Exercise solutions

 

Exercise 1 - Attach URLs of large files

(a) There are two main ways to attach a file containing your own data to view in Ensembl. Either:

From the Ensembl homepage, click on Use my own data in Ensembl, then click on Custom tracks to add a new track.

Or:

Click on the Custom tracks button in any Region in detail view in Ensembl.

A dialogue box labelled ‘Add a custom track’ will appear. We can name our data, for this exercise we will label our data ‘Illumina reads’.

Paste the URL of the BAM file itself (http://www.ebi.ac.uk/~emily/Workshops/BAM/GRCh38.20.illumina.merged.1.bam) into the data box.

Since this is a file, the interface is able to detect the “.BAM” file extension, thus it automatically labels the format as BAM. Click on Add data and close the menu.

(b) Search for the CDH22 gene and click on the Location tab. Click on Configure this page, and then on Your data in the menu. Select the Unlimited track style for your ‘Illumina reads’ track. Close the menu.

You can see that there are more RNASeq reads that map to the exons than reads that map to the introns of the gene.

(c) Zoom in to see the sequence itself by dragging out boxes in the view to zoom in or use the scale bar in the top right of the Region in detail image.

(d) Click on Configure this page and turn off this ‘Illumina reads’ track by selecting Off as the track style of the Your data track.

You can also remove the custom data by clicking on the tab Personal Data and then clicking on the ‘Trash’ icon associated with this data.

Exercise 2 - Track Hubs

(a) There are two ways to add the ENCODE Analysis Hub to view in Ensembl. Either:

Search for Encode from the Track Hub Registry homepage (https://trackhubregistry.org). Find the ENCODE Analysis Hub in the search results, click on View in Genome Browser and select Ensembl.

Once the Track Hub is added, search for the BRCA2 gene in the GRCh37 human genome assembly. Switch to the Location tab.

Or:
Search for the BRCA2 gene in the GRCh37 human genome assembly. Switch to the Location Tab.

Click on the Custom tracks button. Click Track Hub Registry Search and Search for Encode. Click Attach this hub for the ENCODE Integrative Analysis Data Hub.

(b) Click on Configure this page and click on ENCODE Histone Modifications Peaks. Turn on all available tracks for HeLa-S3 cells by hovering over the cell line name and clicking Select all HeLa-S3 in the pop up window (the boxes for HeLa-S3 will turn blue).

Click on ENCODE Transcription Factor Peaks. Turn on all available tracks for HeLa-S3 cells by hovering over the cell line name and clicking Select all HeLa-S3 in the pop up window (the boxes for HeLa-S3 will turn blue).

Close the menu to add the selected tracks.

(c) A number of different Transcription Factors and Histone Modifications, mainly surrounding the BRCA2 5’ region, are annotated.

Transcription Factors:
USF2, STAT1, Pol2S2, Mxl1, MAX, lnl1, E2F6, E2F4, MYC, C-MYC, CEBPB, POLR2A, POL2, POL2B

Histone Modifications:
H3K4me3, H3K9ac, H3K79me2, H3K4me3, H3k4me2, H3K36me3, H3K27ac

(d) Click on Configure this page and click on ENCODE Histone Modifications Signal. Turn on all available tracks for HeLa-S3 cells by hovering over the cell line name and clicking Select all HeLa-S3 in the pop up window (the boxes for HeLa-S3 will turn blue).

Click on Configure this page and click on ENCODE Transcription Factor Signals. Turn on all available tracks for HeLa-S3 cells by hovering over the cell line name and clicking Select all HeLa-S3 in the pop up window  (the boxes for HeLa-S3 will turn blue).

By comparing the signal intensity and annotated peaks for each of the Histone Modifications and Transcription Factors, you can see that the increased signal intensity corresponds to the regions where a peak has been annotated.

(e) Click on Custom tracks and click the ‘Trash’ icon from the Actions section of the ENCODE Analysis Hub.