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Epigenomics Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.

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Epigenomics Help [Internet].

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Epigenomics Help

Created: ; Last Update: June 2, 2014.

How to Use the Sample and Experiment Browser

Summary

Learn how searching and filtering can be performed to identify samples and experiments in the Epigenomics database and how to select, save and view these records.

Searching and Filtering

All experiments and their corresponding samples currently in the Epigenomics database are displayed by default in the Browser window. Clicking the Experiments/Sample toggle button allows you to customize the Browser view to show either Experiment or Sample records (A). Additionally, Experiment and Sample records can be filtered by entering text in the filter box found within the sample browser (B). Search terms can include such things as cell lines (i.e. H1, IMR90), cell types (i.e. stem cell, fibroblast), tissue types (i.e. lung, spleen), and assayed features (i.e. H3K27me3). Additionally, there are three preset filtering options in the sample browser allowing you to filter by "Species", "Biological Source" or "Feature" (C).

Within the Browser window, a series of columns are displayed that indicate the various attributes assigned to experiments and samples. Columns with additional attributes can be added. Click on the "Configure" icon and a pop-up dialog appears which allows you to choose the attributes you wish to display (D). Columns can be sorted alphabetically by clicking on the arrows in the column headings. Mouse over the column headings to reveal the arrows.

A count indicating the total number of experiments or samples available in the browser is indicated on the page to the left of the Browser window (see “All experiments” or “All samples”). “New experiments” or “New samples” include all records that have been added to the Epigenomics database in the past three months. “Recently viewed” indicates a count of the records that have been viewed in the past 8 hours. If you are logged in with a “My NCBI” account, it includes all records viewed in the past 6 months.

Selecting and Viewing Records

Experiments or Samples can be selected by clicking the check boxes on the left side of the Browser window. All records can be selected or deselected by clicking the “Select: All, None” links in the table header (E).

Clicking on an "Experiment ID" for a particular Experiment in the Browser window will bring you to the Experiment page. This page provides information about the experimental data track and provides additional experimental details such as the technique (i.e. ChIP-seq, DNase-seq, etc.) assay type and instrument used. Links are provided that allow viewing or downloading the data track (if available).

Clicking on a "Sample ID" for a particular sample in the Sample Browser window will bring you to the Sample page. This page indicates what data tracks are available for viewing and downloading for that sample. Biological attributes and data source information are also indicated on this page.

After records are selected, notice that several icons become active within the Browser window presenting you with new options. Clicking on the "View on Genome" button will bring you to a page where track data and viewing options are presented for the sample(s)/experiment(s) selected (F). Selecting the “Download” button will present a drop down with the options to download epigenomic track data or export the contents of the Browser window (G). Selecting the “View record details” icon will redirect you to the selected records (H).

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How To Manage Collections of Samples

Summary

Learn how to create and edit collections of Experiments or Samples and how to use My NCBI for maintaining those collections.

Creating and Editing Collections

Data selected from the Browser can be saved to the Clipboard, for temporary storage, or a Collection, for long term storage. After selecting samples, click the “Clipboard” icon to add samples to the clipboard (A). Selecting the “Collection” icon reveals a drop-down menu. You can create and name a new Collection, or you can add samples to an existing Collection by selecting it from the drop down menu. After you have made your selection, clicking the "Copy" button completes the action. If you created a new Collection it will now be listed under the "My Collections" heading on the left side of the page (C). Please note, an individual collection can contain both Experiment and Sample records, however the count reflecting the number of records in the collection will only show the number of Experiments or Samples depending on whether the Browser is set to display Experiments or Samples.

When a Collection is selected, the experiments or samples within the Collection will be displayed in the Browser window. Individual records can be selected by clicking the check box in the left column. Selected records can be removed from the collection by clicking the "Remove" icon. Additionally, members of existing Collections can be copied to the Clipboard, other Collections, or to a new Collection.

Maintaining Collections Through My NCBI

If you do not have a "My NCBI" account, your Collections will only be stored for 24 hours. If you have an account these Collections are stored indefinitely. More information about My NCBI accounts can be found here: http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/sites/myncbi/

Your collections can be accessed and managed from the "My NCBI Home" page. Click Collections and a list of your current collections are displayed. From here, Collections can be merged or deleted. Additionally, you can create a URL to share the collection by clicking on the Private link under sharing and following the instructions.

