Journal: Nature Communications

Article Title: Multiplexed transcriptomic analyzes of the plant embryonic hourglass

doi: 10.1038/s41467-024-55803-9

Figure Lengend Snippet: Longitudinal cryosections of Stage 1 embryos embedded in optimal cutting temperature compound (OCT; ( a – b ) two replicates) or in paraffin ( c – d ) six replicates, for use in10x Visium TM spatial transcriptomics analysis of embryo sections. The Toluidine Blue-stained sections ( a , c ) are overlayed with the10x Visium TM spatial map ( b , d ); the various color-coded circles correspond to the capture spots within which spatial cDNA libraries were generated. Scale bars = 100 μm. e Spatial clustering of Visium TM spatial transcriptomic analysis of the Stage 1 embryo. The spatial embryonic origins of each cluster are indicated by the color-coded embryo cartoon; numbers correspond to the cluster designations on the UMAP. f Longitudinal sections of paraffin-embedded Stage 1 embryo for use in LM-RNA-seq. g Enlarged view of a Stage 1 embryo showing regions microdissected for LM-RNA-seq; all LM-RNA-seq analyzes included three replicates. Figure labels: scu, scutellum; uc, upper coleoptile; lc, lower coleoptile. Scale bars =100 μm. h Heatmap illustrating the correlation between the single-cell (sc) clusters ( y -axis) and Visium TM spatial clusters ( x -axis). The significance level is marked by −log 10 p. The p values were calculated based on the cumulative distribution function (CDF) of the one-tailed hypergeometric distribution (for exact p values, please refer to Source Data). i Expression of candidate genes identified in microdissected embryonic organs. Cell clusters exhibiting elevated candidate gene expression of the specific markers are indicated; expression values are log 2 transformed, i.e., log 2 (TPM + 1). sc_cluster, single-cell cluster; V, Visium TM spatial cluster; scu/Scu, scutellum; epi, epidermis; hypo, hypocotyl; ab, abaxial; ad; adaxial; sus, suspensor; col, coleoptile; emb_endo, embryo-endosperm boundary; UC, upper coleoptile; LC; lower coleoptile.

Article Snippet: To further validate the identification of Stage 1 embryo single cell clusters, eight individual Stage 1 embryo sections were processed using the 10X Genomics Visium TM spatial transcriptomics pipeline (Fig. and Supplementary Data ).

Techniques: Staining, Generated, RNA Sequencing Assay, One-tailed Test, Expressing, Transformation Assay

Journal: Nature Communications

Article Title: Multiplexed transcriptomic analyzes of the plant embryonic hourglass

doi: 10.1038/s41467-024-55803-9

Figure Lengend Snippet: a A Venn diagram of embryonic transcriptomics identifies 130 genes co-expressed in initiating embryonic organs. b Normalized expression of these 130 genes at the Proembryo stage (PE), Transition stage (T), Coleoptilar stage (C), Stage 1 scutellum (Scu), Stage 1 upper coleoptile (UC), Stage 1 lower coleoptile (LC), Stage 1 leaf (L), as well as P0 and P1 of the 14 day-after-germination seedlings. The letters above the boxplots represent significance levels (non-overlapping letters indicate significant differences at p < 0.05 using the Tukey-Kramer HSD test (for exact p values, please refer to Source Data). The middle line reflects the median value; the box shows the 25 th and 75 th percentiles and the whiskers reflect 1.5 times the interquartile range. c and d WGCNA ( c ) and hdWGCNA test ( d ) hierarchical cluster tree graph of transcriptomic similarities among tissue-specific co-expression modules, respectively. The height ( y -axis) scales the length of tissue-specific branches, indicating the transcriptomic distances among modules. The hierarchical cluster trees were constructed based on topological overlap dissimilarity, derived from a signed (one-sided) adjacency matrix calculated using the Pearson correlation. In d the significance levels of coexpression module-sc cluster correlations are marked by color-coded circles (significance levels were calculated via −log 10 p; red or blue colors represent relatively strong or weak correlations, respectively); colored branches indicate correlated structures (red branches represent Scutellum-Coleoptile super-cluster; and blue branches represent the SAM&hypocotyl-Leaf super-cluster). The p values (see Supplementary Fig. ) were calculated based on the cumulative distribution function (CDF) of the one-tailed hypergeometric distribution. e Heatmap illustrating expression correlations of the gene set in Maize ( y -axis) and Arabidopsis ( x -axis) during multiple embryonic stages. Heatmap colors are determined by correlation coefficient (r) via Pearson correlation test with significance level p < 0.05 (*) or p < 0.01 (**) (for exact p values, please refer to Source Data). Scu, Stage 1 scutellum; Col, Stage 1 coleoptile; epi: epidermis; hypoc, hypocotyl; M, co-expression modules; sc_cluster, single-cell cluster; PE, Proembryo; T, Transition stage; C, Coleoptilar stage; L: Stage 1 leaf.

