From 94c781179a78cbe466825163d2a5b564d8c12d3d Mon Sep 17 00:00:00 2001 From: wardDeb Date: Tue, 1 Sep 2026 12:42:51 +0200 Subject: [PATCH] public data info --- README.md | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/README.md b/README.md index 4fa541f..1054764 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,5 @@ +[![DOI:10.5281/zenodo.21529137](https://img.shields.io/badge/DOI-10.5281/zenodo.21529137-yellow.svg)](https://doi.org/10.5281/zenodo.21529137) + # deeptools 25 repo ## Setup @@ -36,3 +38,51 @@ In case you want to run either the benchmark of the example via slurm, an exampl The results generated from both workflows (benchmark and example workflow), as well as the code to generate figure 1 are included in this repository. To collate/generate the figures in the `figures` directory, simply run: > pixi run bash figures/collate_figures.sh + +## Public data +Both the benchmark as well as the example use publicly available data. The processed version of this data is included in the zenodo archive (and will be downloaded automatically by the respective workflows), the original source data can be retrieved through the accessions listed here. + +| Purpose | Modality | Organism | SRA | BioProject | GEO | doi | +| --- | --- | --- | --- | --- | --- | --- | +| benchmark | ChIP - H3K9me3 | Human | SRR28592124 | PRJNA1097546 | GSE263436 | 10.1073/pnas.2412258121 | +| benchmark | RNA | Human | SRR28012902 | PRJNA1078228 | GSE256091 | 10.1158/0008-5472.CAN-23-1551 | +| benchmark | WGS | Human | SRR15494527 | PRJNA752223 | / | / | +| benchmark | ChIP - CENH3 | Wheat | SRR1686799 | PRJNA268976 | GSE63752 | 10.1105/tpc.19.00133 | +| benchmark | RNA | Wheat | SRR27822150 | PRJNA1071712 | GSE254797 | 10.3389/fpls.2024.1401135 | +| benchmark | WGS | Wheat | SRR27887047 | PRJNA956839 | / | 10.1038/s41586-024-07808-z | +| example | NPC_9sca_ctrl_H3K27ac_rep1 | Mouse | SRR15829033 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_H3K27ac_rep2| Mouse | SRR15829034 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_H3K27me3_rep1| Mouse | SRR15829036 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_H3K27me3_rep2| Mouse | SRR15829037 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_H3K4me1_rep1| Mouse | SRR15829042 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_H3K4me1_rep2| Mouse | SRR15829043 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_H3K4me3_rep1| Mouse | SRR15829045 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_H3K4me3_rep2| Mouse | SRR15829046 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_H3K9me3_rep1| Mouse | SRR15829048 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_H3K9me3_rep2| Mouse | SRR15829049 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_input_rep1| Mouse | SRR15829058 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_input_rep2| Mouse | SRR15829059 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_RNA_rep1| Mouse | SRR15829077 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_RNA_rep2| Mouse | SRR15829078 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_ATAC_rep1| Mouse | SRR15829121 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_ATAC_rep2| Mouse | SRR15829122 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_BS_rep1| Mouse | SRR15829019 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ctrl_BS_rep2| Mouse | SRR15829020 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_ATAC_rep1| Mouse | SRR15829084 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_ATAC_rep2| Mouse | SRR15829085 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_BS_rep1| Mouse | SRR15829089 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_BS_rep2| Mouse | SRR15829090 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_H3K27ac_rep1| Mouse | SRR15829101 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_H3K27ac_rep2| Mouse | SRR15829102 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_H3K27me3_rep1| Mouse | SRR15829103 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_H3K27me3_rep2| Mouse | SRR15829104 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_H3K4me1_rep1| Mouse | SRR15829107 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_H3K4me1_rep2| Mouse | SRR15829108 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_H3K4me3_rep1| Mouse | SRR15829109 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_H3K4me3_rep2| Mouse | SRR15829110 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_H3K9me3_rep1| Mouse | SRR15829111 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_H3K9me3_rep2| Mouse | SRR15829124 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_input1_rep1| Mouse | SRR15829131 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_input1_rep2| Mouse | SRR15829132 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_RNA_rep1| Mouse | SRR15829149 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 | +| example | NPC_9sca_ko_RNA_rep2| Mouse | SRR15829150 | PRJNA762170 | GSE183764 | 10.1038/s41586-023-06781-3 |