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Extracellular RNA Atlas

Abbreviation:exRNA Atlas

General Information

The exRNA Atlas is the data and metadata repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas 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. ERCC-developed quality metrics are uniformly applied to the datasets. The exRNA Atlas accepts submissions for RNA-seq or qPCR data.

Homepage https://exrna-atlas.org

Countries that developed this resource United States

Created in 2016

Taxonomic range

Homo sapiens

Mus musculus

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: exRNA Atlas; Extracellular RNA Atlas; DOI: https://doi.org/10.25504/FAIRsharing.xcvp6a; Last edited: April 16, 2021, 6:44 p.m.; Last accessed: Apr 21 2021 6:39 p.m.

Publication for citation exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. Murillo OD. et al.; Cell ; 2019; 10.1016/j.cell.2019.02.018;

This record is maintained by thistlew ORCID and brl-exrna

Record added: Sept. 11, 2018, 6:33 p.m.
Record updated: April 16, 2021, 6:44 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.xcvp6a' by 'The FAIRsharing Team' at 18:44, 16 Apr 2021 (not approved):

	'publications' has been modified:
		Before:
			Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.|Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A|Journal of Extracellular Vesicles|2015
			The NIH Extracellular RNA Communication Consortium.|Ainsztein AM, Brooks PJ, Dugan VG, Ganguly A, Guo M, Howcroft TK, Kelley CA, Kuo LS, Labosky PA, Lenzi R, McKie GA, Mohla S, Procaccini D, Reilly M, Satterlee JS, Srinivas PR, Church ES, Sutherland M, Tagle DA, Tucker JM, Venkatachalam S|Journal of Extracellular Vesicles|2015
			exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.|Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A|Cell|2019
		After:
			Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.|Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A|Journal of Extracellular Vesicles|2015
			The NIH Extracellular RNA Communication Consortium.|Ainsztein AM, Brooks PJ, Dugan VG, Ganguly A, Guo M, Howcroft TK, Kelley CA, Kuo LS, Labosky PA, Lenzi R, McKie GA, Mohla S, Procaccini D, Reilly M, Satterlee JS, Srinivas PR, Church ES, Sutherland M, Tagle DA, Tucker JM, Venkatachalam S|Journal of Extracellular Vesicles|2015
			exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.|Murillo OD. et al.|Cell|2019
		Added:
			exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.|Murillo OD. et al.|Cell|2019
		Removed:
			exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.|Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A|Cell|2019

Edits to 'https://fairsharing.org/FAIRsharing.xcvp6a' by 'thistlew' at 21:25, 22 Apr 2019 (approved):

	'related_databases' has been modified:
		Before:
		After:
			Gene Expression Omnibus
			Database of Genotypes and Phenotypes
		Added:
			Gene Expression Omnibus
			Database of Genotypes and Phenotypes
		Removed:

	'standardsImplemented' has been modified:
		Before:
		After:
			JavaScript Object Notation for Linking Data
		Added:
			JavaScript Object Notation for Linking Data
		Removed:

	'accessPoints' has been modified:
		Before:
		After:
			REST|https://exrna-atlas.docs.stoplight.io/|exRNA Atlas JSON-LD API
		Added:
			REST|https://exrna-atlas.docs.stoplight.io/|exRNA Atlas JSON-LD API
		Removed:

	'tools' has been modified:
		Before:
			extra-cellular RNA processing toolkit (exceRpt)|4.6.2|https://rkitchen.github.io/exceRpt/
		After:
			extra-cellular RNA processing toolkit (exceRpt)|4.6.2|https://gersteinlab.github.io/exceRpt/
			XDec (Expression Deconvolution)|1.0.2|https://github.com/BRL-BCM/XDec
		Added:
			extra-cellular RNA processing toolkit (exceRpt)|4.6.2|https://gersteinlab.github.io/exceRpt/
			XDec (Expression Deconvolution)|1.0.2|https://github.com/BRL-BCM/XDec
		Removed:
			extra-cellular RNA processing toolkit (exceRpt)|4.6.2|https://rkitchen.github.io/exceRpt/

	'publications' has been modified:
		Before:
			Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.|Subramanian SL, Kitchen , Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A|Journal of Extracellular Vesicles|2015
			The NIH Extracellular RNA Communication Consortium.|Ainsztein AM, Brooks PJ, Dugan VG, Ganguly A, Guo M, Howcroft TK, Kelley CA, Kuo LS, Labosky PA, Lenzi R, McKie GA, Mohla S, Procaccini D, Reilly M, Satterlee JS, Srinivas PR, Church ES, Sutherland M, Tagle DA, Tucker JM, Venkatachalam S|Journal of Extracellular Vesicles|2015
		After:
			Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.|Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A|Journal of Extracellular Vesicles|2015
			The NIH Extracellular RNA Communication Consortium.|Ainsztein AM, Brooks PJ, Dugan VG, Ganguly A, Guo M, Howcroft TK, Kelley CA, Kuo LS, Labosky PA, Lenzi R, McKie GA, Mohla S, Procaccini D, Reilly M, Satterlee JS, Srinivas PR, Church ES, Sutherland M, Tagle DA, Tucker JM, Venkatachalam S|Journal of Extracellular Vesicles|2015
			exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.|Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A|Cell|2019
		Added:
			Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.|Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A|Journal of Extracellular Vesicles|2015
			exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.|Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A|Cell|2019
		Removed:
			Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.|Subramanian SL, Kitchen , Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A|Journal of Extracellular Vesicles|2015

