Written by: C. Titus Brown
Primary Source: Living in an Ivory Basement
A few months back, I announced the khmer protocols project, an effort to write down an explicit, open protocol for transcriptome and metagenome assembly. This project was started during the summer of 2013 at the Woods Hole Marine Biological Lab, in collaboration with Joshua Rosenthal. I’d met Josh at the CephSeq meeting the year before, and we reconnected at MBL in 2013; there, motivated in part by discussions at CephSeq, I started writing the eel-pond protocol.
During the summer, Josh and I found that we were both incredibly frustrated by the general failure of researchers to share data pre-pub, and so we started to chat seriously about some ideas we’d independently had about incentivizing the opening of transcriptome data. This eventually led to the Open Marine Transcriptome project, which is still in its formative stages.
However, in the meantime I am happy to report that Josh assembled a bunch of squid transcriptomes and is willing to make them available to all. In addition, Josh did some skim Illumina sequencing (~40x coverage) of the squid genome, and my lab assembled it; we are making a really basic draft genome available as well. (Here, by squid, we mean Loligo pealeii, or the Longfin inshore squid — “loligo” for short. It is also sometimes called “Doryteuthis pealeii”.)
It should be noted that one of the transcriptomes was made from carefully dissected Giant Fiber Lobe neurons. These are the cell bodies for the well-studied squid giant axon. Thus this transcriptome should provide “molecular support” for all the cell biology and neurophysiology that has focused on this most famous of preps.
In addition, Josh and Brenton Graveley of the University of Connecticut Health Center did some skim Illumina sequencing (~40x coverage) of the squid genome, and my lab assembled it a basic draft genome.
We are pleased to announce the availability of this data, in two formats.
First, you can download the assembled and annotated transcriptome data in FASTA format:
- Loligo pealeii buccal ganglion transcriptome (v1.0)
- Loligo pealeii giant fiber lobe (v1.0)
- Loligo pealeii optic lobe (v1.0)
- Loligo pealeii stellate ganglion (without giant fiber lobe) (v1.0)
- Loligo pealeii vertical lobe (v1.0)
as well as the (unannotated) genome assembly: Loligo pealeii genomic data (v0.2)
Second, we have also made available a public BLAST server where you can search the individual transcriptomes, a database of the concatenated transcriptomes, and the genomic sequence. (The BLAST server is not on a particularly powerful machine so I may turn it off if thousands of squid enthusiasts start pounding on it ;)
The various tissues were dissected by Josh Rosenthal and sequenced using an Illumina HiSeq. Raw data and details will be made available as part of a data paper. Assembly and annotation was done per the khmer protocols v0.8.4, with the exception of using the uniprot database for annotation instead of mouse.
The genomic data was similarly sequenced with a HiSeq by Benton Gravely and was then subjected to a variant of the Kalamazoo metagenome protocol: specifically, we did three-pass digital normalization and then assembled with Velvet. This will be described in more detail in the data paper.
Why are you making these data available?
How should I use them?
Heck if we know. Impress us!
How should I cite them?
We will post a citation handle to figshare shortly. If you desperately need to cite us, please contact us a few days in advance of when you need to cite ;).
What if the transcripts or contigs are wrong?
Every assembly is at least a little bit wrong, but we’re reasonably confident that our assembly approaches work OK. We’ve also tried to maximize sensitivity of the genome assembly, at the expense of contig length; we believe this means that misassemblies are also somewhat unlikely.
That having been said, it is your responsibility to validate your own analyses. Caveat emptor.
You may, of course, also pretend that the data is not available and then not use it for anything.
What data sharing license are these data under?
We’re releasing these data under Creative Commons 0, the most liberal of the Creative Commons licenses. This is a public domain dedication: do with the data what you will. If you publish something based on this data, it is standard academic practice to cite us (see above).
Hey, can I repost these on my own site?
Sure thing. Just remember that standard academic practice is to cite the origin of the data, so even if you do something super cool in terms of remixing the data with other data sets, we’d appreciate a link and guidance for users of your data set to cite us.
Why aren’t you trying to get a Science or Nature paper out of all this? Aren’t your reputations going to suffer for doing all this work without trying to milk the data for all it’s worth?
We’re pretty sure our reputations won’t suffer from making a bunch of useful data available. Heck, we’re pretty sure your reputation wouldn’t suffer from making a bunch of useful data available (hint).
The genome is, like, completely useless!? The N50 is about 250 bases!
Yep. Sorry! If you give us $200k we will give you a better genome in ~6 months (annotations not included). In the meantime, we think that this genome is extremely useful for determining exon structure and avoiding degenerate PCR at all costs. In fact, this genome shows near-complete coverage of the ORFs from a handful of cDNAs cloned Back When.
I’m serious about the $200k. And that’s direct, not direct+indirect.
Do you want to collaborate? I have a bunch of analyses that you can do for me — Science/Nature paper guaranteed!
Nope, sorry, too busy. I am, however, happy to not collaborate — see the open marine transcriptome project. Send us your tired, your poor, your huddled transcriptomes…
We’d love your thoughts on these questions of ours in the comments below.
- Is this a good way for us to post the data? Is there a better way?
- How important is raw data (raw reads) to you? Should we accelerate the posting of the raw data? (You can have it now for all we care, but we don’t have a good place to post really big files.)
We’d also love any other feedback, but I reserve the right to publicly post negative feedback that is particularly entertaining.
Latest posts by C. Titus Brown (see all)
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