This repository documents scripts that generate figures related to our manuscript in which we performed chromatin interaction (Hi-C) and modification profiling (CUT&RUN for H3K4me3 and H3K27me3) across human kidney anatomic regions.
The work is published on Scientific Data in 2024.
For citation (DOI: https://doi.org/10.1038/s41597-024-03648-8) (PMID: 39025878):
Li, H., Li, D. & Humphreys, B.D. Chromatin conformation and histone modification profiling across human kidney anatomic regions. Sci Data 11, 797 (2024). https://doi.org/10.1038/s41597-024-03648-8
All primary data have been deposited in NCBI’s Gene Expression Omnibus and are available through GEO Series accession number GSE253634 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE253634), including (1) raw fastq files of Hi-C sequencing data, (2) processed Hi-C contact matrices for all Hi-C libraries (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE253632), (3) raw fastq files of CUT&RUN sequencing data and (4) processed bigwig files for all CUT&RUN libraries (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE253630).
Supporting data files, including donor clinical information, Hi-C chromatin contact domain finding results, Hi-C chromatin loop finding results, CUT&RUN peaks.stringent.bed data outputs obtained from both hg19 and hg39 alignment, are available at https://doi.org/10.5281/zenodo.11955175.