A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues
This repository provides the scripts used in the paper "A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues".
High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we used sheep as an animal model for low-to-high altitude translocation. We generated multi-omics data including 49 whole genome sequencing, 1,277 time-resolved bulk RNA-Seq, 66 ATAC-Seq and 6 single-cell RNA-Seq datasets from multiple tissues as well as phenotypic data from 20 bio-indicators. Our study provides valuable resources and insights for future hypoxia-related studies in mammals.
Our work is out now on Nature Communications: https://doi.org/10.1038/s41467-024-48261-w.
There are five main parts of analysis in our study, including WGS, RNA-Seq, scRNA-Seq, ATAC-Seq and Hi-C. Scripts for scRNA-Seq data analysis have been uploaded to https://github.com/tian6067/WeiwtCAU-sc-RNA_seq.
Genome reference and annotation files used in this study are downloaded from Ensembl genome browser: https://asia.ensembl.org/Ovis_aries_rambouillet/Info/Index (i.e., Oar_rambouillet_v1.0).
To enhance the reusability and reproducibility of our data, and fully facilitate them for secondary analysis and novel discoveries, we uploaded "Data table.xlsx" which includes sample collection, information for sequencing sample, and metatables for sequencing datasets. You can find the details about newly generated sequencing data and public data in this study directly.
We provide integrated expression matrix, consensus peak set with metatables and measurement phenotypic data in our study, which have been uploaded to Google Drive: https://drive.google.com/file/d/1iTbn5IVPGVGEp7nkeNCgjDvtqjXjPQQ8/view?usp=sharing.
High-throughput sequencing data in this study are publicly available for download without restriction, which was deposited in the Sequence Read Archive (SRA) database in NCBI under accession numbers: PRJNA1053506 (WGS), PRJNA1000743 (bulk RNA-Seq), PRJNA1001016 (bulk RNA-Seq) and PRJNA1001505 (scRNA-Seq, ATAC-Seq).
Yan, Z., Yang, J., Wei, WT. et al. A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues. Nat. Commun. 15, 3970 (2024).
Contributor: Ze Yan, Fenghua Lv. Any questions, please feel free to contact yanze@cau.edu.cn.