Article Snippet: To further validate the identification of Stage 1 embryo single cell clusters, eight individual Stage 1 embryo sections were processed using the 10X Genomics Visium TM spatial transcriptomics pipeline (Fig. and Supplementary Data ).

Techniques: Expressing, Construct, Derivative Assay, One-tailed Test

Journal: Communications Biology

Article Title: Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets

doi: 10.1038/s42003-024-05877-4

Figure Lengend Snippet: a – h USC control sample sequenced by three library preparation methods: bulk RNA-Seq with ribosomal depletion, bulk RNA-Seq without ribosomal depletion (polyA), and spatial transcriptomics (10x Visium platform). i – l All GEO+ samples ( n = 463); ( m–p ) all GTEx samples ( n = 1107). Definitions: Total RNA-Seq Reads = FASTQ reads prior to alignment; MT Benchmark Coverage = average mitochondrial sequencing depth measured from two 250 bp segments within the RNR1 and CYB genes ; Deletion Read Rate = deletion reads/MT Benchmark Coverage. MTG (middle temporal gyrus); AM (amygdala); SN (substantia nigra); TL (temporal lobe); DLPFC (dorsolateral prefrontal cortex); CER (cerebellum); HIPP (hippocampus); PFC (prefrontal cortex); VTA (ventral tegmental area); LCM (laser capture microdissection); PD (Parkinson’s Disease); CTRL (control); AD (Alzheimer’s Disease); SCZ (schizophrenia); BD (bipolar disorder); MDD (major depressive disorder). Abbreviations for GTEx tissues are shown on figure.

Article Snippet: Spatial transcriptomics datasets were processed using the 10x Genomics Visium pipeline instructions ( https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome ).

Techniques: Control, RNA Sequencing, Sequencing, Laser Capture Microdissection

Journal: Communications Biology

Article Title: Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets

doi: 10.1038/s42003-024-05877-4

Figure Lengend Snippet: Summary of 12 GEO + RNA-Seq datasets evaluated for mtDNA deletions

Article Snippet: Spatial transcriptomics datasets were processed using the 10x Genomics Visium pipeline instructions ( https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome ).

Techniques: Control, Sample Prep, Hybridization, FACS

Journal: Nature Genetics

Article Title: Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s disease

doi: 10.1038/s41588-024-01961-x

Figure Lengend Snippet: a , We performed ST experiments in the human frontal cortex and the mouse brain using 10x Genomics Visium. Human samples— n = 10 cognitively normal controls, n = 9 early-stage AD, n = 10 late-stage AD and n = 10 DSAD (median 1,316 genes per spot; n = 115,251 ST spots; Supplementary Table ). Mouse samples— n = 10 WT and n = 10 5xFAD aged 4 months; n = 10 WT and n = 10 5xFAD aged 6 months; n = 10 WT and n = 10 5xFAD aged 8 months; n = 8 WT and n = 12 5xFAD aged 12 months (median 2,438 genes per spatial spot; n = 212,249 ST spots; Supplementary Table ). b , Two representative human ST samples from each of the disease conditions, each spot colored by cortical annotations from BayesSpace clustering analysis. c , One representative mouse ST sample from WT and 5xFAD at each time point, each spot colored by brain region annotations derived from BayesSpace clustering analysis. d , We performed snRNA-seq in the frontal cortex and PCC from cognitively normal control donors ( n = 27 FCX and n = 27 PCC) and DSAD donors ( n = 21 FCX and n = 21 PCC). We also included snRNA-seq data from three previous studies of the cortex in AD – ( n = 27 controls, n = 23 early-stage AD and n = 48 late-stage AD). e , UMAP plot depicting a two-dimensional view of the cellular neighborhood graph of 585,042 single-nuclei transcriptome profiles. Each point in this plot represents one cell, colored by their cell-type annotations derived from Leiden clustering analysis. EX, n = 229,041; INH, n = 90,718; MG, n = 20,197; ASC, n = 57,443; OPC, n = 23,053; ODC, n = 153,182; PER, n = 4,659; END, n = 3,637; FBR, n = 2,403 and SMCs, SMC, n = 709. See Table for additional cluster name abbreviations. Illustrations were created with Biorender.com . EX, excitatory neurons; INH, inhibitory neurons; MG, microglia; ASC, astrocytes; ODC, oligodendrocytes; PER, pericytes; END, endothelial cells; FBR, fibroblasts; SMCs, smooth muscle cells.

Article Snippet: Sequencing reads from the human and mouse Visium experiments were processed using the 10x Genomics Spaceranger (v1.2.1) pipeline, with GRch38 and MM10 as the respective reference transcriptomes.

Techniques: Derivative Assay, Control