A collection called “Genome Viewer” is displayed by default. This collection is created by NCBI Epigenomics and is populated automatically with tracks that have been most recently viewed in the genome viewer interface (see below).

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How To View Genome Tracks

Summary

Learn how to use the View on Genome page to choose and view your genomic region of interest, genome browser and data tracks from selected samples.

Getting Started

After you have selected Experiments or Samples, clicking on the "View on Genome" button will bring you to the View page where you can select and set viewing options for genome track data and explore epigenomic data in gene-specific contexts. Alternatively, you can access the View page from the Sample, Study or Experiment pages by clicking on the "View on Genome" links. The View page in the Epigenomics database integrates the NCBI Sequence Viewer tool and search functionality that provides the ability to quickly navigate to queried genes and locations throughout the selected genome.

View on Genome

When you first come to the View page, you will be prompted to enter a gene or chromosome location into the “Gene or Location” box (A). Alternatively, you can select to view an entire chromosome by clicking on the respective buttons above the NCBI Sequence Viewer interface (B). When you perform a query for a particular gene, the results of the search are populated in the box below the query box (C). Autocomplete functionality has been incorporated and as you enter a gene name into the query box a list of possible matches is displayed. The query searches the NCBI Gene database and the list represents these results. If a specific chromosome is entered or specific chromosomal coordinates are entered, a list of genes found within these regions will be displayed in the results box under the query box. If a specific gene is searched for and found, the gene is highlighted in the query result box and the sequence viewer window will show the gene of interest with the data tracks that had been previously selected (D). If no data tracks had been selected previously a set of default tracks that have been manually curated will be displayed. Additional tracks can be added to the viewer interface. Clicking on the “Browse” button under the Add tracks heading will return you to the browser interface where additional tracks may be selected or deselected. Clicking on the “View on genome” button will return you to the viewer with the newly selected tracks being displayed in addition to the tracks that were previously being viewed (E). Clicking on the “Upload” button will redirect you to a page where tracks can be uploaded and then added to the viewer interface.

Tracks can also be viewed on the UCSC Genome Browser. Clicking on the “View on UCSC” button will load your selected tracks to the UCSC browser (F). If you have specified a gene or location on the Epigenomics View page, the UCSC browser will display the data at the same location.

By default, all genome tracks for the previously selected experiments or associated with the selected samples will be displayed. Please note this is conditional. Experiments or samples must be from the same species and use the same genome assemblies in order to be displayed at the same time. If you have samples from multiple species or assemblies you can use the “Species” drop down menu to select the species and genome assembly of interest (G).

Finally, a glossary feature in included. It will provide helpful information regarding which epigenomic features are currently being viewed. Additionally, experimental techniques may be briefly described.

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Configuring the Sequence Viewer interface

Below the window in which track data in displayed, there is a configuration panel that provides customization options for the sequence viewer interface (H). The “Active tracks” tab lists the tracks that are currently displayed (I). This will include the data tracks selected from epigenomics, and other tracks such as genes, translations, genomic variations, etc. Tracks in this tab can be re-ordered, selected, or deselected which impacts what is being displayed. The “Epigenomics” tab specifically lists the tracks that have been selected from the Epigenomics database (J). After making changes such as selecting, deselecting or reordering tracks, clicking on the “Configure” button will reload the sequence viewer with these changes (K). For more details about Sequence Viewer customization, please refer to the help documentation provided at the NCBI Sequence Viewer page (http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/projects/sviewer/). An informative instructional video is also available on the NCBI YouTube Channel (http://www.youtube.com/ncbinlm#p/c/2/TQOx2w18SW8).

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How To Download Genome Tracks

Summary

Learn how to use the Download page to select data tracks and file formatting options.

Getting Started

After you have selected records, clicking on the "Download" button in the Browser window will bring you to a page where you can select and set downloading options for genome track data.

Individual data tracks can be selected for download by using the checkboxes found in the table (A). Additionally, you can select species and alternate genome assemblies using the drop down menu that appears when tracks are selected from multiple species or from different genome assemblies (B). Clicking the "Download" button on this page will download all data associated with the samples selected(C). This list of tracks can be sorted by "Data type" (i.e. H3K27me3, BS-seq) "Sample" or “Feature” by clicking on the arrows in the column headers that appear when moused over,

The track data will be downloaded as .wig files. Raw data used to generate these .wig files, if available, can be found at the Gene Expression Omnibus (GEO) web site (http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/geo).

