Golden Hamster Genome
Marianna Zazhytska
Matthew Speir
UCSC Cell Browser, Quality Assurance and Data Wrangler
Human Cell Atlas, User Experience Researcher
UCSC Genome Browser, User Support
UC Santa Cruz Genomics Institute
Revealing life’s code.
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Marianna Zazhytska
Chikara Takeuchi
Hello Mariana,
I am a former grad student in Siomi lab and replying to you on a behalf of Dr. Siomi. Sorry for your inconvenience, but you can download data from our website. http://siomilab.med.keio.ac.jp/?page_id=26.
Or from this link
[golden
hamster genome sequence] MD5:c575be09457eaac35d4fe98d80254d53
[golden
hamster gff3 annotation] MD5:24c1cfb0ba0c9d20a171d7610fae4ae7
[golden
hamster transposon annotation (repeatmasker .out file)] MD5:dbacf099e330b419238c1deaed3ae5ac
Let me know if there are any problems with downloading these data, and we would be happy if you could cite Ishino K et al, NAR 2021 when you use this data.
Best,
Chikara
差出人:
Marianna Zazhytska <mz2...@columbia.edu>
日付:
日曜日, 2023年10月29日
18:21
宛先:
Matthew Speir <msp...@ucsc.edu>
CC: 竹内力 <chika...@keio.jp>, Haruhiko Siomi <awa...@keio.jp>, gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
件名:
Re: [genome] Golden Hamster Genome
Dear Matthew,
Thank you so much for your reply!
Dear Dr. Siomi,
Would you be so kind as to share FASTA and GTF files for MesAur2.0 assembly? Presently I'm working on the smell loss caused by Covid-19 infection using hamster as a model. I'm trying to visualize some ATAC-seq data, but I was using the MesAur1.0 assembly which is not compatible with the UCSC Genome browser.
Thank you so much,
Best regards,
Marianna
On Sun, Oct 29, 2023 at 4:54 PM Matthew Speir <msp...@ucsc.edu> wrote:
Hello, Marianna.
Thank you for your question about downloading data from the UCSC Genome Browser.
The MesAur2.0 assembly you're referring to is provided as an assembly hub by an external collaborator, the Siomi lab at Keio University School of Medicine. I've cc'd their contact email in my response. Hopefully they can provide you with the FASTA and GTF annotation files for this assembly.
If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Matthew Speir
UCSC Cell Browser, Quality Assurance and Data Wrangler
Human Cell Atlas, User Experience Researcher
UCSC Genome Browser, User Support
UC Santa Cruz Genomics Institute
Revealing life’s code.
On Tue, Oct 24, 2023 at 9:13 AM Marianna Zazhytska <mz2...@columbia.edu> wrote:
Hello,
I'm trying to download MesAur2.0 data and have difficulties with it either using the command line or through a web browser. I can clearly see the genome with gene annotation on the web but when I follow the link with genome data the only hamster I can find is a Chinese hamster.
Would you be so kind as to point me in the right direction to get fasta and gtf files?
Thank you so much!
Marianna
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Marianna Zazhytska
Chikara Takeuchi
Hi Marianna,
No problems! For your questions, you can find the details of this reference in the original article, Ishino K et al, NAR 2021 (https://academic.oup.com/nar/article/49/5/2700/6137370?login=true#231957800)
In short, this is a chromosome length scaffold(summarized in Table 1), and we use just liftover for gene annotation(see the Methods and materials section). Although our annotation is not de novo transcriptome assembly, we can see a good mapping rate with this annotation for in early embryo and ovary RNA-seq data.
Thanks,
Chikara
From:
Marianna Zazhytska <mz2...@columbia.edu>
Date: Monday, October 30, 2023 at 11:40 AM
To: Chikara Takeuchi <Chikara....@UTSouthwestern.edu>
Cc: Matthew Speir <msp...@ucsc.edu>, Haruhiko Siomi <awa...@keio.jp>, gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] Golden Hamster Genome
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