Tweet
Hi Dear, I want to run a de novo transcriptome project by Roche 454 with a species of fish cDNA library that its genome size is about 3*10^9, which kind of picotiter plate region is better for me and why? 1/2 or 1/4 or 1/8 ?
-
-
If the genome is 3E9 bp (similar to Homo sapiens)), then the transcriptome will be at least 3E6 bp. I'm not sure even 1/2 plate will have enough yield to cover your transcriptome, as there will be > 1000x difference between some transcript yields. You may need to use Illumina or Proton instead. -
I have run a devo transcriptome assembly using 454 on a fish with a similar sized genome (slightly larger than human genome). I ran 4 individuals in a whole 454 FLX run.
i used 3' targeted cDNA (however I seem to remember reading that for some reason this isnt the ideal protocol when using 454...?).
If memory serves I got around 30,000 contigs when aligning to a closely related reference transcriptome, and a bunch more via de novo assembly. From the 30, 000 contigs there were ~50K SNPs/indels identified....around 9K of these suited my criteria for a high quality putative SNP.
In theory 3' target cDNAs should increase yield of homologous fragments between individuals, and a full 454 plate seemed to give us good representation of the transcriptome.Last edited by JackieBadger; 10-07-2012, 11:43 AM.Comment
-
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM -
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM
Comment