Epigenomic landscape of the human dorsal root ganglion - A study on chromatin accessibility

Study Purpose: This study was conducted to characterize the chromatin accessibility in the human dorsal root ganglia (hDRG), with the goal of creating a resource to better understand regulatory sequences in genes associated to nociception.

Data Collection: ATAC-seq was performed on 17 DRGs from 13 human organ donors. Sequencing alignment to the human genome GRCh38 was performed using Bowtie2 and Chromap. Aligned read information was obtained.

Primary Conclusion: Transcription factor binding sites for EGR1/3, SP1/4, and JUN/FOS were found to be enriched in the hDRG. Differential analysis between sexes showed higher chromatin accessibility in GABAergic, glutamatergic and IFN-related genes in females in hDRG, while some Ca2+-signaling-related genes were found to be more accessible in male hDRG.

Curator's Notes

Experimental Design: Assay for Transposase-Accessible Chromatin (ATAC) sequencing was used to characterize the accessible chromatin in the human dorsal root ganglion using two experimental procedures: bulk ATAC-seq and spatial ATAC-seq. Bowtie2 was used to map paired-end reads to the reference genome GRCh38/hg38 on L4 or L5 dorsal root ganglia (DRGs) from 9 human organ donors for Bulk ATAC-seq data set. After mitochondrial DNA and duplicates filtering, filtered aligned reads were uploaded in a BAM file format. For spatial ATAC-seq, Chromap was used to perform the alignment of sequences to the human genome GRCh38/hg38 on L4 or L5 DRGs from 8 human organ donors. ArchR was used to process fragment files. Fragment files were uploaded in a .tsv file. Further, a tissue_positions_list.csv, tissue images, and experiment metadata were added for the spatial component of the data. Together, these files can help further processing of spatial ATAC-seq using ArchR.

Completeness: This dataset is part of a larger study: " Epigenomic landscape of the human dorsal root ganglion: A study on chromatin accessibility."

Subjects & Samples: Samples from male (n=7) and female (n=6) human donors were used in this study.

Primary vs derivative data: The Primary data folder is organized by subject and sample name and contains aligned sequences in .BAM format for spatial ATAC-seq. Additionally, the folder includes a tissue_positions_list.csv, tissue images, and experiment metadata related to the spatial component of the data. There is no derivative data folder.