Introduction

The TransOmicsData ExperimentHub package contains datasets spanning various biological contexts such as in vitro embryonic and tissue-specific development in mouse and human. It covers multiple omics sequencing technologies such as (single-cell)-RNAseq, mass spectrometry and ChIP-seq. This package was developed to provide convenient access to raw or pre-processed data for comparative trans-omics analysis.

Installation

The package is currently available through Bioconductor (version 3.19):

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TransOmicsData")

Table of Data

Title	Description	Omics	Species	Reference
chen-organoid	cerebral organoid differentiation	phosphoproteome, proteome, transcriptome, single-cell transcriptome	human	Chen et al., Cell Reports, 2024
xiao-myogenesis	C2C12 myogenesis differentiation	phosphoproteome, proteome	mouse	Xiao et al., iScience, 2022
yang-esc	mouse ESC to epiLC differentiation	epigenome, phosphoproteome, proteome, transcriptome	mouse	Yang et al., Cell Systems, 2019

Shiny App

Explore the human cerebral organoid trans-omic data interactively on http://shiny.maths.usyd.edu.au/hCOmultiome/.

Explore the mouse ESC to epiLC differentiation trans-omic data interactively on http://www.stemcellatlas.org/

Citation

If this work was useful, please consider citing the original publications:

1. For chen-organoid dataset, cite: Carissa Chen, Scott Lee, Katherine G. Zyner, Milan Fernando, Victoria Nemeruck, Emilie Wong, Lee L. Marshall, Jesse R. Wark, Nader Aryamanesh, Patrick P.L. Tam, Mark E. Graham, Anai Gonzalez-Cordero, Pengyi Yang (2024) Trans-omic profiling uncovers molecular controls of early human cerebral organoid formation, Cell Reports, 43(5):114219. Fulltext
2. For xiao-myogenesis dataset, cite: Di Xiao, Marissa Caldow, Hani Jieun Kim, Ronnie Blazev, Rene Koopman, Deborah Manandi, Benjamin L. Parker, Pengyi Yang (2022) Time-resolved phosphoproteome and proteome analysis reveals kinase signaling on master transcription factors during myogenesis, iScience, 25(6):104489. Fulltext
3. For yang-esc dataset, cite: Pengyi Yang, Sean J. Humphrey, Senthilkumar Cinghu, Rajneesh Pathania, Andrew J. Oldfield, Dhirendra Kumar, Dinuka Perera, Jean Y.H. Yang, David E. James, Matthias Mann, Raja Jothi (2019) Multi-omic profiling reveals dynamics of the phased progression of pluripotency, Cell Systems, 8(5):427-445.e10. Fulltext

For the package citation, please enter:

citation("TransOmicsData")