how can I search for a new release data?

Question

[yoingchinchina]

Hello,

I would like to know if I want to start a new study on a new data!

How can I search for a release dataset? For example in next generation sequencing is there any website or tricks you may know to help me finding new data sets

Thank you

Answer 1

[Josh Herr]

If you're looking for data from already published works I usually read the literature -- most journals require data to be submitted to data repositories. I then comb SRA, ENA, and DDBJ for public data for meta-analysis that was cited in a study I am interested in.

[yoingchinchina]

@Josh Herr can you please site one your publication that you did this strategy?

[Josh Herr]

I am currently working on a manuscript using public data but I do not have a citation for this strategy -- it's not really a strategy per se -- you are just using public data to address a hypothesis you have.

What is your hypothesis? Can you address your hypothesis with public data?

Answer 2

[Adrian Pelin]

Not sure about non-American databases, but typically what I do is go here "http://www.ncbi.nlm.nih.gov/" and in the Search Field I pick "All Databases" and then enter the species I am interested in. For example, if you enter "glomus", you will find "http://www.ncbi.nlm.nih.gov/gquery/?term=glomus" that there are 17 SRA experiments (NGS data), but also there are many submitted Nucleotide sequences as well as predicted ESTs. It's a nice page because it gives you a nice overview on the type and amount of data available.

[yoingchinchina]

@Adrian Pelin can you please site one your publication that you did this strategy?

[Adrian Pelin]

Josh is going to laugh at this lol, but the first thing that comes to mind is this paper www.ncbi.nlm.nih.gov/pubmed/21876220 in M&M they say "Putative meiotic genes were initially searched using reciprocal TBlastX and TBlastN (Altschul et al. 1997) searches of publicly available expressed sequence tags from G. irregulare deposited in GenBank (National Center for Biotechnology Information [NCBI]).". So they didn't do a text search, but they used sequence search algorithms to search these public databases. Another paper www.ncbi.nlm.nih.gov/pubmed/23376943 just says "Three of these Illumina
read sets have been obtained from the NCBI SRA database (accession numbers SRX002289, SRX002287, SRX002285;"

[yoingchinchina]

@Adrian Pelin thanks Adrian! actually I am searching for RNA seq. my main goal is to find some data sets and try to compare different sequencing techniques. I could not find a paper which for example did RNA sequencing and provided their data to reproduce what they did! I searched through the http://www.ncbi.nlm.nih.gov/ however, there are so many files coming up and I don't know which to select etc. I will appreciate any guide!

[Adrian Pelin]

np. Here try this http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0108550 they compare 454 and illumina "Raw data have been deposited on the Short Read Archive under accession numbers SRR1346108 and SRR1352724." If anything the litreture review should be helpful.