Files are downloaded as a single compressed .zip file containing the individual tracks. A readme file provides detailed information regarding the downloaded data.

Image epi_help_doc-Image005.jpg

How To Upload Genome Tracks

Users can also upload custom data tracks. Selecting the “Upload” button will redirect the user to a page from which custom data can be uploaded. A My NCBI account is required to use this functionality. In order to maintain privacy and to support long-term data storage, it is necessary for users to have and account and be signed in prior to uploading tracks. Accounts are free and may be established in the My NCBI part of the site (be aware that quotas on number of uploaded tracks per account may be adjusted over time depending on demand). For more information about My NCBI please refer to http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/myncbi .

On the upload page, certain pieces of information are required prior to beginning the upload. The user must specify a species and which genome assembly the data is aligned to (A). A feature type field is also required (B). Feature types include specific histone modifications (e.g. H3K4me3, H3K27me3), DNA methylation, chromatin accessibility etc. An autocomplete function is provided for this entry, but free text can be entered as well. This upload functionality supports popular file formats including BED and WIG. An auto-detect function determines file type.

Optional metadata fields are also available. User can assign biological attributes including cell types, cell line, tissue type as well as many others (C). When complete, users can drag and drop a local file into the “Add data” box below the attributes (D) or select the “Add data” button (E). This will allow local navigation to the file of interest on the user’s computer. Uploading will begin automatically upon selection of file or dropping into the “Add data” box. A progress bar displays the status as the data upload is proceeding.

Image epi_help_doc-Image006.jpg

Upon completion several options are presented: The data track can be viewed in the genome viewer interface, additional data tracks can be uploaded, or the user can return to the browser interface. If the user chooses to view the uploaded data, it will be displayed in the genome viewer above any other tracks. The data track title will be shown in the track header (F). Additional tracks can be added to the viewer be clicking the “Browse” button under the “Add tracks” heading. Selecting the adjacent upload button will return you to the upload page and repeat the upload process (G).

Image epi_help_doc-Image007.jpg

After tracks have been uploaded they will be displayed in the browser interface as an experiment and the user provided metadata will be displayed in the appropriate columns (H). This allows for uploaded data tracks to be selected for operations such as viewing in concert with other database tracks or adding to user created collections. All of a user’s uploaded tracks will be found in the “My Uploads” collection (I). Users can delete uploaded data tracks from the system when in the “My Uploads” collection. PLEASE NOTE: By using the My NCBI system, all of a user’s data is only visible and viewable by them. This information cannot be viewed, downloaded or used by any other users of the Epigenomics resource and is maintained privately. When a user logs out of the My NCBI system, these tracks are maintained, but will no longer be displayed.

Image epi_help_doc-Image008.jpg

How to Search for Studies and Samples

Summary

Learn how to use basic search, limits and advanced searching to more efficiently find Samples, Studies and Experiments of interest.

Getting Started

The Epigenomics database is indexed in Entrez. To search Epigenomics, type a word or phrase into the query box, then click on the Search button or press the Enter key. Combine search terms with connector words: "AND", "OR" or "NOT" using upper case letters.

Using Limits

"Limits" is available from a link above the search box on all Epigenomics pages, including the homepage. Restrict a search to items with links to full text, and make multiple choices within categories. Click the Search button after making selections to run the search. A "Limits Activated" message will appear above the search results list. Limits remain in effect until removed.

About Data Sources

Currently, NCBI Epigenomics does not take direct submissions of data. Data are selected from Gene Expression Omnibus (GEO) database and subjected to additional processing and tracking. GEO is a database of large-scale molecular abundance data generated for functional genomics studies. Because most of the experiments in scope for epigenomics are based on sequencing methodologies, there are often companion submissions to the Sequence Read Archive (SRA) database. Genome tracks may be attached to GEO submissions as supplementary files in a wide variety of formats. For molecular abundance graphs, we currently accept WIG and bigWig files. These data are subjected to computational analysis to identify the likely genome assembly and to ensure that all genome coordinates are in a valid range. Tracks are given accession numbers and changes are tracked using revision numbers and update dates. In some cases, submitted tracks that had been constructed using an older genome assembly may be remapped to reflect the current state of the genome. In this case, the derived track has a separate accession number and revision chain to keep it distinct from the original submission.

