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We began analyzing https://pmc.ncbi.nlm.nih.gov/articles/PMC6086938/, but it redirected us to https://pmc.ncbi.nlm.nih.gov/articles/PMC6086938/. The analysis below is for the second page.
Title[redir]:
Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging - PMC
Description:
A highly multiplexed cytometric imaging approach, termed co-detection by indexing (CODEX), is used here to create multiplexed datasets of normal and lupus (MRL/lpr) murine spleens. CODEX iteratively visualizes antibody binding events using DNA ...
Title[redir]:
Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging - PMC
Description:
A highly multiplexed cytometric imaging approach, termed co-detection by indexing (CODEX), is used here to create multiplexed datasets of normal and lupus (MRL/lpr) murine spleens. CODEX iteratively visualizes antibody binding events using DNA ...
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Keywords {🔍}
cell, cells, codex, figure, mrllpr, spleen, types, tissue, data, expression, iniche, iniches, antibodies, analysis, observed, balbc, interaction, spleens, figures, doi, interactions, staining, image, normal, cat, type, red, splenic, table, disease, cycles, early, frequency, imaging, cycle, signal, antibody, model, ratio, panel, rrid, niche, top, heatmap, change, samples, marker, index, mrl, found,
Topics {✒️}
cd106+/cd16/32+/ly6c–/cd31– stromal cells cell-specific tcr-fluorescein isothiocyanate cd106+cd16/32–ly6c+cd31+ phenotype x-shift phenotype-mapping algorithm mrl-mp/lpr-lpr mice cell-surface-marker expression depends codex dna-tagged tcr-β [google scholar] gerdes late-stage mrl/lpr spleens tcr-β-positive cd4 positive double-stranded oligonucleotide tag pmc beta search expert hand-labeled nuclei late mrl/lpr based org/experiments/1688 acknowledgments gradient-tracing watershed algorithm z-score transformed matrices cd106+cd16/32–ly6c+cd31+ �activation primer”-based extension data-driven i-niche analysis low-pass fft filtering fluorescence-activated cell sorting subsets/morphological units constituting double-stranded oligonucleotide tags paraffin-embedded cancer tissue long single-stranded oligonucleotides mrl/lpr mice monitored illustrate i-niche-dependent variability largely exclusive mega-clusters highest improvement f-values hand-labeled cell center surface-marker phenotypes recognizable early mrl/lpr spleen hand-labeled cell identification online repository page define single-cell boundaries early mrl/lpr stage early-stage mrl/lpr rare cell-type detection i-niche window slides cd4/cd8 double-negative b220+ /nolanlab/codex vortex environment cell-cell pairs observed cell-type interaction landscape ][5′-c1-4/t1-4-3′]n-ttctgcaagatgctaccgttcggctggaddc-3′ mrl/lpr genotype allowed high sample-specific variation panel-specific activator oligonucleotide early mrl/lpr spleens distinct peri-follicular space
Questions {❓}
- A corollary to this is the question of whether the presence of these cells, and new i-niches dependent on these cells, somehow changed the observable biology of the cells they contact?
- So, while there was no obvious gross rearrangement of the tissues, many homotypic and heterotypic cell-cell associations were altered, prompting a key question: what are the main factors driving this disruption?
- This raises interesting questions—can new cell types, or functional subsets, be discerned by this approach?
- What could be the drivers of changes in frequency of pairwise cell-cell contacts?
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