News & Updates
October 14th, 2016
We have currently changed the news page to direct HERE. All news articles you see below have also been moved to this new page.
Cheers,
ENCODE DCC
October 3rd, 2016
127 new ENCODE experiments released in September 2016 on the ENCODE portal, including,
- 55 ChIP-seq experiments
- 32 shRNA-followed by RNA-seq experiments
- 20 eCLIP experiments
- 8 DNase-seq experiments
- 7 RBNS experiments
- 5 ChIA-pet experiments
August 25th, 2016
111 Annotation File Sets of promoter-like and enhancer-like regions have been released! More information on how the DAC called these enhancer-like and promoter-like regions can be found under Encyclopedia, about page. You can also go directly to the DAC websites: Methods for calling Enhancer-like Regions and Methods for calling Promoter-like Regions.
August 3rd, 2016
With collaborations from the DAC (Data Analysis Center), a total of 336 Annotation File Sets of promoter-like and enhancer-like regions have been released! More information on how the DAC called these enhancer-like and promoter-like regions can be found under Encyclopedia, about page. You can also go directly to the DAC websites: Methods for calling Enhancer-like Regions and Methods for calling Promoter-like Regions.
The DAC's code repository for promoter-like and enhancer-like regions are found here. Huge thank you to Michael Purcaro and Jill Moore for the help.
July 20th, 2016
Happy to annouce the release of mouse e10.5 histone ChIP-seq dataset from from the Ren lab, available on the portal here.
July 6th, 2016
Data release: 367 modERN datasets
We are pleased to announced that a whopping 367 modERN datasets have just been released in the ENCODE portal.
June 29th, 2016
182 new datasets were released in June 2016.
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
Human:
Check them all out here |
May 24, 2016
Data release: 50 more modERN experiments
We are pleased to announce 50 more modERN ChIP-seq experiments ENCODE portal, with now great total of 198 experiments released this month.
May 13, 2016
Data release: First Hi-C data for the ENCODE Project
We are pleased to announce the first release on the ENCODE portal of Hi-C data, from Job Dekker's lab. We have released the fastq files and associated metadata, and look forward to hosting analysis and visualization files soon.
May 10, 2016
Data release: modERN (model organism encyclopedia of regulatory networks)
We are pleased to announce the first release on the ENCODE portal of modERN data, an extension of the modENCODE effort led by Robert Waterston at UW. We have released today 39
May 5, 2016
Data release: Genomics of Gene Regulation
We are pleased to announce the first release on the ENCODE portal of Genomics of Gene Regulation data, an RNA-seq and a DNase-seq treatment time series of 100nM dexamethasone on the A549 cell line from the Reddy Lab at Duke University.
May 3rd, 2016
180 new datasets were released in April 2016.
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
Human:
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Mouse:
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Fly:
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April 26th, 2016
Kudos to our ENCODE collaborators, the Yeo lab, for their recent publication in Nature Methods. Check out all the eCLIP-seq (enhanced CLIP-seq) data here.
April 15, 2016
Abstract deadline for talk consideration at the 2016 ENCODE Users Meeting is May 16th, 2016. Register and submit abstract here!
April 1, 2016
Data release: 306 human and 188 mouse datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal since the beginning of 2016:
- Human:
- 112 shRNA RNA-seq assays, 19 CRISPR RNA-seq assay
- 89 ChIP-seq
- 60 RNA-seq
- 9 microRNA counts
- 8 microRNA-seq
- 5 whole genome bisulfite sequencing
- 4 RAMPAGE
- Mouse:
- 77 ChIP-Seq
- 43 microRNA counts
- 58 microRNA-seq
- 10 ATAC-seq
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to metadata quality standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
March 22, 2016
We are happy to announce that the second annual ENCODE Users Meeting will be held at Stanford University on June 8th-10th, 2016.
More details at www.encode2016.org
October 6, 2015
Roadmap Epigenomics metadata integrated
The Roadmap Epigenomics Mapping Consortium (Roadmap) metadata has been fully incorporated into this site including the standardization of terms and ontologies. The experimental metadata can now be searched and explored alongside the ENCODE data. However, the raw data is still housed at dbGAP and the hg19 processed data is housed at GEO. Each Roadmap experiment has a link to the corresponding GEO submission..
We are pleased to announce that 3127 Roadmap experiments have been released on the ENCODE Portal including:
- ChIP-seq: 1884 experiments
- Dnase-seq: 373 experiments
- RNA-seq: 345 experiments
- shotgun bisulfite-seq assay: 145 experiments
June 23, 2015
Data release: 3 human and 91 mouse datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 3 RNA Bind-n-Seq ssays
- Mouse: 64 ChIP-Seq, 15 RNA-seq, 12 whole genome bisulfite sequencing ssays
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
June 17, 2015
Data release: 12 human datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 10 RNA-seq, 2 DNAse-seq assays
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
May 28, 2015
Changelog
A key feature of the ENCODE Portal is the ability to programmatically query metadata and URLs to files via the REST API. To improve transparency about the changes to the objects that comprise the ENCODE metadata schema, we are publishing changelogs for each object. To view the changelog, replace the following URL with the object name:
https://www.encodeproject.org/profiles/changelogs/[object_name].md
For example, viewing the changelog for the file.json object would be
https://www.encodeproject.org/profiles/changelogs/file.md
May 18, 2015
Data release: 12 human datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 8 RNA-seq, 3 RNA Bind-n-Seq, 1 iCLIP assays
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
May 13, 2015
Updates to publications using ENCODE data
The community publication page at the ENCODE Portal has been updated to include 519 new publications that use ENCODE data, published by authors not funded by ENCODE. The addition of these publications brings the total of community publications to 1195. Please contact Mike Pazin at NHGRI to suggest publications to add to these lists.
April 13, 2015
Data release: 28 human datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human:16 RAMPAGE, 12 RNA Bind-n-Seq assays
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
March 31, 2015
Data release: 4 human datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 4 DNase-seq assays
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
March 11, 2015
Graphical display of pipelines
Experiment pages have been updated to show a graphical display of the pipeline used to generate the processed files associated with that experiment. The graphical display includes the software used to generate a file, the version of that software (when known), and the accessions of the files that are inputs and outputs of that software. The graphical display of which steps in a pipeline generated which files demonstrates the data provenance of those files.
See data from ENCSR181KQJ, an RNA-seq assay on the mouse G1E-ER4 cell line.
March 9, 2015
Batch Download
The links to download data files for a search result of assays can now be downloaded via the Batch Download feature. Click on the "Download" button once a list of assays has been identified. When clicked, instructions on how to download the files (using xargs -n 1 curl -O -L < files.txt) and a link to the Batch Download help doc explaining the columns that are included in the metadata.tsv spreadsheet. Click on "Download" again to begin downloading the files.txt file that contains the URLs to the metadata.tsv as well as each file.
March 3, 2015
First announcement: ENCODE Users Meeting
An ENCODE User's meeting will be held at at the Bolger Center in Potomoc, MD from June 29 - July 1, 2015. Attendees will learn how to navigate, analyze, use, and integrate ENCODE data and analysis pipelines. Visit http://encode2015.org for the most current information.
February 12, 2015
Data release: 1 human and 3 mouse datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 1 ChIP-seq assay (control)
- Mouse: 3 RNA Bind-n-Seq assays
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
January 8, 2015
Data release: 5 human and 3 mouse datasets
We are pleased to announce that the following datasets that are part of the Lin S, et al. (2014) Proc Natl Acad Sci U S A 48:17224 publication have been released on the ENCODE Portal:
- Human: 8 RNA-seq assays
- Mouse: 3 RNA-seq assays
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
December 17, 2014
Data release: 114 human and 98 mouse datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 78 shRNA knockdown followed by RNA-seq, 15 RNA-seq, and 21 RNA Bind-n-Seq assays
- Mouse: 15 RNA-seq, 74 ChIP-seq, 9 whole genome bisulfite sequencing assays
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
Read the new data release policy.
December 8, 2014
Data release: 88 human and 11 mouse datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 10 RNA-seq
- Mouse: 10 RNA-seq, 15 ChIP-seq
- Fly: 108 RNA-seq
This release includes new fly RNA-seq data from an extension of the modENCODE project.
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
Read the new data release policy.
December 1, 2014
Updates to publications using ENCODE data
The publication page at the ENCODE Portal has been updated to include the supplemental sites for the modENCODE/ENCODE worm-fly-human comparison publications as well as the mouse-human comparison publications. In addition, more than 250 publications that have used ENCODE and modENCODE data in their work have been added to the portal. Please contact Mike Pazin at NHGRI to suggest publications to add to these lists.
