Question: How to see if a gene is expressed in mouse undifferentiated embryonic stem cell?
1
gravatar for auryndb
21 months ago by
auryndb60
Canada
auryndb60 wrote:

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.

rna-seq • 574 views
ADD COMMENTlink modified 21 months ago by jotan1.1k • written 21 months ago by auryndb60
3
gravatar for jotan
21 months ago by
jotan1.1k
Australia
jotan1.1k wrote:

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.

ADD COMMENTlink written 21 months ago by jotan1.1k

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

ADD REPLYlink written 21 months ago by auryndb60
1

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:

enter image description here

ADD REPLYlink modified 21 months ago • written 21 months ago by jotan1.1k
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