New chromosome-level genome assembly for Chinese Hamster

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Andrew Belmont

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Jul 8, 2021, 3:07:27 PMJul 8
to gen...@soe.ucsc.edu
Hello,

    We are interested in doing genomic work with CHO cells.  The
assembly that you have available, however, is near impossible for us to
work with as it has many thousands of scaffolds.

    There is a new chromosome-level assembly that came out for Chinese
Hamster in 2020 and we are interested in using it with the UCSC browser.

    This seems to be the place to download the Chinese Hamster assembly
and annotation files: https://www.ncbi.nlm.nih.gov/assembly/GCF_003668045.3

    The paper describing this assembly is attached.

    Here is a link to a website that collects genomic information for
Chinese Hamster and CHO cells: https://www.chogenome.org/JBrowse.php

    It would be wonderful if this chromosome-level assembly could be
used to update the available Chinese Hamster assembly to one that allows
viewing entire chromosomes.

Andrew

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Andrew S. Belmont, MD, Ph.D
Professor
Department of Cell and Developmental Biology
Institute of Genomic Biology
Biophysics and Quantitative Biology
University of Illinois, Urbana-Champaign
B107 Chemical and Life Sciences Building
601 S. Goodwin Ave
Urbana, IL 61801
Office: 217-244-2311

CHO_genome_2020_assembly_2020.pdf

Gerardo Perez

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Jul 9, 2021, 12:44:42 PMJul 9
to Andrew Belmont, genome

Hello, Andrew.

Thank you for your interest in the Genome Browser and for letting us know about the Chinese Hamster assembly (GCF_003668045.3).

We offer this Chinese Hamster assembly (GCF_003668045.3) as an assembly hub:
https://genome.ucsc.edu/h/GCF_003668045.3

The supporting download files can be found here:
https://hgdownload.soe.ucsc.edu/hubs/GCF/003/668/045/GCF_003668045.3/

You can read about assembly hubs here: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly.

I hope this is helpful. 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.

Gerardo Perez
UCSC Genomics Institute


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Andrew Belmont

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Jul 12, 2021, 1:16:25 PMJul 12
to Gerardo Perez, genome

Thanks Gerardo and others!

    But I am afraid I am still confused.  The assembly that you pointed me to still does not appear to be chromosome level.  It doesn't recognize "Chr2:" , etc and seems to be just showing just individual scaffolds of limited size if I search for a specific gene- ie HSPA1A.  This is because the average scaffold sizes are quite small.

    The article I attached previously used Hi-C and other methods to align these scaffolds and group them onto chromosome-level scaffolds.

    The NCBI lists a chromosome level assembly: CriGri-PICRH-1.0 with accession numbers:

    I am looking for a way to visualize entire chromosomes at once.  The 4D Nucleome data I visualize involves features such as LADs, NADs, TADs, etc which are larger than many of the scaffolds and we are interested in seeing many such consecutive features covering typically tens of Mbp or entire chromosome arms when we look at our data.

Andrew

Dan Schmelter

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Jul 14, 2021, 3:14:11 PMJul 14
to Andrew Belmont, Gerardo Perez, genome

Hello Andrew,

Thanks for following up to get clarity on this topic. The assembly we previously linked you to is exactly the one you requested, RefSeq Assembly Accession GCF_003668045.3. You can access this browser below:

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_2100979_GCF_003668045.3

Instead of using chromosome names (chr2), we use RefSeq names (NC_048595.1) because they are more universal across assemblies. This is something we're working on making more clear. You can see an equivalency table here, which means that searches or custom tracks with any of the names listed should work for this assembly:

https://genome.ucsc.edu/cgi-bin/hgTracks?chromInfoPage=&hgsid=1133134125_UaHnrcp8NdqiBa7KluqFpnpUqtxf&db=hub_2100979_GCF_003668045.3

For chromosome-scale visualization, you can zoom out to entire chromosomes. It may be slow to load if you have many tracks turned on, so I recommend keeping your tracks minimal or in "Dense" modes at first. I hope this is helpful!

For further communication, please reply-all to gen...@soe.ucsc.edu. Those emails are archived in a public help forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu.

All the best,
Daniel Schmelter
UCSC Genome Browser


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