November 20, 2014
Data release: 88 human and 11 mouse datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 57 shRNA knockdown followed by RNA-seq, 19 RNA-seq, 11 RAMPAGE, 1 ChIP-seq
- Mouse: 10 RNA-seq, 1 ChIP-seq
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
Read the new data release policy.
November 19, 2014
Mouse ENCODE Consortium papers published
Recent findings from the mouse ENCODE Consortium investigating the genomic elements in the mouse model organism and its comparison to human are now published. The list of publications and data used in these publications are detailed on the supplemental website.
November 19, 2014
Create custom track hubs from a search result
Data from a search results of assays can now be visualized at the UCSC Genome Browser. Once a list of assays has been filtered to under 500 experiments based on assay type, a biosample type, or any arbitrary set of searches or filters, the "Visualize" button will be active. When clicked, the button will activate the assembly of all the experiment signal files (in bigWig format) and peak files (in bigBed format) available from the search result into a track hub for display at the UCSC Genome Browser. Once at the UCSC Genome Browser, the display parameters can be adjusted for the entire track hub or each individual track.
The ability to generate a track hub based on a search result allows custom subsets of experiments to be visualized. These subsets of experiments may not be the default view at the UCSC Genome Browser or any other browser that supports track hubs. For example, one search result might include all ChIP-seq assays that use mouse stem cells while another search result might include all RNA-seq, RAMPAGE, and CAGE assays for a search of K562. Like all track hubs, the track hub from a search will remain in your session until it is disconnected.
October 16, 2014
First version of the ENCODE genomics annotations
The first version of the ENCODE genomic annotations have been released. The set of annotations includes an expression matrix, transcription start sites, and candidate enhancers as well as a comprehensive set of publications that contain proposed annotations in the supplemental data.
The list of annotations is available by selecting "Annotations" from the "Data" menu in the toolbar.
October 16, 2014
Data release: 85 human datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 85 shRNA knockdown followed by RNA-seq
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
Read the new data release policy.
October 9, 2014
Antibody pages updated
The antibody pages representing lots of antibodies that are used by the ENCODE project have been updated to reflect the new antibody characterization standards. New features on the page include a listing of all cell types, in any species, that have been characterized using the antibody lot, images and documents supporting the characterization of that antibody lot in that cell type, and a list of experiments that used that specific antibody lot. Also displayed on the page for the antibody lot and each characterization is a status, such as "compliant" or "eligible for new data", representing whether the antibody has been characterized to the standards defined by the Consortium.
Search and filter for antibody lots used by the ENCODE project by selecting "Antibodies" from the "Data" menu in the toolbar or entering an antibody accession (e.g., ENCAB929ZIJ), protein target (e.g., select antibodies after a search for CTCF), or product information (e.g., search for Active Motif 39137) into the search box.
Additional detail about the information displayed on the new pages is available on the antibody characterization help document.
September 29, 2014
Data release: 13 human and 3 mouse datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 3 RNA-seq
- Mouse: 13 RNA-seq
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
Read the new data release policy.
September 12, 2014
Data release: 23 human and 5 mouse datasets
We are pleased to announce that the following datasets have been released on the ENCODE Portal:
- Human: 16 ChIP-seq, 4 iCLIP, and 3 RAMPAGE
- Mouse: 4 RNA-seq and 1 Shotgun Bisulfite-seq
This release includes a new assay:
- iCLIP (individual-nucleotide resolution UV-cross-linking and immunoprecipitation): identifies the binding site of RNA-binding proteins at individual nucleotide resolution (PMID: 20601959, PMID: 2155900)
These data, along with other released ENCODE data, are available at the ENCODE Portal. Recently released data can be identified by selecting a month under the "Date released" filter. View data from this current release.
The new data are released under a rapid release policy by which primary data (e.g., fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for these data.
Read the new data release policy.
August 28, 2014
modENCODE and ENCODE comparison papers published
Publications from the modENCODE and ENCODE consortia comparing the expression, regulatory features, and chromatin structure in D. melangoster, C. elegans, and H. sapiens are now available at Nature. The data used in the analyses of these publications as well as companion papers are listed on a supplemental web site.
August 19, 2014
New ENCODE portal released
We are pleased to announce the release of the new ENCODE portal at https://www.encodeproject.org/. The ENCODE portal serves as the primary and comprehensive source for data and information about the ENCODE project. The portal contains tools for browsing and searching data generated by the ENCODE consortium via assays, biological samples, and experimental reagents used. View the Getting Started document for an introduction to the new ENCODE portal.
