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Add image of experimental design
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markdunning committed Oct 24, 2023
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6 changes: 5 additions & 1 deletion index.html

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7 changes: 6 additions & 1 deletion index.md
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Expand Up @@ -202,6 +202,11 @@ R-based methods such as `edgeR` (implemented in Degust) and `DESeq2` have their

We will use a previously-published count matrix. This was downloaded from the Gene Expression Omnibus (GEO) under the accession number [GSE60450](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60450). Note that we have shortened the column headings and added gene symbols to help with visualisation and annotation

The experimental design is as follows:-

![](https://training.galaxyproject.org/training-material/topics/transcriptomics/images/rna-seq-reads-to-counts/mouse_exp.png)

(image from https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html)

::: exercise
Download the counts from [this link](GSE60450_Lactation-GenewiseCounts_rename_symbol.csv)
Expand Down Expand Up @@ -485,7 +490,7 @@ There are several popular online tools for performing enrichment analysis We wil
4. Make sure that **Method of interest** is set to `Over-Representation Analysis (ORA)`
5. Select **Functional Database** `geneontology`
+ you can change this later if you wish
6. Keep **Select Gene ID Type* as `Gene symbol`
6. Keep **Select Gene ID Type** as `Gene symbol`
7. Paste the gene symbols corresponding to DE genes in *Basal pregnant vs Basal Lactation* from your Excel spreadsheet into the Upload Gene List box.

- **The shortcut CTRL + SPACE will let you select an entire column**
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