From eebdec1d66b7175a8f4d10b37bdc7e6a9e3ad0f6 Mon Sep 17 00:00:00 2001
From: dibbelab <51884459+dibbelab@users.noreply.github.com>
Date: Tue, 1 Feb 2022 11:34:36 +0100
Subject: [PATCH] Update README.md
---
README.md | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index 490f999..e28f04a 100644
--- a/README.md
+++ b/README.md
@@ -28,7 +28,7 @@ On-line single cell BC Atlas available at [http://bcatlas.tigem.it](http:
Figure 3 – Transcriptional heterogeneity in breast cancer cell lines and its impact on drug response. (A) Percentage of cells expressing the indicated genes in each of the 32 cell lines. (B) Fluorescence cytometry of HCC38, MDA-MB-361 and AU565 cell lines stained with a fluorescent antibody against HER2. (C) Expression of HER2 protein in MDA-MB-361 cells is dynamic and re-established in less than 3 weeks. (D) Cell cycle phase for the HER2+ and HER2- subpopulations of MDA-MB-361 cells. p-value refers to the Fisher’s exact test. (E) Enriched pathways (GSEA, FDR<10%) across differentially expressed genes between the HER2+ (orange) and HER2- (blue) MDA-MB-361 cells. (F) Gene expression versus drug potency for four anti-HER2 drugs. Each dot corresponds to a cell line with percentage of cells expressing ERBB2 or EGFR in the cell line [y-axis] versus the experimental drug potency2 as Area Under the Curve (AUC) [x-axis]. PCC (Pearson correlation coefficient) and its p-value are also shown. (G) PCC values computed as in F for 66 drugs for which the cognate drug targets is known. The PCC distribution when choosing a random gene is also shown. (H) Bioinformatics pipeline for the identification of drug sensitivity biomarkers for 450 drugs. (I) The top 250 most expressed genes in a single cell are used as input for a GSEA against the ranked list of genes correlated with drug potency for each one of the 450 drugs to predict its drug sensitivity. (J) Performance of DREEP in predicting drug sensitivity of 32 cell lines in the atlas to 450 drugs in terms of PPV (Positive Predicted Value) versus Recall. (K) Dose-response curve in terms of cell viability following treatment with either afatinib or etoposide at the indicated concentrations on sorted MDA-MB-361 cells (triplicate experiment). (L) Percentage of HER2+ cells in MDA-MB-361 after 72h treatment with either afatinib or etoposide, and (M) cell viability. (N) Percentage of HER2+ cells in MDA-MB-361 cell-line at the indicated time-points either following 48h of afatinib pre-treatment (red bars) or without any afatinib pre-treatment (black bars) and (O) the relative number of cells rescaled for the number of cells at the beginning of the experiment. Source data are provided in a Source data file.
-## How to dowload RAW data of the Atlas
+## How to download RAW data of the Atlas
Raw UMI counsts before to be normalized with [GFICF package](https://github.com/dibbelab/gficf) are arevailable on figshare at following DOI [10.6084/m9.figshare.15022698](https://figshare.com/articles/dataset/Single_Cell_Breast_Cancer_cell-line_Atlas/15022698). Specifically raw UMI count matrix of the 35,276 cells is available in two main formats:
1. R dataset as rds file [RAW.UMI.counts.BC.cell.lines.rds](https://figshare.com/ndownloader/files/28893384)
2. MatrixMarket format (like cell ranger output)
@@ -36,7 +36,7 @@ Raw UMI counsts before to be normalized with [GFICF package](https://github.com/
2. Cell name file file [barcodes.tsv.gz](https://figshare.com/ndownloader/files/30469065)
3. Gene name file [features.tsv.gz](https://figshare.com/ndownloader/files/30469065)
-## How to dowload Processed data of the Atlas
+## How to download Processed data of the Atlas
Processed data with [GFICF package](https://github.com/dibbelab/gficf) are arevailable on figshare at following DOI [10.6084/m9.figshare.15022698](https://figshare.com/articles/dataset/Single_Cell_Breast_Cancer_cell-line_Atlas/15022698). Specifically you have to download the file [GFICF.processed.counts.gficf](https://figshare.com/ndownloader/files/33943715)