5.2. Step-by-step instructions for creating datasets (‘omics)

5.2. Steps

You are welcome to use a dataset of your interest or alternatively download one from open TG-GATES, a large, publicly available, toxicological study from Japan: http://toxico.nibio.go.jp/open-tggates/search.html.

TG-GATEs toxicogenomics dataset

i)  Select acetaminophen (or another chemical of interest) – search (use the English language version of the site, selector top right hand corner).


TG-GATEs toxicogenomics dataset


Select your organism (for example Human – in vitro – CEL files). Download all files: Extract the zip archive (for example acetaminophen.Human.in_vitro.Liver.zip). Rename “Attribute.tsv” to “Attribute.txt” and inspect in Excel. Make sure your file does not contain blank columns or special characters (such as μ). The labels in the “Attribute.txt” file are explained in the appendix (Chapter 6).

TG-GATEs toxicogenomics dataset change extension

TG-GATEs toxicogenomics dataset attributes

iii) Data fields:
  This is a dose-response study of acetaminophen. Fields are as follows:
  Barcode: Array Barcode
Exp_ID: TGP internal experiment identifier
iv) Start the SEURAT configured ISAcreator by double-clicking on the ISAcreator executable (ISAcreator.jar on PC, ISAcreator.app on the mac).

Proceed to:

5.3. Step-by-step instructions for creating datasets (‘omics):

5.3. Mapping your annotation to ISA-tab, PART 1