The Spatial-Cell-ID EquipEx+ platform provides equipment and expertise for single-cell spatiotemporal transcriptomics (aka #spatialtranscriptomics)
Lyon, France
Joined January 2022
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Spatial-Cell-ID retweeted
🚨Preprint alert!
tinyurl.com/2zkmynsd
Did you ever dream of generating spatial maps of #enhancer activity at #singlecell resolution in a multicellular organism using massively parallel enhancer-reporter assays?
Then spatial-scERA is the method for you!
Spatial-Cell-ID retweeted
It's tomorrow!!
We're expecting a full room for an exciting day of science and spatialOMICs discussions 🤩
Join us in Lyon for the annual Spatial-Cell-ID day!
We will welcome @DenisSchapiro (@UniHeidelberg) and Marco Grillo (@MatsNilssonLab @scilifelab) as keynote speakers.
Full program available here:
spatial-cell-id.ens-lyon.fr/…
Spatial-Cell-ID retweeted
🔔Proud and excited to share our latest preprint!
We asked this simple question: do TADs really act as strong boundaries or can functional enhancer-promoter interactions be established across TAD boundaries?
biorxiv.org/content/10.1101/…
A 🧵on our main conclusions: (1/n)
Spatial-Cell-ID retweeted
Using transcriptomic similarity and spatial coordinates, PASTE allows aligning and integrating spatial transcriptomics data generated from adjacent tissue slices. @RonZeira @benjraphael
nature.com/articles/s41592-0…
Spatial-Cell-ID retweeted
I’m so happy to present our spatial multi-omics work out today! nature.com/articles/s41467-0… #spatial #transcriptomics #citeseq #smomics
Spatial-Cell-ID retweeted
Spatial-CUT&Tag! @ScienceMagazine, unfolding a new chapter of #spatialomics 🤗 . From my phenomenal postdoc @DengYanxiang of @YaleSEAS
@YaleBME, @yalepathology @YaleMed @YaleCancer
Thanks to awesome collaborators @GoCasteloBranco @marekbartosovic @PKukanja science.org/doi/10.1126/scie…
Spatial-Cell-ID retweeted
It's great to see our article about the multimodal omics analysis framework muon out!
Many thanks to everyone who provided feedback along the way. 🙌
See a few highlights in the thread below.
MUON, from @gtcaa, Kats & @OliverStegle, a package for organizing, analyzing, visualizing & exchanging multi-omics data. It is based around MuData, an open data structure for multimodal data. An example given is ATAC-seq and RNA-seq from single cells genomebiology.biomedcentral.…
ALT Alternative example workflows for integrating multiple omics for latent space inference and clustering
Spatial-Cell-ID retweeted
New Resource online now at Dev Cell: A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants - zpr.io/6nU8Z95mJ8qS
Spatial-Cell-ID retweeted
"Spatial components of molecular tissue biology", review wrote with @davidsebfischer @fabian_theis and Aviv Regev is out in @NatureBiotech. We outline biological questions and computational challenges in spatial analysis of tissues. 1/N nature.com/articles/s41587-0…
Spatial-Cell-ID retweeted
How to efficiently analyse & process large-scale spatial transcriptomics data from different techs?
We've developed Spacemake that does this and much more
biorxiv.org/content/10.1101/…
Spatial-Cell-ID retweeted
Power analysis for spatial omics | bioRxiv biorxiv.org/content/10.1101/…
Spatial-Cell-ID retweeted
Spatially resolved transcriptomics and its applications | Nice review from Prof. Mingyao Li's group @DrMingyaoLi Statistical and machine learning methods for spatially resolved transcriptomics with histology sciencedirect.com/science/ar…
Spatial-Cell-ID retweeted
How cool is it to be able to visualize multiresolution #InSituSequencing and #SpatialTranscriptomics images with millions of overlaying points from your phone browser!? 🔬📱
TissUUmaps 3 allows it: visit our gallery for more examples tissuumaps.github.io/gallery…
Spatial-Cell-ID retweeted
Optocoder: a computational tool that decodes spatially indexed bead arrays. Optocoder processes spatial transcriptomics microscopy images to extract bead locations and their barcodes (led by fantastic PhD student @nssenel at @N_Rajewsky lab) (1/4)
biorxiv.org/content/10.1101/…
Spatial-Cell-ID retweeted
Interested in spatial omics? Plz check out our squidpy tool, bringing together omics & image analysis to enable a scalable description of spatial molecular data. Out today @naturemethods thx to @g_palla1, @HannahSpitzer1 & team! nature.com/articles/s41592-0… github.com/theislab/squidpy
Spatial-Cell-ID retweeted
Very happy about all the work done by the TissUUmaps team! 💪
TissUUmaps 3: Interactive visualization and quality assessment of large-scale spatial omics data
shorturl.at/dBQV1
You can visit the website to access TIssUUmaps 3 learn more about it: tissuumaps.github.io/
Spatial-Cell-ID retweeted
Our review paper on spatial transcriptomics came online today: frontiersin.org/articles/10.…. We reviewed 10 experimental methods, which cover 1) spatial barcoding, 2) in situ hybridization, and 3) in situ sequencing. We also reviewed 32 computational methods, which cover tools for /1
Spatial-Cell-ID retweeted
@Spatial_Cell_ID relevant preprint here
We can now obtain subcellular maps for both RNA and protein in the same experiment and show the dynamic changes in location of both in the unfolded protein response. Introducing LoRNA (the LOPIT for RNA) biorxiv.org/cgi/content/shor…
Spatial-Cell-ID retweeted
(1) Finally out, after one of the most painful and long reviews (with nitpicky reviews, see my last comment) is a method that I am extremely proud of and excited about. One of the best in my career: nature.com/articles/s41592-0…
Spatial-Cell-ID retweeted
"Spatial Isoform Transcriptomics (SiT)" combining @10xGenomics #Visium and @nanopore long-read to characterize full-length transcripts in brain sections. Great collab between @pbarbry @joalunatkthse labs. @fr_genomics, @cnrs, @humancellatlas, @cziscience, disq.us/t/3r8gopa