@lylaatta

MD-PhD Candidate @JHUBME. spatial transcriptomics at https://xitter.cf/t.co/S5zk0oAaQ1. she/her

 Baltimore, MD
lylaatta.github.io/
Joined December 2020
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Check out our now published investigation into how experimental design and analysis choices can affect downstream results when analyzing imaging-based spatial transcriptomics data. rdcu.be/dKFby
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Finally, based on our results we provide a decision tree for investigators deciding on which normalization method to use with their data.
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Thanks to @kalen_clifton, @manjari_017, @Gohta_Aihara, who contributed to this project, to @JEFworks for guidance and mentorship, and to the reviewers for providing thoughtful feedback that greatly improved the work!
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Excited to share some updates and recommendations on normalization approaches for #singlecell imaging-based targeted #spatialtranscriptomics data. See more in our pre-print: bit.ly/jefworks-imSRT-norm
Dr. Jean Fan@JEFworks7 Mar 2024
We've updated our #bioRxiv preprint investigating the potential impact of #geneexpression normalization methods with different gene panels in analysis + interpretation of #singlecell imaging-based targeted #spatialtranscriptomics data. Check it out: biorxiv.org/content/10.1101/… 🧵1/n
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Check out our new #bioinformatics method to characterize cell-type spatial relationships across length scales in #singlecell #spatialomics data Preprint: biorxiv.org/content/10.1101/… Software: github.com/JEFworks-Lab/CRAW… Led by @rdsantospeixoto + @bf_miller_ w/ @BruskoMaigan +team 🧵👇
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This results in region- and cell type-specific false +ve/-ve differential gene expression tests and different sign log fold changes. We see these effects across single-cell imaging-based spatial transcriptomics technologies.
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These issues can be mitigated with larger gene panels or gene panels that are more representative of the gene expression of the tissue's component cell types.
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We hope that this work is useful to folks looking to leverage the high throughput and spatial resolution of single-cell imaging-based spatial transcriptomics' technologies to ask new biological questions that help us understand how cells behave within their spatial contexts.
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We find that when using count based normalization methods such as library size normalization, downstream differential gene expression and fold change analyses give different results with different gene panels.
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Given advancing imaging-based spatial transcriptomics tech and many new datasets to interrogate spatial biology, we (@kalen_clifton, @manjari_017, @JEFworks, and I) wanted to explore how experimental design choices and gene expression normalization can affect downstream analyses.
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Happy to share some of what I've been working on recently! See 🧵 below for a summary. And this 🧵for more details: xitter.cf/JEFworks/status/169904… And check out the preprint for all the details: biorxiv.org/content/10.1101/… #spatialtranscriptomics #singlecell #scRNAseq
Dr. Jean Fan@JEFworks5 Sep 2023
How should we normalize #singlecell #geneexpression counts from imaging-based #spatialtranscriptomics? We kept getting asked this so we wrote a paper about it! #bioRxiv preprint: biorxiv.org/content/10.1101/… Led by @lylaatta w/ @kalen_clifton + @manjari_017 #AcademicTwitter 🧵1/n

Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

Recent advances in imaging-based spatially resolved transcriptomics (im-SRT) technologies now enable high-throughput profiling of targeted genes and their locations in fixed tissues. Normalization of...

biorxiv.org
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.@JohnsHopkins says that termination, discrimination, sexual assault, and health and safety don't deserve protections in a contract. We demand better and are willing to fight for our workplace rights. #NotSafeatJHU #MyRightsMyContract #JohnsHopkins
I'm not safe at work if I do not have consistent access to free high-quality masks or COVID-19 testing during a global pandemic that kills and disables hundreds in the US daily.

ALT I'm not safe at work if I do not have consistent access to free high-quality masks or COVID-19 testing during a global pandemic that kills and disables hundreds in the US daily.

Public health is a workplace issue!!

ALT Public health is a workplace issue!!

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JHU closed on-site employee COVID-19 testing due to "reduced demand". I was repeatedly denied testing after a known exposure. @JohnsHopkinsSPH claims to be the #1 school of public health, but JHU refuses to provide access to public health protections during an ongoing pandemic.
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Replying to @JohnsHopkins
@JohnsHopkins says that termination, discrimination, sexual assault, and health and safety don't deserve protections in a contract. We demand better and are willing to fight for our workplace rights. #NotSafeatJHU #MyRightsMyContract #JohnsHopkins
I'm not safe at work if I do not have consistent free access to high-quality masks for COVID -19 testing during a global pandemic that kills hundreds in the US daily. We deserve a contract that protects us!

ALT I'm not safe at work if I do not have consistent free access to high-quality masks for COVID -19 testing during a global pandemic that kills hundreds in the US daily. We deserve a contract that protects us!

Public Health is a workplace issue!!

ALT Public Health is a workplace issue!!

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Thrilled to share our #bioinformatics tool for aligning #spatialtranscriptomics data using #LDDMM across technologies, partial matched tissues, to 3D atlas 📰 biorxiv.org/content/10.1101/… 🖥️ github.com/JEFworks-Lab/STal… #Python Congrats @kalen_clifton @manjari_017 w/ collab @UCLA @JHUBME
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