Journal: Nature communications

Article Title: Single-cell analysis identifies conserved features of immune dysfunction in simulated microgravity and spaceflight.

doi: 10.1038/s41467-023-42013-y

Figure Lengend Snippet: Fig. 6 | Simulated microgravity induces distinct modifications to immune cell cytoskeletal morphology and cytokine production. A Super-resolution micro- scopy analysis of actin in 2D for cell area (left), intensity (middle), and texture as punctate over diffuse index (PDI, variance/mean, right) between 25 hours of 1G or simulated uG. Dots represent individual PBMCs (n = 159 cells for 1G, and n = 154 cells for uG) from 4 independent donors. Donors were male (25 years old), and females (35, 38, and 46 years old). One outlier for actin intensity and actin PDI from each condition is removed based on Grubbs’ test. Two-tailed Welch’s t test was used for all comparisons. ***p ≤0.001. Data are plotted as mean ± standard error of the mean (SEM) and source data are provided with this paper. B Representative super- resolution microscopy images (2D left, 3D right) of PBMCs from 1G and simulated uG (25 hours) from donor 1 (35 yr F) and donor 2 (25 yr M; 2 of total 4 donors from A are shown here). 3D images better highlight changes to overall cell shape and actin protrusions in simulated uG. Scale bar = 2 μm and 1 μm, respectively. C Sixteen-channel granularity spectrum measurement of PBMCs stimulated with TLR7/8 agonist (9 hours stimulation, 16 hours conditioning prior to stimulation) from 1G (pink line) and uG (brown line) minus the corresponding unstimulated cells (25 hours total culture). The effect of simulated microgravity on unstimulated granularity spectrum is plotted in gray. Asterisks compare pink vs brown lines only. P values generated from unpaired two-tailed t test. n = 3 donors tested from A, 35- year-old female sample was not used. **p ≤0.01, *p ≤0.05. Data are plotted as mean ± SEM, and source data are provided with this paper. D Super-resolution

Article Snippet: A UMAP plot of unstimulated PBMCs single-cell transcriptomes (10X Genomics), pooled together from a male (36 years old) and a female (25 years old) donor, that underwent either 1G or simulated microgravity (uG) for 25 hours total.

Techniques: Two Tailed Test, Super-Resolution Microscopy, Generated

Journal: Human Genetics

Article Title: Advances in long-read single-cell transcriptomics

doi: 10.1007/s00439-024-02678-x

Figure Lengend Snippet: Currently available long-read scRNA-Seq library preparation protocols

Article Snippet: scCOLOR-seq , Drop-seq , Long-read (ont) , Low Cell capture efficiency (10%) , Overcome the low base-calling accuracy of Oxford Nanopore sequencing; provides a simplified and more robust method to perform quantitative long-read transcript sequencing on large numbers of cells , Error correction of single cell sequencing barcodes, with over 80% recovery of reads when using an edit distance of 7, or over 60% recovery when using a conservative edit distance of 6. Uniquely, UMIs can be deduplicated with a high level of accuracy, approaching 100% in simulated data , Philpott et al. ( ) .

Techniques: Sequencing, Modification, Illumina Sequencing, Nanopore Sequencing, Reverse Transcription, Amplification

Journal: Human Genetics

Article Title: Advances in long-read single-cell transcriptomics

doi: 10.1007/s00439-024-02678-x

Figure Lengend Snippet: Different aspects of short-read and long read Seq

Article Snippet: scCOLOR-seq , Drop-seq , Long-read (ont) , Low Cell capture efficiency (10%) , Overcome the low base-calling accuracy of Oxford Nanopore sequencing; provides a simplified and more robust method to perform quantitative long-read transcript sequencing on large numbers of cells , Error correction of single cell sequencing barcodes, with over 80% recovery of reads when using an edit distance of 7, or over 60% recovery when using a conservative edit distance of 6. Uniquely, UMIs can be deduplicated with a high level of accuracy, approaching 100% in simulated data , Philpott et al. ( ) .

Techniques: Sequencing, Variant Assay

Journal: Nucleic acids research

Article Title: SCAR: Single-cell and Spatially-resolved Cancer Resources.

doi: 10.1093/nar/gkad753

Figure Lengend Snippet: Figure 1. Ov ervie w of SCAR_S T module. ( A ) Tumor spatial transcriptomic datasets of three species included in the SCAR_S T module: i.e. human, mouse and zebrafish. ( B ) Selection of genes from lymphoma showcasing spatial expression patterns in the SCAR_ST module, including top 10 spatially variable genes in lymphoma ( 56 ). Schematics were created with BioRender.com.

