Tools & Resources

Below are some of the tools and resources developed by the Slotkin Lab:

All-in-One (AIO) RNA sequencing Data Pipeline and Machine Learning

From: (2025) M.C. Kramer, T.S. Ratnayake, S.A. Edwards, H.L. Lowrey, G. Klaas, L. Sidorenko, B.A. Rowan, R. Michelmore, B.C. Meyers and R.K. Slotkin. Identification of a cleaved aberrant RNA associated with the initiation of transgene silencing. The Plant Cell 37: koaf219. Github repository available here. This repo contains the scripts for all data analysis steps for “All-in-One” RNA-seq, Random Forest machine learning, small RNA sequencing, and RMarkdown files for each figure in the manuscript.

Image Resources for plant growth under high CO2 conditions

From: (2023) K. Panda, B. Mohanasundaram, J. Gutierrez, L. McLain, S.E. Castillo, H. Sheng, A. Casto, G. Gratacós, A. Chakrabarti, N. Fahlgren, S. Pandey, M.A. Gehan and R.K. Slotkin. The plant response to high CO2 levels is heritable and orchestrated by DNA methylation. New Phytologist. Images available here.

Resources for in vivo Protein-RNA tethering

Plasmids and seeds available from the ABRC: Link From: A plant tethering system for the functional study of protein-RNA interactions in vivo (2022). D. Cuerda-Gil, Y.-H. Hung, K. Panda and R.K. Slotkin. Plant Methods 18: 75.

Improved annotation of Arabidopsis Transposable Elements

Long-read cDNA Sequencing Enables a ‘Gene-Like’ Transcript Annotation of Arabidopsis Transposable Elements. K. Panda and R.K. Slotkin. Annotations are available on GitHub.

Software Tools

Analyze CRISPR knock-in insertion junctions with amplicon sequencing - Analyze the CRISPR junction intactness using GATK on amplicon reads and visualize basepair insertions and deletions.

Analyze CRISPR on and off target insertion rate using Insertion-seq analysis pipeline Whole-genome CRISPR off-target insertion screening, and visualization of unintended insertion events.

CHIP-seq data processing snakemake pipeline. Snakemake based CHIP-seq processing pipeline for HPCs. Generates bam files and normalized bigwig tracks

Small RNA-seq data processing snakemake pipeline. Snakemake based sRNA-seq processing pipeline for HPCs. Generate Genome mapped bam files and count files.

DNA Methylation Analysis - Bisulfite Amplicon sequencing (BSAS-seq) processing wrapper Analyze Bisulfite Amplicon sequencing reads, map reads using methylpy, generate allC files, count methylation percentage, coverage and stats.

Tool to determine the stength of RNA-directed DNA Methylation (RdDM). From: An siRNA-guided Argonaute protein directs RNA Polymerase V for the first round of RNA-directed DNA methylation (2021). M. Sigman, K. Panda, R. Kirchner, L.L. McLain, H. Payne, J.R. Peasari, A.Y. Husbands, R.K. Slotkin, A.D. McCue.Nature Plants 7: 1461-1474. 2026 - Improved pipeline to calculate RNA-directed DNA Methylation (RdDM) strength from bisulfite amplicon sequencing data using Bismark.

EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels. J. Daron and R.K. Slotkin. Genome Biology v18:7704. Available on GitHub.

image-right Kismeth: Analyzer of Plant Methylation States Through Bisulfite Sequencing. E. Gruntman^*, Y. Qi^*, R.K. Slotkin^*, T. Roeder, R.A. Martienssen and R. Sachidanandam. BMC Bioinformatics v9: e371.^*These authors contributed equally to this manuscript. Available as an web-based tool.

Teaching Resources

R.K. Slotkin. Designing a Better Laboratory Course. Teaching Guide for Graduate Student Instructors 2005-2006, University of California Press.