Wednesday, June 27, 2012

From stem cells to eye precursor with differentiated retinal cells in human

From a stem cell culture to the optic cup with fully differentiated retinal cells: photoreceptors, bipolar cells and ganglion cells.


This may be of substantial importance in the future treatments of eye diseases or injuries where the transplant of retinal cells is needed. One may imagine that in the future embryonic stem cells will be taken at birth and differentiated into multiple eye precursors and frozen in case needed.  

Link:
Link to the article where the same was performed in mice:

Friday, June 22, 2012

Differences between RNA-Seq and DNA-Seq may come from mapping artifacts

The follow-up to the previous post
http://milospjanic.blogspot.com/2011/08/widespread-sequence-differences-between.html

The wide-spread differences between RNA and DNA sequencing are most probably artifacts and not RNA editing events as suggested previously in the Science paper, except A to I editing (an I is read as a G) and C to G
The reason why they have such a large number of artifacts is most probably the presence of systematic mapping errors. Reads coming from RNA-Seq will rather be mapped by a mapping software in one piece to the wrong location (even if they map with few mismatches to the wrong location) than be spliced between exons. Thus lot of reads will map to non-functional pseudo-genes, for example, or some other homologous locations with mismatches. The sequence will be different from the underlying DNA sequence and thus it will be called a RNA editing event.


Also the confirmation with PCR may be erroneous as the primers may be designed poorly and may amplify 'the wrong' homologous sequence as well. This may give the false conclusion that the DNA sequence is different from the RNA sequence at the gene locus.


More details can be found here:
http://www.genomesunzipped.org/2012/04/guest-post-accurate-identification-of-rna-editing-sites-from-high-throughput-sequencing-data.php#more-4944

Changing decimal separator in LibreOffice 3

I didn't find the way to change decimal separator in LibreOffice, the way you can do it in Excel.
(Blog post http://milospjanic.blogspot.com/2011/04/changing-decimal-separator-in-excel.html)

However you can do the following:
Go to Tools/Options/Language Settings/Languages
Change Locale setting to the one that has decimal separator you need, e.g. to English US if you want dot (.) to be the separator.
Leave checked Decimal separator key: Same as locale setting
And you are done.