The portal includes all released ENCODE data from the production phase of the project, including newer data for 700+ assays that have been released under a rapid release policy. This policy releases the primary data (e.g., fastq sequence files) immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. There is no moratorium on external use for this data. For more detail, view the new data release policy.
The ENCODE tools, genome browser tracks, and downloads developed during the first production phase will remain available at the UCSC Genome Browser site, http://genome.ucsc.edu/ENCODE. Questions about the new ENCODE portal can be sent to encode-help@lists.stanford.edu.
July 17, 2014
Data Release from ENCODE: 760 experiments of ChIP-seq, RNA-seq, ChIA-Pet and 3 new assay types in human and mouse
The ENCODE Data Coordination Center is pleased to announce the first public release of data from the third phase of ENCODE. This phase represents a continuation of ENCODE and Mouse ENCODE through an additional four years of high-throughput whole-genome data production, with additional resources and emphasis on uniform data processing, analysis and functional validation. View the participants and projects in this phase of ENCODE.
This data release includes the following datasets:
- Human: 257 ChIP-seq, 164 RNA-seq (includes 25 with shRNA knockdown), 22 RAMPAGE, 7 ChIA-PET, 20 RNA Bind-n-Seq
- Mouse: 260 ChIP-seq, 2 RNA-seq, 28 Shotgun Bisulfite-seq (WGBS)
New assays in this phase of ENCODE include:
- RAMPAGE: Identifies transcriptional start sites with quantification (PMID: 24510412, PMID: 22936248)
- Shotgun Bisulfite-seq (WGBS): Analyzes DNA methylation at high resolution (PMID: 19829295)
- RNA Bind-n-Seq: Identifies binding sequences and measures affinity of protein binding to RNA, using a cell-free system (PMID: 24837674)
This data, along with all files from the previous phase of ENCODE, are available from the new ENCODE DCC website (encodedcc.org).
Going forward, the DCC website and ENCODE portal will merge to provide a single site with comprehensive information about the ENCODE project and extensive user tools for locating data of interest from all phases of ENCODE production. The ENCODE tools, tracks, and downloads developed during the first production phase will remain available at the UCSC Genome Browser site, http://genome.ucsc.edu/ENCODE. For newer data, the 'Visualize Data' button under the Files section of the new site's Experiment pages launches a Genome Browser view for processed data suitable for visualization.
The new data is released under a rapid release policy by which primary data (e.g. fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for this data. View the new data release policy.
June 16, 2014
Visualize tracks on the UCSC Genome Browser via track-hubs-on-the-fly
Since the new ENCODE Portal focuses on access to the data via metadata searches, the ability to visualize tracks at the UCSC Genome Browser via track hubs has been released. When there are data suitable for visualization, the 'Visualize Data' button under the Files section of the new site's Experiment pages launches a Genome Browser via a track hub-on-the-fly feature.
March 24, 2014
Updated data release policy
The ENCODE data release policy has been updated so that the scientific community may freely download, analyze and publish results based on any ENCODE data without restrictions as soon as they are released. We request that researchers who use ENCODE datasets (published or unpublished) in publications and talks cite the ENCODE Consortium. Further details are described in the full ENCODE data release policy.
March 17, 2014
Antibody characterization standard updated
The ENCODE consortium has developed guidelines and best practices to ensure high-quality immunoprecipitation-based data. Characterization of an antibody's specificity and sensitivity are included as part of these guidelines (PMID:22955991). The antibody characterizations have been updated to include chromatin regulators and RNA binding-proteins.
The updated antibody characterization document is available for download along with other experimental guidelines.
February 13, 2014
ENCODE data with expanded metadata released on new DCC portal
The ENCODE DCC has released its preview of the new ENCODE portal containing ENCODE data with an expanded set of metadata. The metadata associated with biosamples and assays have been mapped to ontologies. In addition, the assays have been grouped as experiments that reflect the number of replicates that were performed as part of the experiment. Metadata can be searched using the search box or browsed using the faceted search interface.
November 12, 2013
Materials from ENCODE/Roadmap Epigenomics Tutorial at ASHG2013 available online
We are happy to announce that handouts from the ASHG tutorial are available online now:
http://www.genome.gov/27555330
You can access this page by going to the tutorials page under the Help menu item. Then select the "ENCODE Tutorials available from NHGRI" link.