Overview

Introduction to the exRNA Atlas

The exRNA Atlas is the data repository of the Extracellular RNA Communication Consortium (ERCC), which includes small RNA sequencing and qPCR-derived exRNA profiles from human and mouse biofluids.
All RNA-seq datasets are processed using version 4 of the exceRpt small RNA-seq pipeline and ERCC-developed quality metrics are uniformly applied to these datasets.

There are two different versions of the exRNA Atlas:
  • a public version (accessible by everyone) and
  • a private version (accessible only by ERC Consortium members).
    • The private version of the Atlas stores additional exRNA profiles that are not yet available to the public.
    • You must log into your Genboree account in order to access the private version of the Atlas.
    • If you are a member of the ERC Consortium and are unable to log in to the private atlas, please contact the Data Coordination Center () for assistance.

If you are interested in submitting data to the Atlas, visit the Data & Metadata Processing Guide page to learn more about the submission process.

Selecting Profiles

Using the ncRNA Search Bar

Faceted Charts

Viewing Selected Biosamples in Grid via Faceted Charts

Biosample Partition Grids

Viewing Biosamples in Biosample Partition Grid

Drill-down Sub-setting of Biosamples via Linear Tree

Viewing Selected Biosamples in Grid via Linear Tree

Downloading Profile Data and Metadata from the exRNA Atlas

Downloading Data and Metadata from the exRNA Atlas

Viewing exRNA Profiling Datasets

Viewing exRNA Profiling Datasets

Viewing Atlas Statistics

Viewing Atlas Statistics

Running Analyses and Viewing Analysis Results Using the exRNA Atlas

Running Analyses and Viewing Analysis Results Using the exRNA Atlas

BedGraphs

BedGraphs are publicly accessible, base pair level coverage maps of the genome and are present for every sample in the exRNA atlas. You can find them inside the CORE_RESULTS archives for any sample within a study (studies are defined by an accession such as EXR-TEST1-AN) . There will be 3 bedGraph files you can use
  • endogenousAlignments_genome_Aligned.bedgraph.xz - Shows where reads that aligned to the host genome fell
  • endogenousAlignments_genomeUnmapped_transcriptome_Aligned.bedgraph.xz - Has reads that did not align to the host genome
  • endogenousAlignments_genomeMapped_transcriptome_Aligned.bedgraph.xz - Shows where reads that aligned to the host genome fell in the transcriptome

Tools

Data Slicing

You can select regions of interest across the genome and samples of interest across any study present in the atlas and perform "data slicing" and retrieve a matrix with the coverage of your regions (rows) per sample (columns) by using the downloadable exRNA Data Slicer tool found here.

Genome browser

You can view which regions are detected in the atlas using the UCSC genome browser. These coverage files have been split by biofluid and library preparation kit i.e. you can see regions of the genome where at least one plasma samples processed by the TruSeq library preparation kit has reads. We provide two coverage cut offs: 1 read and 5 reads. Files can also be downloaded here.

RNA binding proteins (RBPs)

  • For the publicly available 150 RBPs where ENCODE/ENCORE have performed eCLIP (a method to determine where a protein binds across the genome), we have intersected regions bound by the RBPs with exRNA reads. Two versions of files where the RBP binding regions are present are available. All of these files are present inside each study (an accession EXR-TEST1-AN). Please note though there are 150 RBPs, there will be 296 files. This occurs because ENCODE/ENCORE profiled the RBPs in one OR two different cell lines. For RBPs profiled in 1 cell line there is only one file. For those profiled in two cell lines there are 3 files = one for HepG2, one of K562, and one for a merged file where we have merged regions found in both cell lines.

1) For each study, you can view reads that fall into a give RBP's binding sites across samples. You can find these in the postProcessedResults files. Through the atlas datasets page, you can download All Summary Files using the download icon in the bottom right of each dataset card or you can access them through the FTP. There is a folder name _intersect_individual_RBP.combined_samples.tgz which houses the RBP coverage files for that study.

2) For each sample, you can look at coverage of reads that fall into all 150 RBPs. On the atlas, you can select samples in the sample viewer and download the Core Results Archives - inside the fastq folder there will be a endogenousAlignments_genome_Aligned_intersect_individual_RBP.tgz folder which houses the 96 files for each sample. These regions have been intersected so if RBP A binds to chromosome 1, 1:10 and RBP B binds to chromosome 1, 5:15 then three regions will be created 1:5, 5:10, and 10:15. In these files, the rows are the overlapping regions and the columns are for each RBP.

exRBPs

Data for the exRBPs that have been intersected with the atlas data is available in forms

  • For the publicly available 150 RBPs where ENCODE/ENCORE have performed eCLIP (a method to determine where a protein binds across the genome), we have intersected regions bound by the RBPs with exRNA reads. Two versions of files where the RBP binding regions are present are available. Please note though there are 150 RBPs, there will be 296 files. This occurs because ENCODE/ENCORE profiled the RBPs in one OR two different cell lines. For RBPs profiled in 1 cell line there is only one file. For those profiled in two cell lines there are 3 files = one for HepG2, one of K562, and one for a merged file where we have merged regions found in both cell lines.

1) For each study, you can view reads that fall into a give RBP's binding sites across samples. You can find these in the postProcessedResults files. Through the atlas datasets page, you can download All Summary Files using the download icon in the bottom right of each dataset card or you can access them through the FTP. There is a folder name _intersect_individual_RBP.combined_samples.tgz which houses the RBP coverage files for that study.

2) For each sample, you can look at coverage of reads that fall into all 150 RBPs. On the atlas, you can select samples in the sample viewer and download the Core Results Archives - inside the fastq folder there will be a endogenousAlignments_genome_Aligned_intersect_individual_RBP.tgz folder which houses the 96 files for each sample. These regions have been intersected so if RBP A binds to chromosome 1, 1:10 and RBP B binds to chromosome 1, 5:15 then three regions will be created 1:5, 5:10, and 10:15. In these files, the rows are the overlapping regions and the columns are for each RBP.

Explorer Tool

The exRNA Atlas Explorer tool allows you to visualize the RBPs across any dataset or sets of datasets in the atlas. The tool is available here

Learn More About the exceRpt small RNA-seq Data Analysis Pipeline

exceRpt Homepage

Genboree Tutorial for Using exceRpt

Understanding Your exceRpt Results

exceRpt Version Updates

exRNA Atlas v3

exRNA Atlas v3

Using ~6,500 exRNA profiles from human serum, plasma, cerebrospinal fluid, urine, and saliva across 60 datasets, this study identifies >30 million unique extracellular RNA genomic loci (exGLs) covering >18% of the human genome expressing exRNA. All exGLs are viewable via UCSC Genome Browser track hub

Datasets used to generate exGLs are available here

We assigned each exGL to a unique identifier, exGLids. exGLids and their annotations can be accessed via User Interface or programmatically via APIs or as TSVs

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