4
$\begingroup$

First of all I have to say that I have no biology background since I'm a undergraduate computer science student. Nowadays, for my research I need to use some of the databases related with bioinformatics (modENCODE and NCBI-GEO). Currently, I'm searching RNA-Seq data and I have found the following one in modENCODE website which is stored in NCBI-GEO database.RNA-Seq data

In the description part of it, it is written that:

Synchronized L1 worms cultured at 25degC for about 91 hrs to a point at which ~100% worms are resistant to 1% SDS treatment. Illumina sequencing of C. elegans dauer daf-2(el370) sample 2-1 DauerDAF2-2-1 polyA+ RNAseq random fragment library This sample is available through the modENCODE DCC (www.modencode.org) as: DauerDAF2-2-1 Local library name: DauerDAF2-2-1 Quality values are ASCII encoded Phred + 33.

Regarding with this paragraph, I want to ask that, what is C. elegans dauer daf-2(el370) . I've searched on the internet and I have found that dauer is kind of development stage of C. elegans. However, I could not find any information about the daf-2(el370) part (Actually all I found was that daf-2 is name of a gene of C. elegans). Actually, my primarily concern is whether this RNA-Seq data contains the C. elegans' whole transcriptome or it contains only mRNAs related with daf-2 gene.

$\endgroup$
  • 1
    $\begingroup$ I might be wrong here, but daft-2(el370) looks an awful lot like a nomenclature of a transgenic worm. And RNA Seq doesn't do it on a gene by gene basis if I remember my basics. It does it on the whole transcriptome. $\endgroup$ – Rover Eye May 16 '15 at 13:22
  • $\begingroup$ @RoverEye Although I have limited information, I agree that RNA-Seq does it on the whole transcriptome, I just wanted to be approved. Thanks for the information. $\endgroup$ – stackunderflow May 16 '15 at 13:26
  • $\begingroup$ I think it is daf-2 mutant which prolongs dauer stage. Did you read the corresponding paper?? $\endgroup$ – WYSIWYG May 16 '15 at 19:49
  • $\begingroup$ @WYSIWYG corresponding paper is not available to publicly access therefore I could not read it. $\endgroup$ – stackunderflow May 16 '15 at 20:40
  • 1
    $\begingroup$ @stackunderflow Here you go: genome.cshlp.org/content/19/4/657.long $\endgroup$ – mdperry May 17 '15 at 14:10
4
$\begingroup$

Have you discovered wormbase yet? It will become your new best friend. In worms gene names reflect the loss-of-function (lf) phenotype. Daf means "abnormal DAuer Formation," so daf-2 was the second daf gene identified (ref). The mutations are called alleles and each worm lab has their own allele designation. e was for England and in that lab's strain list the daf-2 allele was the 1,370th on their list. So daf-2(e1370) designation means that the strain carries a lf mutation in the daf-2 gene, and the specific allele is one that was isolated in Cambridge, UK. I believe that allele is temperature-sensitive (ts) dauer-constitutive. So at 25⁰C 100% of the animals were dauers. That is when they harvested RNA. It is the entire transcriptome. It sounds like you may be familiar with modENCODE Data Warehouse. You can still ask questions about modENCODE datasets at help@modencode.org. While the modENCODE Data Coordination Center was mothballed at the end of the NIH funding period, there are a few people who still field queries like yours, to the Helpdesk. Also, moving forward the new ENCODE DCC has taken over curation of archival modENCODE metadata.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.