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Processed imaging and feature data for: Gene transcription and chromatin packing domains form a self-organizing system"

Year: 2026
Type: dataset
Abstract: #### README This repository contains the processed data and imaging feature data used in **"Gene transcription and chromatin packing domains form a self-organizing system"** (Carter, Almassalha, et al., *bioRxiv*, 2026; doi: [10.64898/2026.03.15.711889](https://doi.org/10.64898/2026.03.15.711889)). This data is archived on Zenodo: **[ZENODO DOI — pending submission]**. The code used to generate this data and produce the figures in this publication is available in a separate GitHub repository: [BackmanLab/Pol-II-Transcription-Project](https://github.com/BackmanLab/Pol-II-Transcription-Project), archived separately with its own permanent identifier at Zenodo: [10.5281/zenodo.22090110](https://doi.org/10.5281/zenodo.22090110). See that repository's `FIGURES.md` for the complete figure-to-script index, and each analysis subfolder's own README for which scripts consume which files in this deposit. To regenerate the analysis, clone the GitHub repository, download this data deposit, and update paths in the relevant scripts to point to where you have stored this data locally. **Sequencing data (raw and processed) is hosted separately at GEO, not in this deposit:** - [Total RNA-seq](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279127) — GSE279127 - [Hi-C](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279166) — GSE279166 - [CUT&Tag, POLR2A](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279081) — GSE279081 - EU-seq — GEO submission in progress; accession will be added upon assignment - CUT&Tag, H3K4me3 — GEO submission in progress; accession will be added upon assignment - RIP-seq (POLR2A, EZH2) — GEO submission in progress; accession will be added upon assignment For inquiries or issues, please reach out to Lucas Carter at [email protected].
DOI: 10.5281/zenodo.22103264
Authors: Carter, Lucas M, Li, Wing Shun, Acosta, Nicolas, Gong, Ruyi, Pandya, Niyati, Carignano, Marcelo A, Pujadas Liwag, Emily, Wang, Kunlun, Kuo, Tiffany, MacQuarrie, Kyle, Kanemaki, Masato T., Almassalha, Luay, Backman, Vadim
Institutions: Northwestern University, Lurie Children's Hospital, National Institute of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Research Organization of Information and Systems, The University of Tokyo, Northwestern Memorial Hospital
Language: English
Open Access status: green
OpenAlex ID: W7204192755
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