Hi researchers,
I want to look at the mRNA expression data for a certain cell line (if someone has done it) in public database, how can I do that?
For example, if I want to check HepG2.2.15 cell line. I can do this in GEO or other databases?
Thanks.
Hi Strehl,
Thanks for your reply. Can you explain this a bit further? If I use GEO and choose "GEO Profile" to search. Assume I type "p53", can I regard the results are all the microarray that contain p53 expression?
I thought you wanted data of the HepG2.2.15 cell line?
Microarray and RNA-seq data contain usually most genes, so I don't understand your question. You need to specify what you are looking for..
Dear Shuaichen,
GEO is a repository for all the high throughput experiments. So, if you give HEPG2 cell line as search keyword. It will list out all the experiments that are associated with HEPG2(in general experiments would have been done on them). If you want to check for expression of p53 or any other genes, you can download the .CEL or SOFT files for these expts. provided for the experiment you have chosen. The files can then be analysed for expression of your genes of interest ( as the experiments would mostly be data from arrays or NGS, they would have expression for very large number of genes). You can also do your searching in Arrayexpress (from EBI), GEO (from NCBI) and ENCODE (from UCSC). The data from among these 3 databases are interlinked to each other.
Dear Sushri,
Thank you so much for the detailed explanation. Which software you use to analyze the data you download? Genespring or ?
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