Gregory lab #PhD student, Lauren Whaley Powers, attended #SNO25 in beautiful Honolulu & presented her poster:

'Integrative #SingleNuclei #SpatialTranscriptomic profiling of primary and recurrent human #GBM reveals cell-type specific #EGFRvIII expression & #ANXA1 signaling axis' 🧠🧬🔬💻🌺

Are you a PhD interested in #adultneurogenesis and #spatialtranscriptomic in the mouse brain ?
You can apply now for a #JuanDeLaCierva posdoctoral grant from MICIU at our lab @institutocajal.bsky.social @csic.es 🧠🐭
Please, write us before the 5th of December !!
⬇️
aei.gob.es/convocatorias/…

Advice needed: can you distinguish splicing variants by commercial #spatialtranscriptomic (eg visium)? #singlecell #omics

New BBSRC funding supports expansion of transformative spatial science The new system builds on the Institute’s existing spatial transcriptomic infrastructure.

We're excited to share that we've expanded our #SpatialTranscriptomic capabilities with the addition of the @vizgen.bsky.social MERSCOPE Ultra, thanks to funding from the @ukri.org BBSRC ALERT scheme!

🔗 buff.ly/sUekTX5

2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices Imaging-based spatially resolved transcriptomics can localise transcripts within cells in 3D. Cell segmentation precedes assignment of transcripts to cells and annotation of cell function. However, ce...

Have you been bothered that practically every #SpatialTranscriptomic analysis tool assumes data to be 2D? Well, you were right - overlapping cells are a really big problem. Check out our report on bioRxiv: 2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices. t.ly/CQX8K

Finally, our paper studying synovial tissue # DC #DendtriticCells in joint health and #rheumatoidArthritis is out in Immunity!
#scRNAseq #spatialTranscriptomic
From: @ImmunityCP
https://mstdn.science/@ImmunityCP/113557582489769767

In this #codetutorial, I quickly identify spatially variable genes in a #spatialtranscriptomic dataset w/ 377,985 cells by combining our recently developed preprocessing tool SEraster with our existing tool MERINGUE.

Try it out for yourself: jef.works/blog/2024/03...

#AcademicSky #Rstats

Benchmarking sequencing-based #SpatialTranscriptomic methods

#10xVisium
#HDST
#BMKMANUS1000
#SlideseqV2
#Stereoseq
#PIXELseq
#DBiTseq

Different ST methods yield inconsistent cell-cell communication results by #CellChat #CellPhoneDB

bioRxiv 2023
www.biorxiv.org/content/10.1...