How To Use
Exmaple-1: A TERT promoter mutation and its surrounding multi-omics status

A. Show the TERT gene region

1.Go to the top page of DBTSS (https://dbtss.hgc.jp/)

2.Input ‘TERT’ to the keyword field at top left and click the search button.

3.Select the genome browser.

4.The user can see the TERT gene region at the genome browser. TERT is located on the minus strand of the reference genome.
  If the user want to show the plus strand, erase ‘-’ from the genomic position.

5.The user can reset contents by ‘Clear all tracks’ and show the basic items by ‘Show basic public data (Sequence+RefSeq+CpG).’

B. Select the clinical and model datasets

1.Select the cancer dataset. Select ‘Japanese,’ ‘Genome,’ ‘Cancer cell’, ‘Clinical samples’, ‘ICGC’ and ‘SNP_SNV.’
・ICGC Liver Cancer- NCC, Japan

2.Select the Japanese germline variation datasets for references.
Select ‘Japanese,’ ‘Genome,’ ‘Normal cell’, ‘Clinical samples’, ‘HGVD and Japan PGx’ and ‘SNP_SNV.’
・Japan PGx
・Nagahama SNP

3.Select the germline variation in other ethnic groups for references.
・dbSNP
・NHLBI ESP
・1000 Genomes

4.Select the Japanese lung cancer cell line datasets as model systems.
・RERF-LC-Ad1 SNV
・RERF-LC-OK SNV

C. Go to the TERT promoter region

1.For focusing on the TERT promoter mutation, drag and scroll the view to the promoter mutation (chr5:1295113) and zoom-in.
(link )

2.If the user want to display additional information such as the substitution pattern and mutant case numbers, use the setting by right-click.

3.The user also can change the height and color of track in the ‘Detail…’ of the setting.

D. Select the cell line datasets for multi-omics status

1.Reset the browser and search ‘TERT,’ again.

2.Add genome datasets detected (WGS). Select ‘Japanese,’ ‘Genome,’ ‘Cancer cell’ and ‘SNP_SNV.
・RERF-LC-Ad1 SNV
・RERF-LC-OK SNV
・PC-9 SNV’

3.Add epigenome datasets (ChIP-seq).
Select ‘Japanese,’ ‘Epigenome,’ ‘Cancer cell’, ‘Cell lines’, ‘Cell_lines’ and ‘DB_wiggle’ (and click ‘more…’).
・RERF-LC-Ad1 H3K4me3
・RERF-LC-OK H3K4me3
・PC-9 H3K4me3
・RERF-LC-Ad1 Pol II
・RERF-LC-OK Pol II
・PC-9 Pol II

4.Add transcriptome dataset (TSS-seq and RNA-seq).
Select ‘Japanese,’ ‘Transcriptome,’ ‘Cancer cell,’ ‘Cell lines’, ‘Cell_lines’ and ‘TSS’ and ‘RPKM’ (and click ‘more…’).
・RERF-LC-Ad1 TSS
・RERF-LC-OK TSS
・PC-9 TSS
・RERF-LC-Ad1 RPKM
・RERF-LC-OK RPKM
・PC-9 RPKM

E. Go to the surrounding region of the promoter mutation

1.Zoom-out and adjust the region to show the promoter and its downstream gene. (link )

2.Change visualization by the setting (right-click) in each track

How To Use
Exmaple-2: A MT1A promoter mutation represented by new genomic technologies

A. Show the MT1A gene region

1.Go to the top page of DBTSS (https://dbtss.hgc.jp/)

2.Input ‘MT1A’ to the keyword field at top left and click the search button.

3.Select the genome browser.

4.The user can see the MT1A gene region at the genome browser.

5.The user can reset contents by ‘Clear all tracks’ and show the basic items by ‘Show basic public data (Sequence+RefSeq+CpG).’

B. Select the long read datasets

1.Add the Chromium/GemCode linked read dataset. Select ‘Long read,’ ‘Linked read’ and ‘GemCode_Phasing.’
・H1975 GemCode Phasing Pattern

C. Go to the upstream region of MT1A

1.For focusing on the MT1A regulatory mutation, drag and scroll the view to the promoter mutation (chr16:56638440) and zoom-in. (link )

D. Select the epigenome and transcriptome datasets

1.Add epigenome datasets (ChIP-seq and BS-seq). Select ‘Worldwide,’ ‘Epigenome,’ ‘Cancer cell,’ and ‘BS’ and ‘DB_wiggle.’
・H1975 H3K4me3
・H1975 BS

2.Add transcriptome dataset (TSS-seq and RNA-seq). Select ‘Worldwide,’ ‘Transcriptome,’ ‘Cancer cell,’ and ‘TSS’ and ‘RPKM.’
・H1975 TSS
・H1975 RPKM

E. Go to the surrounding region of the regulatory mutation

1.Zoom-out and adjust the region to show the upstream region and its downstream gene. Change visualization by the setting. (link )

F. Select the single cell datasets

1.Add the C1 dataset. Select ‘Single cell,’ ‘C1’ and ‘ppm_distribution.’
・PC-9 C1 RPKM distribution
・LC2/ad C1 RPKM distribution

2.Select the Chromium datasets. Select ‘Single cell,’ ‘C1’ and ‘ppm_distribution.’
・H1975 DMSO Chromium ppm distributionn
・H1975 gefitinib Chromium ppm distribution

G. Go to the gene region of MT1A

1.For focusing on the MT1A expression profile, zoom the MT1A gene region. (link )

H. Go to the page of cellular population diversity

1.Click the summary link in the track item details.

2.Select the dataset and click the result bottun.
・PC-9 gefitinib (+).

3.The user can see the result of clustering analyzed by Cell Ranger (10x Genomics) on the two-dimensional t-SNE plot.

4.Input ‘MT1A’ to the box of the gene name.

5.Click the link of Gene ID ‘ENSG00000205362’, and then, the user can get the results of expression diversities of MT1A gene among individual cells.