Attaching the ENCODE track hub in human

  1. Add the ENCODE Track Hub to the ‘Region in Detail’ view for the genomic region surrounding the BRCA2 gene. Hint: You will need to add and view this Track Hub to the human GRCh37 genome assembly.

  2. Turn on all the available tracks relating to Histone Modification Peaks and Transcription Factor Peaks in HeLa-S3 cells.

  3. Which Transcription Factors and Histone Modifications have features in this region?

  4. Add the Tracks showing Signals for the Histone Modifications and Transcription Factors that have peaks in this region. Compare the signal intensity to the location of annotated peaks.

  5. Remove the ENCODE Track Hub from your list of custom tracks.

  1. There are two ways to add the ENCODE Track Hub to view in Ensembl. You can search for Encode from the Track Hub Registry homepage. From the search results, find the Encode Analysis Hub and select Ensembl in the View in Genome Browser list. Alternatively, you can search for the BRCA2 gene in the Ensembl GRCh37 site. Switch to the Location tab and click on Custom tracks in the left-hand panel. Click Track Hub Registry Search and search for Encode. Click Attach this hub in the ENCODE Analysis Hub option.

  2. Go to Configure this page and click on ENCODE Histone Modification Peaks under ENCODE Analysis Hub in the left-hand panel. On the right, turn on all available tracks for HeLaS3 cells by selecting HeLaS3 from the cell line tab and clicking Select all in the Factor tab. Go to the second step 2. Refine selection and make sure all tracks are on (blue colour). You can turn on the tracks under More filtering options in the right-hand panel and clicking on the individual options. Go to the third step 3. Configure track display to change the track display.

Click on ENCODE Transcription Factor Peaks now. Turn on all available tracks for HeLaS3 cells by selecting HeLaS3 from the Cell Line tab and clicking Select all in the Factor tab. Go to the second step 2. Refine selection and make sure all tracks are on (blue colour). You can go to the third step 3. Configure track display to change the track display or proceed straight to View tracks.

  1. There are features for a number of different transcription factors and Histone modifications, mainly surrounding the BRCA2 5’ region.

    Transcription factors: CTCF, USF2, TBP, STAT1, MAX, POL2S2, POLR2A, POL2, POL2B, MXI1, INI1, E2F1, E2F4, E2F6, HAE2F1, ELK4, MYC, CMYC, CEBPB, TAF1, TFAP2A, TFAP2C, AP2alpha and AP2gamma. Histone Modifications: H3K4me3, H3K9ac, H3K79me2, H3K4me3, H3K4me2, H3K36me3, H3K27ac

  2. Go to Configure this page and click on NCODE Histone Modifications Signal. Turn on all available tracks for HeLaS3 cells by selecting HeLaS3 from the Cell Line tab and clicking Select all in the Factor tab. Go to the second step 2. Refine selection and make sure all tracks are on (blue colour). You can go to the third step 3. Configure track display to change the track display.

Go to Configure this page and click on ENCODE Transcription Factor Signal. Turn on all available tracks for HeLaS3 cells by selecting HeLaS3 from the Cell Line tab and clicking Select all in the Factor tab. Go to the second step 2. Refine selection and make sure all tracks are on (blue colour). You can go to the third step 3. Configure track display to change the track display or proceed straight to View tracks.

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.

  1. Go to Custom tracks and click the Trash icon from the Actions section of the ENCODE Track Hub.

Adding Wiggle files to Ensembl Bacteria

Upload the GD_wiggle.wig file to the Gluconacetobacter diazotrophicus PA1 5 (GCA_000021325) genome in Ensembl Bacteria. View this track across the region Chromosome:2884000-2898000. What is the highest score in this region?

Go to Ensembl Bacteria and put Gluconacetobacter diazotrophicus PA1 5 into the Search for a genome box. Select Gluconacetobacter diazotrophicus PA1 5 (GCA_000021325) to go to the species homepage.

Select Display your data in Ensembl Bacteria to get to the custom track menu. Select Choose file and select the file location. The file type should be automatically selected. Click Add data.

Click on the Nearest region with data in the results page. From the region page you reach, put the coordinates Chromosome:2884000-2898000 into the Location box to jump to the region.

The highest score is 99 and it overlaps the ACI52364 transcript.

Adding BAM files to Ensembl Fungi

Attach the file Spom_all_61G9EAAXX_and_61G9UAAXX.+.sorted.bam, which can be found here, to view in Schizoaccharomyces pombe. Go to the region I:490843-490870, can you see a mismatch between a read and the reference assembly?

Go to the provided public directory and right click on the file Spom_all_61G9EAAXX_and_61G9UAAXX.+.sorted.bam to copy its URL, which is: http://ftp.ebi.ac.uk/ensemblgenomes/pub/misc_data/bam/fungi/Spom/Spom_all_61G9EAAXX_and_61G9UAAXX.%2B.sorted.bam Go to Ensembl Fungi and select Schizosaccharomyces pombe to go to the species homepage.

Select Display your data in Ensembl Fungi to get to the custom track menu. Paste the file URL into the Data box. The file type should be automatically selected. Click Add data.

Close menu and then put I:490843-490870 into the search box.

In the reads there are three red bases which do not match the reference assembly: A on the forward strand, and G and T on the reverse.