Top Tweets for #Dbitseq
On a roll! 🎉 @YanxiangDeng’s lab + @zhouwanding drop a new preprint extending #DBiTseq to co-map DNA methylation 🧬 & RNA in the same tissue slice. Kudos @ChinNLee2021 & Hongxiang Fu!
DNA methylation goes spatial! Introducing Spatial-DMT: a technology that co-profiles DNA methylation and transcriptome in the same tissue section. A fantastic collaboration with @zhouwanding lab. Kudos to Chin Nien Lee @ChinNLee2021 and Hongxiang Fu! https://t.co/895gPK9lKr
Benchmarking sequencing-based #SpatialTranscriptomics methods
#10xVisium
#HDST
#BMKMANUS1000
#SlideseqV2
#Stereoseq
#PIXELseq
#DBiTseq
🐭adult brain/adult olfactory bulb/e12.5 embryo
1⃣Molecular capture efficiency
2⃣Molecular lateral diffusion
Spatial accuracy of mRNA detection, dictated by tissue & permeabilization
3⃣Clustering + Cell state annotation
🧐Different ST methods yield inconsistent cell-cell communication results by #CellChat v1.6 or #CellPhoneDB v4
bioRxiv 2023
https://t.co/khKH10T1Hi
🚨PREPRINT ALERT🚨
Systematic comparison of sequencing-based spatial transcriptomic methods🫶
#ST #benchmark #Visium #HDST #BMKMANUS1000 #SlideSeq #StereoSeq #PIXELSeq #DBiTseq
👉https://t.co/6iQQVJltDU
Thanks for sharing and for the inspiration to this project by publishing #DBiTseq
🤩EXPANDING UNIVERSE OF #DBiT 🤩
Now you can simultaneously map 9 or even more tissue sections in a single DBiT-seq #spatialomics run. Incredible work & beautiful data! Congrats
@Meier_Lab @celia4science @johwirth & team
@PioneerCampus @HelmholtzMunich https://t.co/W9MSMexJfG
Improvements in workflow and #chemistry lead to increased numbers of reads and counts per spot compared to the original #DBiTseq method. An extended #imaging workflow prevents the destruction of image features. 🧬🔬 2/6
I am excited to present multiplexed Deterministic Barcoding in Tissue (xDBiT)🎊. As an extension of #DBiTseq it allows the generation of #spatial #transcriptomics datasets of nine fixed tissue sections in parallel. Paper finally out on @NatureComms📜https://t.co/DfY0UXjBAa 1/6
TLDR:
1. Next-generation sequencing is a procedure for co-mapping of mRNAs and proteins in formaldehyde-fixed tissue.
2. Uses microfluidics to replace the "Solid phase capture of biomolecules on tissues"
#spatialbiology #DBiTSeq #spatialOmics #transcriptomics
Improvements in workflow and #chemistry lead to increased numbers of reads and counts per spot compared to the original #DBiTseq method. An extended #imaging workflow prevents the destruction of image features. 🧬🔬 2/4
I am very happy to present multiplexed Deterministic Barcoding in Tissue (xDbit)🎊. As an extension of #DBiTseq it allows the generation of #spatial #transcriptomics datasets of nine fixed tissue sections in parallel. Preprint is now out on biorxiv📜: https://t.co/4OESTDLz3z. 1/4
Upgraded version of #DBiTseq allowing simultaneous analysis of nine tissue sections with increased read and gene counts per spot
#SpatialTranscriptomics #Microfluidics https://t.co/kHJz8pYMLU
3/4 The liver is highly organized, consisting of hexagonally shaped liver lobules.
Gradients of nutrients and hormones lead to zonation and division of labour of hepatozytes.
#Dbitseq allows us to study the zonation on a transcriptome-wide level.🔬
#YoungScientistsHMGU
2/4 #Dbitseq is a versatile ST method using #microfluidic channels to spatially barcode tissues.
We aim to:
🔝Increase throughput
💰Lower costs
💡Improve usability
🌍Extend application field
As target system for these developments we chose liver zonation.
#YoungScientistsHMGU
Researchers at @Yale developed an in-tissue barcoding approach namely #DBiTseq for spatially revolved #wholetranscriptomesequencing at cellular level, which required no tissue dissociation or #RNA exaction, thus potentially more suited for #FFPEsamples https://t.co/n0QsdMKtMR
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