Article Snippet: Finally, to visualize the cell stemness prediction results, the prediction result and the cell type information of the single cell were simul- t f S I m 1 ( s i d S r S s i w s ‘ C T m r m d l r d d a t t j i a C I C t ‘ p w C P w M w m t r c l ‘ ‘ S T c t c D ow nloaded from https://academ ic.oup.com /nar/article/52/D 1/D 1407/7280550 by guest on 15 January 2024 aneously applied as parameters using the ‘plotCytoTRACE’ unction. patial transcriptomic dataset treatment n total, 41 spatial transcriptomic datasets of 21 human, ouse and zebrafish tissues were obtained from GEO ( 29 ), 0x Genomics ( https:// www.10xgenomics.com/ ), SPASCER 44 ), STOmicsDB ( 45 ), and SODB ( 46 ).

Techniques: Selection, Expressing

Journal: Nature Communications

Article Title: PROST: quantitative identification of spatially variable genes and domain detection in spatial transcriptomics

doi: 10.1038/s41467-024-44835-w

Figure Lengend Snippet: a Boxplot shows the Adjusted Rand Index (ARI) to summarize the domain segmentation accuracy of each method in all 12 sections of the DLPFC dataset. The boxplot’s center line, box limits, and whiskers denote the median, upper and lower quartiles, and 1.5× interquartile range, respectively. Source data are provided as a file. b Hematoxylin and Eosin (H&E) image and the manual annotation of the DLPFC section 151672. c Spatial domains identified by SCANPY, stLearn, HMRF, BayesSpace, SpaGCN, SpaceFlow, STAGATE, BASS, and PROST, respectively, in the DLPFC section 151672. d UMAP visualizations (top) and PAGA graphs (bottom) generated by SCANPY, stLearn, SpaceFlow, STAGATE, and PROST, respectively, for the DLPFC section 151672 dataset. The UMAPs and PAGA graphs were colored by the corresponding layer annotation of spots in ( b ). e Boxplot shows the Moran’s I and Geary’s C values for spatial autocorrelation using 50 top-ranked SVGs detected by Seurat, SpatialDE, scGCO, SPARK-X, SINFONIA and PROST, respectively, in the DLPFC section 151672 dataset. The boxplot legend is the same as ( a ). Source data are provided as a Source Data file. f H&E image (left) and the manual annotation (right) of the DLPFC section 151675. Representative SVGs detected by PROST in the DLPFC section 151672 ( g ) show the same spatial patterns in the DLPFC section 151675 ( h ), demonstrating the transportability of SVGs.

Article Snippet: All data analyzed in this study were downloaded in raw form from the original publications. (1) The 10x Visium DLPFC data is available at LIBD ( http://research.libd.org/spatialLIBD ); (2) The other datasets generated by 10x Visium platform are available at the 10x Genomics website ( https://support.10xgenomics.com/spatial-gene-expression/datasets ); (3) The ST sequencing data used in this study is available in the SpatialDB database: ( http://www.spatialomics.org/SpatialDB ); (4) The processed Stereo-seq data from mouse olfactory bulb tissue is accessible at SEDR ( https://github.com/JinmiaoChenLab/SEDR_analyses ); (5) The mouse somatosensory cortex dataset is available from ( http://linnarssonlab.org/osmFISH/availability/ ); (6) The Slide-seq data is download from ( https://singlecell.broadinstitute.org/single_cell/study/SCP354/slide-seq-study ); (7) The Slide-seqV2 datasets are available at the Broad Institute Single Cell Portal ( https://singlecell.broadinstitute.org/single_cell/study/SCP815/highly-sensitive-spatial-transcriptomics-at-near-cellular-resolution-with-slide-seqv2 ); (8) Simulated gene expression counts are available at ( https://github.com/acheng416/Benchmark-CTCM-ST ); (9) The processed SeqFISH mouse embryogenesis dataset with segmentation information and associate metadata are available at https://crukci.shinyapps.io/SpatialMouseAtlas/ . are provided with this paper.

Techniques: Generated