SpatialTranscriptomics example: PIPELINE="standard" Rscript $STTKIT/st_snormalize.R --infile $SAMPLE/${PIPELINE}_pipeline/${SAMPLE}_${PIPELINE}_ensembl_adjusted.tsv \ --sampleid $SAMPLE \ --hejpeg {SAMPLE}_HE_bw_scaled.jpg \ --outprefix OUTDIR/${PIPELINE}/$SAMPLE/normalize/$SAMPLE \ ...
Single‐Cell RNA Sequencing and Spatial Transcriptomics Reveal Pathogenesis of Meningeal Lymphatic Dysfunction after Experimental Subarachnoid HemorrhageSubarachnoid hemorrhage (SAH) is a devastating subtype of stroke with high mortality and disability rate. Meningeal lymphatic vessels (mLVs) are a ...
Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology Thomas M. Goralski, Lindsay Meyerdirk, Libby Breton, Laura Brasseur, Kevin Kurgat, Daniella DeWeerd, Lisa Turner, Katelyn Becker, Marie Adams, Daniel J. Newhouse & Michael X. Henderson Nature...
Single-cell and Spatial Transcriptomics Reveals Ferroptosis as The Most Enriched Programmed Cell Death Process in Hemorrhage Stroke-induced Oligodendrocyte... Rationale: Within chronic obstructive pulmonary disease (COPD), emphysema is characterized by a significant yet partially understood B cell immune comp...
Single-cell and Spatial Transcriptomics Reveals Ferroptosis as The Most Enriched Programmed Cell Death Process in Hemorrhage Stroke-induced Oligodendrocyte-mediated White Matter Injury. Int J Biol Sci 2024; 20(10):3842-3862. doi:10.7150/ijbs.96262. https://www.ijbs.com/v20p3842.htm Copy Other ...
Multiplexed mRNA profiling in the spatial context provides new information enabling basic research and clinical applications. Unfortunately, existing spatial transcriptomics methods are limited due to either low multiplexing or complexity. Here, we intro
source('/data/xy/UCASpatial_v1.R') # Load the spatial transcriptomics data and the referenced scRNA/snRNA-seq data st_vis <- readRDS('/datapath/ST_data.rds') sc_ref <- readRDS('/datapath/SC_data.rds') # cluster info in 'sc.ref$clust_vr' # Run UCASpatial to map cell ...
therapeutic targets. As high-throughput single-cell technologies mature, their integration into spatial transcriptomics, multiomics, and clinical data analysis will aid in patient stratification and in developing effective treatment plans for patients with or without liver injury due to infectious diseases....
This study used spatially resolved transcriptomics in a mouse model to define the dose-dependent effects of heme exposure in the brain. Our data reinforced the adverse function of heme as a potent inflammatoxin that drives key phenotypic features of secondary brain injury after intracerebral and othe...
Single-cell, single-nucleus and xenium-based spatial transcriptomics analyses reveal inflammatory activation and altered cell interactions in the hippocampus in mice with temporal lobe epilepsy Temporal lobe epilepsy (TLE) is among the most common types of epilepsy and often leads to cognitive, emotion...