I searched gene mRNA expression in last year, finding minus in some cancer cell lines. But recently I searched the same gene in CCLE, the mRNA expression was different with the old. Is there some different computing methods between them? How can I download the old version mRNA expression?
Thank you
Hi. I’d need to do a bit of investigation to understand this. Could you point me to the filename, gene name and quarters on which you did this comparison? -thanks
GSDMA Expression 21Q3 Public.csv (93.4 KB)
This is GSDMA mRNA expression in new version.
This is the old version.
I cannot find connect between them.
I may not be understanding the issue properly, but we haven’t made any significant changes to our rnaseq pipeline in the past year. I’m plotting 21q3 vs 20q1 expression data for GSDMA for your reference. The source of the data is CCLE_expression.csv both downloaded from the public portal, and each dot is a cell line:
The two datasets are almost identical. What is the old DepMap quarter that you’re using?
Emmm，Could you please teach me how to process the 20q1 expression data, in order to show it like the immage?
Where are you getting this image from? I’m not able to find it on the DepMap portal: DepMap: The Cancer Dependency Map Project at Broad Institute
I dowanloaded it last year, you can find many images like this in GOOGLE IMAGES RESEARCH " CCLE mRNA expression". I do not know how to culculate the mRNA data to show it like the image I downloaded before.
Hey,
I tried to look for this image online and could not find it.
To go from this dataset to the plot you are showing, you would need to group samples based on their lineage using a plotting tool like R’s ggplot or python’s matplotlib.
The cell line sample info file in the download section of depmap, lists ACH-ID → lineage associations.
Hope it helps!
Best,
