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Old 05-06-2011, 07:30 AM   #1
tldgID
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Question Publicly available NGS data?

Hello,

I am looking for NGS data, preferably RNA-Seq, which has large number of samples. But all is available (or I could've found) have very few samples, e.g. 3 or 4.

Does anyone know a publicly available NGS data with many samples coming from 2 different conditions, e.g. tumor vs. normal? or any other 2 category data!

Any help is appreciated.
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Old 05-06-2011, 09:15 AM   #2
Daisy-Fu
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Default Yes

I have seen many papers like that, different conditions, different populations of the same species, like that.
Here I attached a link of a paper of sequencing a whitefly, sorry not human, but the same idea, one population is pesticide resistant, and one is susceptible.

http://www.biomedcentral.com/1471-2164/12/56

Hope this helps!
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Old 05-06-2011, 11:03 AM   #3
tldgID
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Thank you Daisy-Fu

I haven't read the whole paper yet, but just looking at the “Methods” section, I see that it says “More than 2,000 adults of each strain were collected in two separate 2 ml Eppendorf tubes and flash frozen in liquid nitrogen.”

and considering that “A single full plate run” has been done, do you know if it means that there is sequence data available for 2000 insects for each condition or some samples are selected from the entire pool?
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Old 05-23-2011, 11:07 AM   #4
tldgID
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Question

I am still looking for publicly available NGS data with reasonably large number of samples. Especially samples form cancer and tumor tissues would be the perfect situation. By using the barcoding, it is possible to run many samples in one flow cell, but still I cannot find such data which provides separate sequence datasets for each sample.

I appreciate any help/hints/comments on this

Daisy-Fu,

About the whitefly paper, I read it and it generates 2 sequence read datasets: one for insecticide susceptible standard strain (TV1) and another for resistant strain from Turkey (TV6). 2000 adults of each strain are pooled together to generate enough material for sequencing. Great deal of work is done here and it is very impressive, but in the point of view of my project, the final experiment produces 2 datasets, one for each strain. Thank you for letting me know about the paper, but I am afraid I cannot use it in my project
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Old 05-23-2011, 10:58 PM   #5
sphil
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Hey,

try out the ncbi sra under:
http://www.ncbi.nlm.nih.gov/sra

SRA abbreviates Short Reads Archive which not only means solexa/abi sequencing. You can just "google" for tissues or experiments and will recive files in SRA-Format. They also provide a tool, namely SRA Toolkit to some kind of decompress fastq, fasta, sff and stuff like that from the SRA-Archive you download. Hope that helps,


best

Philip
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Old 05-24-2011, 06:20 AM   #6
tldgID
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Hey Philip,

Thank you for your help and reply!

I am using SRA. I have already found couple of datasets and working on them. The only issue is that the number of the samples is very small, usually less that 10 in both classes. I am working on a dataset by Dr. T. Wu which is one of the best ones, since it has tumor and adjacent normal tissues. However, still not many samples, 3 for each condition.

I hoped that by posting here, I can hear back if someone knows about a study with many samples

The Cancer Genome Atlas (TCGA) has many samples (based on the records that are publicly visible), but one needs a special permission to access that data.
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Old 05-24-2011, 06:51 AM   #7
sphil
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hey,

i guess you will hardly find free datasets containing more than three run for a specific tissue. Such enormous projects usually don't made their data freely available....nevertheless I wish you all best luck to find some!


if I'll find anything in near future I will contact you whether it is appreciated!
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Old 05-24-2011, 07:00 AM   #8
tldgID
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Thanks Philip and I surely appreciate any help, hints or suggestions.
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Old 05-24-2011, 11:58 PM   #9
steven
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You may be interested in the Encode project, they provide RNA-seq data for plenty of conditions (cell lines, cell compartments..). Data can be browsed at the UCSC Table browser (the expression group proposes several RNA-seq tracks). To download, find the ftp platform. You can also try ModEncode.

Not sure about the number of replicates though
Please keep us in touch
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Old 05-25-2011, 12:01 AM   #10
steven
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Quote:
Originally Posted by tldgID View Post
I am working on a dataset by Dr. T. Wu which is one of the best ones, since it has tumor and adjacent normal tissues.
BTW, which one is that? Could you post the ID or ref please?
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Old 05-25-2011, 02:11 PM   #11
tldgID
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Hi Steven,

Thanks! I'll check it out.

Here is the link to the prostate cancer (and normal) samples:

http://trace.ncbi.nlm.nih.gov/Traces...tudy=SRP003611
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