Supplementary Data for "GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery-center axis"

We offer a nextflow pipeline (https://github.com/BiCroLab/nextflow-radiantkit) based on Radiankit (https://github.com/BiCroLab/radiantkit) to perform image analysis on YFISH images obtained from Genomics loci Positioning by Sequencing (GPSeq) experiment. This help researchers assess the radial digestion of the chromatin by restriction enzyme as indicated in GPSeq protocol.

Here we provide sample data to perform the test run for the nextflow-radiantkit pipeline.

We include an example report generated by the pipeline from a GPSeq experiment performed on hTERT-immortalized retinal pigment epithelial cells (hTERT RPE-1) cell line for a doubling time point series (30 sec, 1 min, 2 min, 4 min, 8 min, 16 min, 32 min, 64 min).

Note: this dataset does not reproduce the radiantkit report as in the Supplementary Data included in this repository. It only help users of the nextflow-radiantkit to ensure all the requirements to run the pipeline are met and the pipeline can run through all processes.

We provide a nextflow pipeline (https://github.com/BiCroLab/nextflow-gpseq) to enable users to analyse GPSeq sequencing data without high level of bioinformatics expertise.

Here we include an example report of generated using MultiQC by the nextflow pipeline from a GPSeq experiment performed on hTERT-RPE-1 cell line for a doubling time point series (30 sec, 1 min, 2 min, 4 min, 8 min, 16 min, 32 min, 64 min).

Raw sequencing data is available on European Nucleotide Archive (accession: PRJEB89772).