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-   -   Costs (http://seqanswers.com/forums/showthread.php?t=6098)

zhiller 07-23-2010 02:13 PM

Costs
 
I have done a couple microarray experiments but am now interested in RNAseq. I am unfamiliar with the technology and would like to know if it's even feasible with my budget. I was confused by a table in the SOLiD brochure that quoted $150/sample??

For two time points, I have three biological replicates with a drug and three without which makes a total of 12 samples. The samples are from a mouse macrophage cell line. I have seen a few core labs offer services for affy chips for between $600 and $800. I want to know if it would cost more or less to do sequencing. By how much? Also, could I use bar codes and only do one or two runs?? I know that prices may vary by quite a bit for a number of reasons, but a ballpark estimate would be helpful. Any information or links to other resources would be great too! Thanks

NextGenSeq 07-23-2010 02:52 PM

It is definitely more to do RNA-Seq than microarrays. To make the library costs ~$100 to $300 and to sequence costs ~$1000 to $2000 depending on the type of run (single read or paired end and length of sequence run).

chinahnzj 08-11-2010 12:37 AM

It is definitely more to do RNA-Seq than microarrays. As I know, to sequence costs ~$1000 to $2000 depending on the type of run and datasize (including library construction), but RNA-Seq has some advantages, such as digital signaling, data throughput, broad detection range, new transcripts detection and antisense transcripts detection, etc.
RNA-seq is used to analyze gene expression of certain biological objects in specific conditions. This technology combines the library construction strategy of transcriptome sequencing with the bioinformatics analysis method of digital gene expression (DGE), it is a highly accurate quantification method and is able to produce high repeatability, wide detection range with low cost. It can be widely used in agricultural research, biomarker identification, environmental improvement, disease related studies, drug screening and many other fields.

james hadfield 08-11-2010 03:04 AM

I would not really agree with the prices quoted as it very much depends on your service provider and the number of reads you think you need. If you are accessing a core lab and are happy for 5-10M reads per sample then a lane will do two at about $1000 for PE50bp (I am guessing a bit about costs in the US compared to the UK).
Illumina's new (but delayed) sample prep kits should be bringing costs down and if you do 'home-brew' then the cost can be at the lower end of NextGenSeq's estimate. Again it very much depends on the number of samples you want to run.
If you can get access to HiSeq the four, six or even eight samples might be possible per lane for RNA-Seq.
It depends very much on your primary interest; transcript abundance, splicing, ASE?

DeWalchNGS 05-25-2011 01:41 PM

Quote:

Originally Posted by zhiller (Post 22307)
I have done a couple microarray experiments but am now interested in RNAseq. I am unfamiliar with the technology and would like to know if it's even feasible with my budget. I was confused by a table in the SOLiD brochure that quoted $150/sample??

For two time points, I have three biological replicates with a drug and three without which makes a total of 12 samples. The samples are from a mouse macrophage cell line. I have seen a few core labs offer services for affy chips for between $600 and $800. I want to know if it would cost more or less to do sequencing. By how much? Also, could I use bar codes and only do one or two runs?? I know that prices may vary by quite a bit for a number of reasons, but a ballpark estimate would be helpful. Any information or links to other resources would be great too! Thanks

These price ranges are very accurate. If you would like more information on RNAseq services feel free to contact me for an accurate quote.

lpatty@dewalch.com

LOH 03-24-2016 04:25 PM

The Sequencing price has been reduced a lot during the last five years. We now offer $280/sample for RNA Sequencing on HiSeq4000, PE150, 10M reads.


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