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In this video, I’ll show you how to search for experiments and samples in the Epigenomics
database, using the Browser tool. I'll start on the Epigenomics home page and select ‘Browse
Experiments’ from the Tools section.
All experiments currently in the Epigenomics database are accessible in the Browser window.
Each experiment represents a single epigenetic feature assayed on a particular biological
sample. You can also view records at the biological sample level by toggling the selector in the
upper left.
Each row in the Browser represents a distinct experiment. A default set of attirbutes are
displayed as columns, and the view can be customized. Columns can be sorted by clicking
on the column headers and additional columns can be added by using the configure button.
Experiments and samples can be filtered by entering text in the filter box, using terms
for cell types, cell lines, tissues, and epigenetic feature types. Or, you can use these pre-set
filter options.
For example, if I'm interested in experiments performed on human embryonic stem cells, specifically
the H1 cell line, I can filter by entering those terms into the free text filter, or
by using the pre-set filters. I’ll select *** sapiens, then ‘embryonic stem cell,
H1’ and finally, H3K4me3, for the feature, histone H3 lysine 4 trimethylation. The Browser
now displays the results of these filters.
Experiments can be selected by clicking the check boxes, and all samples can be selected
or deselected by clicking the text in the table header.
Clicking an experiment ID redirects you to a record where more detailed information can
be found. After selecting experiments, notice that several
icons become active within the Browser window. Clicking on the “View on Genome” button
loads your selected experiments to the Sequence Viewer.
Selecting the download button presents options to download epigenomic track data, or export
the content of the Browser window as a table.
Selecting the “View details” icon redirects you to the selected experiment or sample records.
Selected experiments can be copied to the Clipboard for temporary storage, or if you
have a MyNCBI account, to a collection for long term storage.
That’s the end of this demonstration. Note the link to Help documentation, and send questions
or comments by using the ‘Write to the Help Desk’ link.