DNA methylation in the chromatin landscape of healthy and injured cell types in the human kidney

*** To access this data, please go to Kidney Precision Medicine Project (KPMP) 

Whole Genome Bisulfite Sequence WGBS in human kidney tissue. There are 13 nephrectomies, two biopsies each split into two kidney compartments glomerulus (GLOM) and tubule interstitium (TI). One of the nephrectomies was sequenced in the first and second batches to evaluate the sequence quality. Then we had 30 kidney samples plus three blood samples added like controls with 2 negative and 1 positive.Genomic DNA is isolated using the PureLink Pro 96 Genomic DNA Kit (Cat# K182104A). DNA quantity and quality are assessed using the Qubit Fluorometer 4.1 (Invitrogen). Bisulfite conversion was performed using the EpiTect Fast DNA Bisulfite Kit (Qiagen Cat# 59824). An input of 10 ng was used for library prep. Library prep with QIAseq Methyl DNA Library Kit (Cat# 180502) was used to amplify and laminate Illumina adaptors. Library purification was performed using QIAseq Beads. The library quality was assessed using the Agilent Bioanalyzer 2100 and Qubit Fluorometer 4.1. Multiple libraries were pooled in equal molarity. A final concentration of 300 pM was loaded onto the NovaSeq 6000 sequencer (Illumina) for 150 bp paired-end sequencing. Approximately 200 million read pairs (400 million reads total) were generated per library. An EpiTect Unmethylated DNA control (Qiagen Cat# 59568) was used for the first and second batches. The EpiTect Methylated DNA control (Qiagen Cat# 59655) was sequencing run the second batch. Sequencing quality control, mapping, and methylation analysis were performed using the pipeline with FastC 0.11.5, MultiQC v1.8 TrimGalore 0.6.7 to remove Illumina adapter sequences and 10 bp 5' prime and 5bp 3' prime. Bismark 0.23.1 DNA Mapping: Non-directional mapping to the hg38/GRCh38. The data in Zenodo are the bigwig for each experiment  33 (15 GLOM and 15 TI and blood 2 Negative 1 Positive), There are two merged bigwigs for GLOM and TI samples and a metadata file.

Published in: DOI: 10.1038/s41467-023-44467-6