sequencing data analysis—hosted on GitHub. These stacks include ready-to-use notebooks for bulk RNA-seq, single-cell, spatial transcriptomics, and multi-omics workflows, all built on Jupyter Docker Stacks. They provide reproducible and streamlined analysis environments for lab members and collaborators. Documentation and links to the container images are available on GitHub.
Some of our protocols have found their way into methods papers:
Anna Dowbaj*, Timo N Kohler*, Lucía Cordero-Espinoza, Florian Hollfelder, Meritxell Huch
Generation of liver mesenchyme and ductal cell organoid co-culture using cell self-aggregation and droplet microfluidics.
STAR Protoc, 4(2) Art. No. 102333 (2023) DOI
Zixuan Zhao*, Xinyi Chen*, Anna Dowbaj*, Aleksandra Sljukic*, Kaitlin Bratlie*, Luda Lin*, Eliza Li Shan Fong, Gowri Manohari Balachander, Zhaowei Chen, Alice Soragni, Meritxell Huch#, Yi Arial Zeng#, Qun Wang#, Hanry Yu#
Organoids
Nat Rev Methods Primers, 2 Art. No. 94 (2022) DOI
Laura Broutier, Amanda Andersson-Rolf, Christopher J Hindley, Sylvia F Boj, Hans Clevers, Bon-Kyoung Koo, Meritxell Huch
Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation.
Nat Protoc, 11(9) 1724-1743 (2016) DOI