A melange of mouse research had scientists tweeting up a storm this week.
It all started with “two huge spatial atlases of the whole mouse brain,” tweeted Lukas Valihrach of the Czech Academy of Sciences.
‼️ Two huge spatial atlases of the whole mouse brain generated by two technologies ‼️
Q: Do you prefer Slide-seq or MERFISH?????????https://t.co/0ch9v8oM0R (data online at https://t.co/M5dudcFRAD)
????https://t.co/jo9ydkA6pz (need to know a companion preprint https://t.co/Clgk2I3TB5) pic.twitter.com/UCzq51zIJl— Lukas Valihrach (@LukasValihrach) March 9, 2023
One atlas, developed by researchers at the Allen Institute in Seattle, Washington, combines two single-cell datasets: an RNA sequencing dataset of about 7 million cells, along with a spatial transcriptomic dataset of about 4.3 million cells profiled by way of multiplexed error-robust fluorescence in situ hybridization (MERFISH), a technique Spectrum covered in November 2018.
Extremely excited to share our bioRxiv preprint posted yesterday, on “A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain”! A huge team effort from @AllenInstitute and collaborators, combining scRNA-seq and MERFISH. https://t.co/Dp1PXfP9YU
— Hongkui Zeng (@HongkuiZeng) March 7, 2023
The atlas “is a foundational resource for deep and integrative investigations of cellular and circuit function, development, and evolution of the mammalian brain,” tweeted Hongkui Zeng of the Allen Institute for Brain Science, in a thread describing her team’s research.
The whole-mouse-brain cell atlas is a foundational resource for deep and integrative investigations of cellular and circuit function, development, and evolution of the mammalian brain.
So much more to learn from the data! A truly incredible treasure trove.— Hongkui Zeng (@HongkuiZeng) March 7, 2023
“A new Allen brain atlas for mouse. This is huge, in all aspects,” tweeted Li Wang of the University of California, San Francisco.
A new Allen brain atlas for mouse. This is huge, in all aspects. https://t.co/Shu7dwmCDQ
— Li Wang (@LiWang_neuro) March 7, 2023
Carlos Alvarez of Ohio State University Medical Center asked if Zeng’s team had found “evidence of sex-specific neurons.”
Zeng replied that the team had found a small set that are sex specific or sex dominant in the hypothalamus, amygdala and pallidum areas.
Yes, we identified a small set of clusters that are sex specific or sex dominant. They were found in hypothalamus, amygdala and pallidum areas. This is described in the last section of Results.
— Hongkui Zeng (@HongkuiZeng) March 8, 2023
“The spatial combined with the single cell is just [star-struck emoji] – looking forward to using this data!” tweeted Julie Siegenthaler of the University of Colorado.
That is the best part and soon all the data we generated in this study will be released for all to use. I can’t wait to see what scientist around the world pull from it.
— Delissa McMillen (@Delissa76) March 7, 2023
Delissa McMillen of the Allen Institute replied that “soon all the data we generated in this study will be released for all to use. I can’t wait to see what scientist around the world pull from it.”
Anirban Maitra of the University of Texas MD Anderson Cancer Center shared this image from the paper and quipped, “Jackson Pollock or spatial profiling?”
Jackson Pollock or spatial profiling?
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brainhttps://t.co/yHVP8cjrGO
Preprint @AllenInstitute of whole mouse brain atlas, comprised of >11 million single cells profiled with scRNA seq & MERFISH ???? pic.twitter.com/1jxdLlOQBa— Anirban Maitra (@Aiims1742) March 6, 2023
The second mouse atlas comes from researchers at the Broad Institute in Cambridge, Massachusetts, who used “Slide-seq, a recently developed spatial transcriptomics method with near-cellular resolution,” according to the preprint published 8 March. Spectrum covered Slide-seq in May 2019.
The data underlying the atlas are available online at BrainCellData.org.
“We find minimal marker sets for all cell types, explore activity-regulated genes, and perform analyses of heritability enrichment,” tweeted lead investigator Evan Macosko, a member of the Broad Institute.
Excited to release our cell type atlas of the adult mouse brain! Here’s our portal:https://t.co/9OkNhUM5zP
And preprint:https://t.co/4FhnGfBBsU
We find minimal marker sets for all cell types, explore activity-regulated genes, and perform analyses of heritability enrichment.
— Evan Macosko (@macosko) March 8, 2023
“Another incredible whole-brain dataset — what a week!” tweeted Joel Geerling of the University of Iowa.
Another incredible whole-brain dataset — what a week! https://t.co/3YlUwxljMj
— Geerling Lab (@geerling_lab) March 9, 2023
In another mouse study, published this week in Current Biology, researchers questioned the assumption that female mice complicate experiments because the “estrous cycle makes all female mouse behavior more variable” than males,’ tweeted Sandeep Robert Datta of Harvard University, in a thread describing his team’s research.
Female mice are studied less than males in part because of a belief held by some that the estrous cycle makes all female mouse behavior more variable. But is this true? Check out our latest, led by @danarubilevy in collab with @shanskylab! https://t.co/xTYF0rsAa2
— Sandeep Robert Datta (@Datta_Lab) March 7, 2023
The team examined the open-field behavior of female mice at different phases of the estrous cycle, using an approach Datta’s lab pioneered called motion sequencing (MoSeq). The hormonal cycle only negligibly affected female mouse behavior, which is actually less variable than that of males, the team found. Both sexes should be used in experiments, the researchers concluded — and “if you were forced to pick a single sex to use when studying spontaneous exploration, our data suggest that sex should be female,” Datta tweeted.
Of course, for many important reasons everyone should use both sexes in their experiments. But if you were forced to pick a single sex to use when studying spontaneous exploration, our data suggest that sex should be female.
— Sandeep Robert Datta (@Datta_Lab) March 7, 2023
“Just another nail in the ‘female data are too messy’ coffin!” tweeted Rebecca Shansky of Northeastern University College of Science, who was involved in the study.
Just another nail in the “female data are too messy” coffin!
— Shansky Lab (@ShanskyLab) March 7, 2023
“This is super important because even in studies of diseases that predominantly affect women, male mice are used with the assumption that they are more ‘reproducible,’” tweeted Saba Valadkhan of Case Western Reserve University.
This is super important because even in studies of diseases that predominantly affect women, male mice are used with the assumption that they are more “reproducible”.
Which means relevance to the disease in human populations is considered a minor concern. https://t.co/DCT8YwVPOx— Dr. Saba Valadkhan (@SValadkhan) March 8, 2023
Liisa Galea of the University of British Columbia pointed out that “the implication that hormones don’t matter is not correct,” as they do matter, just not more in one sex than the other.
Yes but the implication that hormones don’t matter is not correct. They matter just not more on one sex than the other
— Dr. Liisa Galea (@LiisaGalea) March 8, 2023
“No more excuses for excluding female mice from studies,” tweeted Silvia Maioli of Karolinska Institutet.
No more excuses for excluding female mice from studies.. https://t.co/0bOGLJNJcG
— Silvia Maioli (@silvia_maioli) March 7, 2023
That’s it for this week’s Community Newsletter! If you have any suggestions for interesting social posts you saw in the autism research sphere, feel free to send an email to [email protected].
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Cite this article: https://doi.org/10.53053/WKSV2572
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