From 11e6af2a22ec839ffbdd7be29dbc5ceccd0c7095 Mon Sep 17 00:00:00 2001
From: YunaBlum <31280664+YunaBlum@users.noreply.github.com>
Date: Sat, 30 Nov 2024 22:20:10 +0100
Subject: [PATCH] Update how-do-i-start.md

adding cancer name
---
 phase-1_2_3/bundle/how-do-i-start.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/phase-1_2_3/bundle/how-do-i-start.md b/phase-1_2_3/bundle/how-do-i-start.md
index 5b8739b..204393c 100755
--- a/phase-1_2_3/bundle/how-do-i-start.md
+++ b/phase-1_2_3/bundle/how-do-i-start.md
@@ -10,7 +10,7 @@ This section will give you a description of the dataset and baseline methods sug
 ### Provided cell population reference data
 
 
-The organizers provide cell population reference profiles for PDAC. Three reference datasets are available: **bulk RNAseq of isolated cell populations, bulk methylation profiles of isolated cell populations and single-cell RNAseq**. All references are using publicly available data. Each reference type contains 5 cell types: immune cells (immune), fibroblasts (fibro), endothelial cells (endo), and classical (classic) and basal-like (basal) tumor cells. 
+The organizers provide cell population reference profiles for PDAC (pancreatic cancer). Three reference datasets are available: **bulk RNAseq of isolated cell populations, bulk methylation profiles of isolated cell populations and single-cell RNAseq**. All references are using publicly available data. Each reference type contains 5 cell types: immune cells (immune), fibroblasts (fibro), endothelial cells (endo), and classical (classic) and basal-like (basal) tumor cells. 
 
   \- **bulk RNAseq cell populations**:  immune cells and fibroblasts transcriptomic profiles were retrieved from the GTEx Analysis V10 ([GTEx portal](https://www.gtexportal.org/home/downloads/adult-gtex/bulk_tissue_expression), link to paper [1](https://www.liebertpub.com/doi/full/10.1089/bio.2015.0032) [2](https://www.nature.com/articles/ng.2653)), endothelial cell transcriptomic profiles were retrieved from GEO [GSE135123](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135123) (link to [paper](https://pmc.ncbi.nlm.nih.gov/articles/PMC6890669/)). Basal-like and classical tumor cell transcriptomic profiles were retrieved from [this paper](https://pmc.ncbi.nlm.nih.gov/articles/PMC6082139/). **Preprocess**: this reference data has been normalized using edgeR.