MIchelle and Julia will be presenting the following topic and papers:
Qian F, et al. Single-cell RNA-sequencing of zebrafish hair cells reveals novel genes potentially involved in hearing loss. Cell Mol Life Sci. 2022 Jun 26;79(7):385. doi: 10.1007/s00018-022-04410-2.PMID: 35753015 Review: •Single-cell RNA sequencing technologies and bioinformatics pipelines. Hwang B, Lee JH, Bang D. Exp Mol Med. 2018 Aug 7;50(8):96. doi: 10.1038/s12276-018-0071-8. Review.PMID: 30089861
16 Comments
HUIXIAN QIU
2/25/2024 07:52:23 pm
I have seen the term heterogeneity of the gene in many literature and it is mentioned again in the review paper. Could you explain what it means by what "gene expression is heterogeneous" means and how do we understand it in the context of the scRNA-sec technique?
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Dianna Xie
2/26/2024 08:15:58 pm
When reading Qian et al.'s article, I was wondering does this gene also causes hearing loss or dysfunction in other organisms? Or does it affect a specific hair cell type, or cause different dysfunctions, or other parts of the body?
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Rebecca Wright
2/27/2024 12:39:58 pm
The Qian et al article discusses a technique known as WISH. What is this technique, and is it in any way similar to the FISH technique?
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Sara Fritz
2/28/2024 11:32:07 am
Can you describe how the researchers create the cluster map from the RNA-seq data and how they determine which clusters belong to which types of hairs? What is the difference between PCA and UMAP?
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Brooke Fuerstenau
2/28/2024 03:24:25 pm
After reading the Qian article, I was wondering if these genes have any similar functions/use the same pathways that could be studied and implemented into future research regarding human hearing loss?
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Rohan Babaria
2/28/2024 03:25:43 pm
In Quian et Al. I was confused why the researchers chose capgb and mb specifically over some of the other genes found and was wondering if you could shed some light on that.
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perla larios
2/28/2024 06:04:10 pm
How could this discovery pave the way for novel therapeutic interventions targeting myoglobin-related pathways in the context of hearing loss or other sensory disorders?
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Joely
2/28/2024 08:13:42 pm
Why do you think the researchers chose WISH (detecting RNA levels) over RNA FISH? Is there a big difference between the two techniques? Or is it the same thing just with different names?
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Kate Stack
2/28/2024 10:35:03 pm
I was very surprised to see myoglobin be a candidate gene in the primary paper! I know that they saw reduced balance ability in ko myoglobin zebrafish, likely due to the reduction hair cells in the ear, but I was wondering if there is anything else that could have caused this as well? Do you have any hypothesis about why myoglobin might be important for the hair cell production?
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Samuel Kivi
2/29/2024 12:40:26 am
Do you think it could be possible for scientists to create genetically-modified zebrafish (or other, closely-related species) that can have cells/tissues extracted as a treatment for hearing loss in humans (similar to cross-species organ transplants that have been pursued as of recent)?
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Zoe Zwick
2/29/2024 01:06:32 am
In the main paper for this week, they did the vestibulo-ocular reflex (VOR) test to test balance of the morphant zebrafish. What is this test and how would they calculate the data for the figure based on the test?
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Madeline Blum
2/29/2024 07:31:37 am
What exactly is dimension reduction in terms of analyzing RNA- seq data? Does this simply mean grouping cells from the results into similar categories? Would the 2D projection of gene expression mean gene expression of these categories, or is there something I am missing?
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2/29/2024 09:23:55 am
For "Single-cell RNA-sequencing of zebrafish hair cells reveals novel genes potentially involved in hearing loss" and other single cell RNA sequencing, were there any specific strategies employed to enhance the capture rate of RNA molecules and to ensure a sufficient sequencing depth for rare transcripts during the library preparation for sequencing?
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Miles Giehtbrock
2/29/2024 10:23:01 am
One of the papers mentioned "A distinctive feature of scRNA-seq data is the presence of zero-inflated counts due to reasons such as dropout or transient gene expression" why would tissue gene expression be inflated in normal rna seq data?
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Maggie Chrostowski
2/29/2024 10:28:23 am
In the Qian et al. paper, section E in Figure 1 discusses the length of kinocilium, does the length of kinocilium affect the function of the hair cells?
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Praneeth Venigalla
2/29/2024 11:42:20 am
Given the rapid evolution of single-cell RNA sequencing technologies and bioinformatics pipelines, what do you consider the most significant challenges currently facing researchers in this field, and how can these be overcome?
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