About Complete Epigenomes

Epigenome Classes as defined by the Roadmap Epigenomics Program

One of the goals of the Roadmap Epigenomics Project is to establish what are called “reference epigenomes.” These are high resolution, genome-wide maps of epigenetic modifications in a variety of human cell lines, primary cell and tissue types. The majority of the reference epigenomes generated will contain information on epigenetic modifications having to do with a core set of histone marks, DNA methylation, and chromatin accessibility, in addition to, gene expression data associating gene activity with the epigenetic modifications. A subset of reference epigenomes will also contain an expanded set of at least twenty additional histone modifications. For an epigenome to be considered complete it must contain, at the minimum, the following information: DNA methylation data, genome-wide mapping of the most informative “core” histone modifications (which currently includes H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H3K36me3), and RNA expression data.

Four classes of “reference epigenomes” have been established which are differentiated by the number of epigenetic features examined. These classes are distinguished as follows.

Class 1 Epigenomes

  • DNA methylation (whole genome bisulfite sequencing)
  • “core” histone modifications and an expanded set of histone modifications
  • RNA sequencing data (RNA-seq)
  • Chromatin accessibility

Class 2 Epigenomes

  • DNA methylation (whole genome bisulfite sequencing)
  • “core” histone modifications
  • RNA sequencing data (RNA-seq)
  • Chromatin accessibility

Class 3 Epigenomes

  • DNA methylation (RRBS, MeDIP-seq, MRE-seq)
  • “core” histone modifications
  • RNA sequencing data (gene expression microarray)
  • Chromatin accessibility (if possible)

Class 4 Epigenomes

  • DNA methylation (RRBS, MeDIP-seq, MRE-seq)
  • “core” histone modifications
  • RNA sequencing data (gene expression microarray)

Roadmap Epigenomics Project Web Resources

To facilitate the dissemination of data from the Roadmap Epigenomics Project, several web based resources have been created. This includes the Reference Epigenome Mapping Consortium page, the NCBI Epigenomics database, the NCBI Gene Expression Omnibus (GEO) data listings page, the Human Epigenome Atlas, and the Roadmap Epigenomics Visualization Hub. While the overall goal of these resources is the same, there are some differences with respect to available features. These features are highlighted below.

BrowserDownload data?Browse dataView DataUpdatesOther FeaturesUpload data?
Reference Epigenome Mapping Consortium HomepageLinks to data downloadClickable data matrix or visual data browserLinks to UCSC browser mirror (Epigenome Browser)Data: At each data freeze (4x/year)Protocols, publications, quality metrics, project and center/group informationNo (but linked Epigenome Browser supports upload)
NCBI Epigenomics Hub.wigSample (i.e. cell/tissue type) browser, experiment (i.e. epigenetic feature) browser, text searchNCBI epigenomics viewer or UCSC browser mirrorContinuously“Compare Samples” tool in development to identify regions of greatest chromatin differences, suggests GO terms and pathways most associated.Being implemented
NCBI Gene Expression Omnibusbed, .wig, .bam and SRABy sample, study, or data matrixNCBI Epigenomics viewerContinuouslyN/A
The Human Epigenome Atlas (on Genboree).bed, .wig by ftp or httpBy sample, assay, or clickable data matrixUCSC browser, Atlas Gene/Pathway browser (read densities across single genes or pathways)Data: At each data freeze (4x/year)Info on metadata, data flow, data quality. Tools for analysis via Genboree workbench (Independent tools and Galaxy pipelines). Data & functionality exposed via HTTP REST APIs for programmatic use and extension
Roadmap Epigenomics Visualization Hub and Load Track HubNoENCODE style data matrixUCSC browser mirror, or remote display at UCSC main site (load track hub)Data: At each data freeze (4x/year)UCSC mirror hosts integrative analysis tracks and summary tracks, tracks viewable at UCSC main siteBeing implemented
Human Epigenome Browser at Wash UYesExpandable data selection matrix and metadata matrixNext generation epigenome browserAt each data freezeGoogle map style zoom and pan, genomic data and metadata viewer, data collation view, pathway/gene set view, statistical analysisYes
Epigenome Browser UCSC mirror.bed, .wig through Table Browser. Individual reads not availableUCSC data selection matrix (ENCODE style)UCSC browser mirrorData: At each data freeze (4x/year)High-utility UCSC mirror tracksYes
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