Edits to 'https://fairsharing.org/FAIRsharing.xcvp6a' by 'The FAIRsharing Team' at 13:58, 15 Oct 2018 (approved):

	'description' has been modified:
		Before: The exRNA Atlas (https://exrna-atlas.org) is the (meta)data repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas 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 (https://rkitchen.github.io/exceRpt/) and ERCC-developed quality metrics (https://exrna.org/resources/data/data-quality-control-standards/) are uniformly applied to these datasets.  If you're interested in submitting your RNA-seq or qPCR data to the Atlas, view our Submission Guide (http://genboree.org/theCommons/projects/exrna-mads/wiki/Data%20Submission%20to%20DCC%20using%20FTP). 
		After: The exRNA Atlas is the data and metadata repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas 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. ERCC-developed quality metrics are uniformly applied to the datasets.  The exRNA Atlas accepts submissions for RNA-seq or qPCR data.

	'dataProcesses' has been modified:
		Before:
			Web Interface
			Automated Pipeline
			Manual Curation
			Manual Release
			Version History
			Data Submission
		After:
			Web Interface
			Automated Pipeline
			Manual Curation
			Manual Release
			Version History
			Data Submission
			exRNA Atlas Quality Control Metrics
		Added:
			exRNA Atlas Quality Control Metrics
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.xcvp6a' by 'The FAIRsharing Team' at 10:20, 17 Sep 2018 (approved):

	'supportLinks' has been modified:
		Before:
			email|thistlew@bcm.edu
			online documentation|http://genboree.org/theCommons/projects/exrna-mads/wiki/exRNA%20Atlas
		After:
			email|thistlew@bcm.edu
			online documentation|http://genboree.org/theCommons/projects/exrna-mads/wiki/exRNA%20Atlas
			online documentation|https://exrna.org/resources/data/data-quality-control-standards/
		Added:
			online documentation|https://exrna.org/resources/data/data-quality-control-standards/
		Removed:

	'dataProcesses' has been modified:
		Before:
			Web Interface
			Automated Pipeline
			Manual Curation
			Manual Release
			Version History
		After:
			Web Interface
			Automated Pipeline
			Manual Curation
			Manual Release
			Version History
			Data Submission
		Added:
			Data Submission
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.xcvp6a' by 'thistlew' at 06:14, 16 Sep 2018 (approved):

	'description' has been modified:
		Before: The exRNA Atlas is the (meta)data repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas 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 (https://rkitchen.github.io/exceRpt/) and ERCC-developed quality metrics (https://exrna.org/resources/data/data-quality-control-standards/) are uniformly applied to these datasets.  If you're interested in submitting your RNA-seq or qPCR data to the Atlas, view our Submission Guide (http://genboree.org/theCommons/projects/exrna-mads/wiki/Data%20Submission%20to%20DCC%20using%20FTP). 
		After: The exRNA Atlas (https://exrna-atlas.org) is the (meta)data repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas 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 (https://rkitchen.github.io/exceRpt/) and ERCC-developed quality metrics (https://exrna.org/resources/data/data-quality-control-standards/) are uniformly applied to these datasets.  If you're interested in submitting your RNA-seq or qPCR data to the Atlas, view our Submission Guide (http://genboree.org/theCommons/projects/exrna-mads/wiki/Data%20Submission%20to%20DCC%20using%20FTP).

Edits to 'https://fairsharing.org/FAIRsharing.xcvp6a' by 'thistlew' at 03:19, 15 Sep 2018 (approved):

	'description' has been modified:
		Before: The exRNA Atlas is the (meta)data repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas includes small RNA sequencing and qPCR-derived <b>exRNA</b> profiles from human and mouse biofluids. All RNA-seq datasets are processed using version 4 of the exceRpt small RNA-seq pipeline (https://rkitchen.github.io/exceRpt/) and ERCC-developed quality metrics (https://exrna.org/resources/data/data-quality-control-standards/) are uniformly applied to these datasets.  If you're interested in submitting your RNA-seq or qPCR data to the Atlas, view our Submission Guide (http://genboree.org/theCommons/projects/exrna-mads/wiki/Data%20Submission%20to%20DCC%20using%20FTP). 
		After: The exRNA Atlas is the (meta)data repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas 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 (https://rkitchen.github.io/exceRpt/) and ERCC-developed quality metrics (https://exrna.org/resources/data/data-quality-control-standards/) are uniformly applied to these datasets.  If you're interested in submitting your RNA-seq or qPCR data to the Atlas, view our Submission Guide (http://genboree.org/theCommons/projects/exrna-mads/wiki/Data%20Submission%20to%20DCC%20using%20FTP).

