How to see if a gene is expressed in mouse undifferentiated embryonic stem cell?

Question

[auryndb]

How can I see if my gene is expressed in mouse ESC using available RNA-seq data? IS there any website that I can simply put the name of my gene down and get a results if it is expressed or not. ( I know about ENCODE, or ESCAPE) but I have not been able to find how to do this in their websites.

Answer 1

[jotan]

You can go to ENCODE on UCSC

http://genome.ucsc.edu/ENCODE/dataMatrix/encodeDataMatrixMouse.html

There's RNA Seq for ES-Bruce4 and ES-E14 in the matrix.

Click on that, check the "visibility" boxes next to the tracks. Hit return to browser. Search for your genes.

[auryndb]

I did that. But how can I know if my gene is there or not?

http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A77851443%2D77873934&hgsid=481968789_9OTOvrJx9kSJKlFmtsByHNaDvoxp

[jotan]

After clicking on ES-Bruce 4 (the E14 tracks are not working for some reason), there are four tracks available.

1. ES-Bruce4 Embryonic day 0 RNA-seq Alignments Rep 1 from ENCODE/LICR
2. ES-Bruce4 Embryonic day 0 RNA-seq Alignments Rep 2 from ENCODE/LICR
3. ES-Bruce4 Embryonic day 0 RNA-seq Signal Rep 1 from ENCODE/LICR
4. ES-Bruce4 Embryonic day 0 RNA-seq Signal Rep 2 from ENCODE/LICR

Leave the first two boxes unchecked. These are showing you actual alignments. Select tracks 3 and 4.

This will show you the RNA seq signal in blue tracks like this: