Hi,
I would like to sequence a few hepatic RNA samples to find out the differential gene expression between different groups. I plan to sequence 9-12 samples (3-4 replicates per group; 3 groups in total), each with 15-20 million reads. To my knowledge, this can be multiplexed in one lane using Hiseq platform.
So far, I haven't been able to get a local service provider to perform the sequencing. I would like to obtain some recommendations from the research community regarding providers who can offer good service.
Thanks.
One of the option might be CyVerse platform. You can create your account and utilize Discovery environment to analyze RNA-seq data. However, it is hard to analyze big data files (more than 1.9 GB).
You can also check on lewis3 system if you are eligible to apply from your University. This server is good for storing and analyzing transcriptome data.
The last option might be computer with Linux system and at least 2 TB of memory. It should be enough for installing all required packages and store a data.
Good luck!
I don't know in Malaysia but I know a lot in The USA. Here is a website where you could find some services. It is https://www.scienceexchange.com. This website is great! Enjoy! !!!
I have a great experience with the jp sulzberger columbia genome center in the New York. I used Hiseq platform. Just like you my samples were liver RNA and the purpose was to get differential gene expression among different groups.I would highly recommend that and good luck!
Thank you all so much for your replies.
Anyway, after getting in touch with some of the local & overseas service providers, I thought it may be helpful to provide a review of my experience so far so that others from the region can make use of the information.
Recommended service providers
1) Monash University Malaysia Genomics Facility (http://www.sci.monash.edu.my/research/mdp/genomics-cluster)
- helpful, provide quick reply (within 1 day, please look for Ms. Lee Yin Peng) and price quote
- However, they have Miseq platform which is not cost-effective for large sequencing project.
2) ScienceVision (http://sciencevision.com.my/)
- helpful, quick reply (within 1 day)
- able to provide excellent advice if you are new to NGS
3) Genome Institute of Singapore (https://www.a-star.edu.sg/gis/our-science/technology-platforms/next-generation-sequencing.aspx)
- efficient, prompt reply (1-2 days)
- able to provide an estimated cost (unofficial) based on your sequencing project besides giving some advice
- plan to outsource my samples to this service providers
Not Recommended Providers (mainly because of no response)
1) Malaysia Genome Institute
- cannot reach by email (some kind of error message was generated when I tried to email them)
- have a "Contact Us" form at their website, but no response even after I filled up and submitted multiple attempt.
2) Malaysian Genomic Resource Centre
- enthusiastic at the beginning (prompt reply, 1-2 days)
- after 3-4 follow-up emails, they became slow (>7 days) and require multiple reminder emails in order to obtain the information
- provided me an estimated cost without breakdown of each component despite I specifically ask them to break it down.
3) First BASE Laboratories
- Did not reply (>1 week) even after I emailed them alongside with the long questionnaire about my project
4) UKM Medical Molecular Biology Institute
- Did not reply
Others...
1) Genome Solutions (http://www.genomesolutions.com.my/)
- prompt reply (1-2days)
- still discussing with the company
Thus far, these are the service providers that I have contacted. I will update the list if I get in touch with other companies.
Hi Hong,
Try submitting a request on Genohub - https://genohub.com/ngs/. You can find services according to your RNA-seq project specifications and submit a request on this web page. Genohub has connections to service providers from all over the world and they can help you find one suitable for your particular project and location preference.
Good luck!
Dear all,
I would like to update the status of my sequencing project so that others (primarily in Malaysia) can have a reference.
Last time I stopped at Genome Solutions. Basically, it is a very responsive company. However, the price quote is a bit higher than expected and so, I did not choose their service.
I ended up outsourcing my samples to another Singapore service provider - NovogeneAIT (http://novogeneait.sg/) which quoted me a very reasonable price (~USD200+ per sample/15 samples/150PE/20M). The sequencing was done at Novogene at Beijing using Hiseq4000. I was extremely satisfied with the sequencing data. I received an average of 25.3M raw PE reads per sample (Q30-92.5%; Q20-97%). The company is very professional and responsive. I would not hesitate to use their service the next time I need to carry out a sequencing project.
I hope this helps.
Hi Hong Sheng and other potential readers,
Just an update that our website is now this: https://www.monash.edu.my/mdp/tmb/research-clusters/genomics-facility
We have an in-house MiSeq system, but even if you require HiSeq output, we do provide Library Preparation and QC services prior to your sequencing step.
Anyone in the South-East Asia region who are interested in NGS service, please contact us at [email protected]
Best wishes!
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