Edits to 'https://fairsharing.org/FAIRsharing.xcvp6a' by 'thistlew' at 03:19, 15 Sep 2018 (approved):

	'description' has been modified:
		Before: The exRNA Atlas is the (meta)data repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas 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 (https://rkitchen.github.io/exceRpt/) and ERCC-developed quality metrics (https://exrna.org/resources/data/data-quality-control-standards/) are uniformly applied to these datasets.  If you're interested in submitting your RNA-seq or qPCR data to the Atlas, view our Submission Guide (http://genboree.org/theCommons/projects/exrna-mads/wiki/Data%20Submission%20to%20DCC%20using%20FTP). 
		After: The exRNA Atlas is the (meta)data repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas includes small RNA sequencing and qPCR-derived <b>exRNA</b> profiles from human and mouse biofluids. All RNA-seq datasets are processed using version 4 of the exceRpt small RNA-seq pipeline (https://rkitchen.github.io/exceRpt/) and ERCC-developed quality metrics (https://exrna.org/resources/data/data-quality-control-standards/) are uniformly applied to these datasets.  If you're interested in submitting your RNA-seq or qPCR data to the Atlas, view our Submission Guide (http://genboree.org/theCommons/projects/exrna-mads/wiki/Data%20Submission%20to%20DCC%20using%20FTP).

Edits to 'https://fairsharing.org/FAIRsharing.xcvp6a' by 'The FAIRsharing Team' at 20:44, 11 Sep 2018 (approved):

	'domains' has been modified:
		Before:
			Data visualization
			Differential gene expression analysis
			Pathway model
			RNA sequencing (RNA-Seq)
			qPCR
		After:
			Data visualization
			Differential gene expression analysis
			Life Science
			Pathway model
			RNA sequencing (RNA-Seq)
			Real time polymerase chain reaction (RT-PCR)
			qPCR
		Added:
			Life Science
			Real time polymerase chain reaction (RT-PCR)
		Removed:

	'licences' has been modified:
		Before:
			Data Access Policy|https://exrna.org/resources/data/data-access-policy-summary/|Data
		After:
			exRNA Atlas Data Access Policy|https://exrna.org/resources/data/data-access-policy-summary/|Data
		Added:
			exRNA Atlas Data Access Policy|https://exrna.org/resources/data/data-access-policy-summary/|Data
		Removed:
			Data Access Policy|https://exrna.org/resources/data/data-access-policy-summary/|Data

In Collections

NIH-supported data repositories

Support

General

support email	William Thistlethwaite
online documentation	exRNA Atlas Documentation
online documentation	Quality Control Metrics

Additional Information

Contact

William Thistlethwaite ORCID

Tools

extra-cellular RNA processing toolkit (exceRpt)	https://gersteinlab.github.io/exceRpt/	4.6.2
XDec (Expression Deconvolution)	https://github.com/BRL-BCM/XDec	1.0.2

Access / Retrieve Data

Conditions of Use

Applies to: Data use

exRNA Atlas Data Access Policy

Data Versioning

Version History

https://exrna-atlas.org/exat/versionHistory

Data Release

Manual Release

No link recorded

Data Curation

Automated Pipeline	No link recorded
Manual Curation	No link recorded
Data Submission	http://genboree.org/theCommons/projects/exrna-mads/wiki/Data%20Submiss ...
exRNA Atlas Quality Control Metrics	https://exrna.org/resources/data/data-quality-control-standards/

Data Access

Web Interface

No link recorded

REST Web Services

exRNA Atlas JSON-LD API

https://exrna-atlas.docs.stoplight.io/

Publications

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.

Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A
Journal of Extracellular Vesicles 2015

View Paper (PubMed) View Publication

The NIH Extracellular RNA Communication Consortium.

Ainsztein AM, Brooks PJ, Dugan VG, Ganguly A, Guo M, Howcroft TK, Kelley CA, Kuo LS, Labosky PA, Lenzi R, McKie GA, Mohla S, Procaccini D, Reilly M, Satterlee JS, Srinivas PR, Church ES, Sutherland M, Tagle DA, Tucker JM, Venkatachalam S
Journal of Extracellular Vesicles 2015

View Paper (PubMed) View Publication

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

Murillo OD. et al.
Cell 2019

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

JavaScript Object Notation for Linking Data

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by thistlew ORCID and brl-exrna

Funds

NIH Common Fund, USA (Government body)

Maintains

Grant Number(s)

1U54DA036134-01 (NIH Common Fund, USA)

Extracellular RNA Atlas

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