Entering edit mode
4.9 years ago
atitparajuli2018
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0
Hi, I am looking for databases containing ESTs of Alfalfa (Medicago sativa L) for my research work. I needed minimum of 1 million ESTs information. I know there are few available in the NCBI (just more than 320000), I need to collect around to generate a library to do exome sequencing.
if you can't get them from NCBI (or EBI/ENA) you will have a hard time tracking them, if they exist at all . If someone has a substantial set of ESTs they likely would have submitted them to any of the above already.
On the other hand: could RNAseq data be of any use? Or ESTs from medicago truncatula?
I used to be personally involved in Medicago (truncatula) genome sequencing (over a decade ago) , but it seems that many of the links or resources from back in the days are dead in the meanwhile. Perhaps you can still find some info in the following document: https://www.noble.org/globalassets/docs/medicago-handbook/bioinformatics-resources.pdf
There are only 320,297 sequences information in NCBI, I need minimum of 1 million sequence information to develop a library. I think RNAseq data would be of use, I don't think ESTs from medicago truncatula would be of any use. I do believe there are other database resources like DDBJ, JGI. I only needed sequence information from them. If I cannot find the minimum amount of sequence then I need to use the information from medicago truncatula.
Thank you for the information
DDBJ (and actually also ENA) are synced resources, meaning they all contain the same info. JGI is indeed separate but they normally submit their data to NCBI as well.
Why (or how) are you so fixed on this 1M number of exome sequencing? I've successfully created exome sequencing libraries of datasets of far less then 1M ESTs
The problem with ESTs using from few library ( I think) is, generally they are taken from the same sample (Treatment) and gene expression at that treatment, so If I use only that source to develop my library, then I think I will be missing other genes not expressed at the particular treatment. My research focuses on identifying genetic variants associated with self-incompatibility in Alfalfa, so I hope to gather as many information available to construct library as possible, which ultimately would be helpful in my research.
having already 300K ESTs might already indicate it will not be from a single (or few) samples. You can always check the metadata for them to get re-assured.
The only thing you have to worry about is the number of genes covered, if I recall correctly they assume that in the alfalfa set they already have >36K genes, so that seems like a quite comprehensive set. There might be some more data or info here btw :http://plantgrn.noble.org/AGED/
You will anyway have to link it back to the truncatula genome otherwise you will have no clue about the exon-intron structure of the genes, so while you're at it you could check if you miss potential interesting genes