6. In April, collaborator Brian Cleary published Composite In Situ Imaging, a compressed sensing method for imaging transcriptomics With Aviv Regev & @eric_lander + contributions from Evan M, @sinhanubhav, @ehshabibi, & @JamieLMars Tweet added by Fei Chen Lab @insitubiology

Fei Chen Lab

2 years

6. In April, collaborator Brian Cleary published Composite In Situ Imaging, a compressed sensing method for imaging transcriptomics With Aviv Regev & @eric_lander + contributions from Evan M, @sinhanubhav , @ehshabibi , & @JamieLMars

Compressed sensing for highly efficient imaging transcriptomics

Nature Biotechnology - Spatial transcriptomics is enhanced by using imaging probes for subsets of genes.

www.nature.com

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Fei Chen Lab

@insitubiology

2 years

Hello, Twitter! We're so grateful that 2021 was filled with exciting science and lab fun! For our inaugural tweet, we want to appreciate our lab members and collaborators by sharing some of their amazing work from the past 12 months Presenting the 2021 Chen Lab Year in Review:

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Fei Chen Lab

@insitubiology

2 years

1. We kicked off 2021 with in situ genome sequencing, a new technique for measuring DNA sequence and structure in intact samples With @Andrew_C_Payne , @z_chiang , @PaulReginato , @eboyden3 , & @JD_Buenrostro

In situ genome sequencing resolves DNA sequence and structure in intact biological samples

A technical approach allows simultaneous sequencing and imaging of genomes in human fibroblasts and early mouse embryos.

www.science.org

zack chiang

@z_chiang

3 years

Introducing IN SITU GENOME SEQUENCING, a new technology to resolve DNA sequence🧬 and structure🔬 A team effort with @Andrew_C_Payne , @PaulReginato , @eboyden3 , @JD_Buenrostro , and Fei Chen This is how it works: (1/8)

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@insitubiology

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2. ExSeq was published just weeks later, combining in situ transcriptomics and expansion microscopy With Shahar Alon, @D_R_Goodwin , @sinhanubhav , Oz Wassie, @geochurch , @AdamMarblestone , & @eboyden3

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

An adaptation of expansion microscopy allows in situ sequencing and multiplexed subcellular mapping of RNAs.

www.science.org

Anubhav Sinha

@sinhanubhav

3 years

We're excited to share that expansion sequencing (ExSeq) is finally out! ExSeq brings together expansion microscopy and a suite of in situ sequencing technologies, enabling spatially precise in situ sequencing in tissues. /1

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@insitubiology

2 years

3. @hattaca dropped inCITE-seq for jointly measuring nuclear proteins and RNA in single cells, which enables quantifying the direct or indirect effects of TFs on gene expression in vivo (supervised by Aviv Regev)

Hattie Chung

@hattaca

3 years

Excited to share our #preprint on inCITE-seq for measuring nuclear protein levels + transcriptome at single cell! Like CITE-seq for cell-surface proteins, we use DNA-conjugated antibodies to measure proteins, but now inside the nucleus + transcriptome.

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Fei Chen Lab

@insitubiology

2 years

4. In February, Dylan Cable published RCTD, a computational approach for deconvolving cell type mixtures in spatial transcriptomics data (with @rafalab )

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Fei Chen Lab

@insitubiology

2 years

5. In March, @SGRodriques & @linlinmc ’s work on RNA timestamps to encode the age of single molecules was released in print (with @eboyden3 )

RNA timestamps identify the age of single molecules in RNA sequencing

Nature Biotechnology - The age of individual RNA molecules at 1-h resolution is inferred by measuring A-to-I editing.

www.nature.com

Sam Rodriques

@SGRodriques

4 years

New paper out today in @NatureBiotech with Linlin Chen, Fei Chen, @eboyden3 , and many other wonderful coauthors, demonstrating how we can encode the age of an RNA into its sequence to achieve "temporal transcriptomics"

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@insitubiology

2 years

7. In June, @ehshabibi and collaborator @DanielaJDiBella released a single-cell atlas of mouse corticogenesis (supervised by Aviv Regev & @ArlottaLab )

Molecular logic of cellular diversification in the mouse cerebral cortex

Nature - A single-cell atlas of the developing mouse cortex provides a temporal and spatial assessment of the molecular logic that drives the establishment and organization of cortical cell types.

www.nature.com

Ehsan Habibi

@ehshabibi

3 years

Very excited to share my paper just out in @NATURE . KUDOS to @DanielaJDiBella from @ArlottaLab , Aviv, Fei, Bob Stickels, Gabriele Scalia, and Tommasso Biancalani for the heroic effort!

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@insitubiology

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8. In October, @JamieLMars shared her work using Slide-seq to map cell neighborhoods in healthy and diseased kidneys With Teia Noel, @qbw_128 , @SilvanaBazua , @haiqi_chen , & @AnnaGreka

Jamie Marshall

@JamieLMars

3 years

Thrilled to share the Kidney Slide-seq pre-print . HUGE thanks to the amazing kidney slide-seq team Teia Noel, @qbw_128 , and @haiqi_chen . Thanks to Evan Murray for the Slide-seq arrays, @SilvanaBazua , and @AnnaGreka , Fei Chen, and @macosko for mentorship!

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@insitubiology

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9. In November, @haiqi_chen released the first spatial transcriptomic atlas of mammalian spermatogenesis Haiqi is starting his own lab @UTSWNews and is recruiting at all levels!

Haiqi Chen

@haiqi_chen

3 years

Excited to share our work published today @CellReports on dissecting spermatogenesis using spatial transcriptomics.

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Fei Chen Lab

@insitubiology

2 years

10. Not a paper, but possibly even more exciting: in December, @soph_liu was awarded an #ImpetusGrant with Karin Gustafsson from the Scadden lab to study immune cell aging

Sophia Liu

@immunoliugy

3 years

Thanks to #ImpetusGrants @MartinBJensen @LNuzhna for funding our project! Grateful for the support from my PI, @insitubiology , and excited to work alongside Karin Gustafsson in David Scadden's lab.

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Fei Chen Lab

@insitubiology

2 years

11. And right before the holidays, Tongtong Zhao and @z_chiang adapted Slide-seq beads to measure DNA and used this technique to study clonal heterogeneity in cancer (with @JD_Buenrostro )

Spatial genomics enables multi-modal study of clonal heterogeneity in tissues

Nature - A technique using barcoded beads for DNA sequencing within tissue sections enables spatial resolution of tumour clonal heterogeneity and can be multiplexed with other analytical techniques...

www.nature.com

zack chiang

@z_chiang

3 years

Just released @Nature : slide-DNA-seq, our new method for spatial DNA sequencing in tissues 🧬 Excited to add a genetic dimension to the rapidly expanding spatial toolbox with the tech dev superteam of Tongtong Zhao, @JD_Buenrostro & @insitubiology (1/6)

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Fei Chen Lab

@insitubiology

2 years

With success comes people moving on, and it was bittersweet to see @Andrew_C_Payne ( @E11BIO ), @PaulReginato (climate tech), Julia Morriss (Harvard CCB), Bob Stickels (Scale Bio), Evan Murray, @JamieLMars (Solid Bio), & @haiqi_chen (UTSW) off to new adventures

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Fei Chen Lab

@insitubiology

2 years

On the other hand, we're thrilled to have new faces Gio, Julie, @dawnchenx , @VerenaVolf , Mehdi, Yifan, @Luyi_T , Simon, Chen, & @AndyRusss ! Looking forward to more exciting science and lab fun in 2022! Happy New Year!

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