GeneWalk
Works out which of a gene's annotated functions are actually relevant in your experimental context, using representation learning on a condition-specific gene network.
Tools & protocols
Experimental and computational methods
We develop methods for studying transcription, RNA processing, RNA flow between cellular compartments and mitochondrial gene expression. Published protocols, software and analysis code are available below and on GitHub; post-publication corrections are listed with the corresponding protocol.
Full tutorial and documentation →
Benchtop protocols
NET-seq, nano-COP, subcellular RNA-seq and mitoribosome profiling — published protocols with PDFs and matching analysis pipelines.
Code
Analysis pipelines for every method we publish, plus GeneWalk itself, live under the churchmanlab organization on GitHub.
Protocols
Protocols from the lab
Transcription and splicing in the nucleus
nano-COP — nanopore analysis of co-transcriptional processing
Drexler HL, Choquet K, Merens HE, Tang PS, Simpson JT, Churchman LS (2021) Revealing nascent RNA processing dynamics with nano-COP. Nature Protocols 16(3):1343–1375.
Correction since publication
Page 18, In-house 10× poly(A) buffer (for poly(A) tailing only) should read: “Contains 25 mM MnCl₂, 10 mM DTT, and 5 mg/ml BSA. Mix 1 μl of 1 M MnCl₂, 4 μl of 100 mM DTT, 4 μl of 50 mg/ml BSA, and 31 μl of nuclease-free water.” 1 M MnCl₂ can be purchased from Sigma (cat. no. M1785).
subRNA-seq — subcellular RNA sequencing
Mayer A, Churchman LS (2017) A Detailed Protocol for Subcellular RNA Sequencing (subRNA-seq). Current Protocols in Molecular Biology 120:4.29.1–4.29.18.
NET-seq in yeast
Churchman LS, Weissman JS (2012) Native elongating transcript sequencing (NET-seq). Current Protocols in Molecular Biology, Chapter 4:Unit 4.14.1–17.
NET-seq in mammalian cells
Mayer A, Churchman LS (2016) Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing. Nature Protocols 11(4):813–833.
NET-seq in metazoans (updated)
Martell-Smart D, Ietswaart R, Smalec B, Churchman LS (2020) Profiling metazoan transcription genome-wide with nucleotide resolution using NET-seq. protocols.io.
Mitochondrial gene expression
Mitoribosome profiling in yeast
Couvillion MT, Churchman LS (2017) Mitochondrial Ribosome (Mitoribosome) Profiling for Monitoring Mitochondrial Translation In Vivo. Current Protocols in Molecular Biology 119:4.28.1–4.28.25.
Human mitoribosome profiling
Soto I, Couvillion M, Churchman LS (2024) Human mitoribosome profiling: a re-engineered approach tailored to study mitochondrial translation. Methods in Molecular Biology 2661:257–280.