transcriptome sequencing  (Macrogen)

Journal: iScience

Article Title: Multi-omics profiling-derived signature links cellular ecosystem to glioblastoma prognosis

doi: 10.1016/j.isci.2026.115982

Figure Lengend Snippet: Transcriptomic and TME characteristics associated with ECMSig in TCGA-GBM cohort (A) Volcano plot showing DEGs between ECMSig-high and ECMSig-low groups. Red dots: upregulated in high-risk; blue dots: upregulated in low-risk. Benjamini-Hochberg adjusted. (B) Gene set enrichment analysis (GSEA) plots showing enrichment of hallmark pathways. Pathways enriched in ECMSig-high and ECMSig-low groups are shown with their running enrichment scores (ESs) and ranked gene lists. Benjamini-Hochberg adjusted. (C) Heatmap showing the activity scores of selected oncogenic and tumor-related signaling pathways (rows) across TCGA-GBM samples (columns), annotated by ECMSig group and ECMSig score. Red indicates high activity, blue indicates low activity. ∗ p < 0.05. Wilcoxon signed-rank test. (D) Heatmap depicting the estimated infiltration levels of various immune and stromal cell types (rows) in TCGA-GBM samples (columns), stratified by ECMSig group and score. Red indicates high infiltration, blue indicates low infiltration. Cells significantly highly infiltrated in ECMSig-high are labeled in red, and those high in ECMSig-low group are in blue. ∗q < 0.05, ∗∗q < 0.01, ∗∗∗q < 0.001. Wilcoxon signed-rank test. Benjamini-Hochberg adjusted. (E and F) Scatterplots showing the spearman correlation between ECMSig score and (E) Macrophage_XCELL infiltration score and (F) immune_score_XCELL. The blue line represents the linear regression fit with 95% confidence interval bands. Spearman correlation test.

Article Snippet: The single-cell transcriptomic sequencing dataset utilizing technology from the 10X Genomics platform was available under the accession number GEO: GSE182109 at the Gene Expression Omnibus (GEO) repository.

Techniques: Activity Assay, Protein-Protein interactions, Labeling

Journal: iScience

Article Title: Multi-omics profiling-derived signature links cellular ecosystem to glioblastoma prognosis

doi: 10.1016/j.isci.2026.115982

Figure Lengend Snippet: Single-cell RNA sequencing analysis revealing ECMSig expression across cell types and identification of prognostically relevant cell states in GBM (A) UMAP visualization of major cell types identified in GBM scRNA-seq data. (B) Dot plot showing the scaled average expression (color intensity) and percentage of cells expressing (dot size) canonical marker genes for each major cell type. (C) Dot plot showing the scaled average expression and percentage of cells expressing the seven ECMSig genes across major cell types. (D) UMAP plots showing the expression levels of individual ECMSig genes and overall ECMSig score across all cells. (E–G) UMAP plots illustrating Scissor-identified prognostically unfavorable (Scissor_Pos, red dashed circle) and favorable (Scissor_Neg, blue dashed circle; Scissor_Others, gray) cell subpopulations within (E) tumor cells, (F) myeloid cells, and (G) endothelial cells. (H–K) Violin plots comparing ECMSig scores among tumor cells grouped by Scissor status (H) and tumor type (I), and myeloid cells (J) or endothelial cells (K) grouped by Scissor status. ∗∗∗∗ p < 0.0001. Wilcoxon signed-rank test. (L) Dot plot showing differentially expressed marker genes between myeloid Scissor_Pos and other myeloid cells. Dot size indicates the fraction of cells in the group expressing the gene; color indicates average expression level.

Article Snippet: The single-cell transcriptomic sequencing dataset utilizing technology from the 10X Genomics platform was available under the accession number GEO: GSE182109 at the Gene Expression Omnibus (GEO) repository.

Techniques: Single Cell, RNA Sequencing, Expressing, Marker

Journal: iScience

Article Title: Multi-omics profiling-derived signature links cellular ecosystem to glioblastoma prognosis

doi: 10.1016/j.isci.2026.115982

Figure Lengend Snippet: Spatial transcriptomic analysis revealing co-localization of ECMSig, hypoxia, Scissor-Positive cells, and pericytes in GBM (A) Spatial feature plots for four GBM samples. Each row represents a sample. Columns show spatial heatmaps of: ECMSig score, hypoxia signature score, tumor Scissor_Pos signature score, myeloid Scissor_Pos signature score, endothelial Scissor Pos signature score, and pericyte marker signature score. Color scale indicates scaled expression or score (low to high). Each dot represents a spatial barcoded spot.

Article Snippet: The single-cell transcriptomic sequencing dataset utilizing technology from the 10X Genomics platform was available under the accession number GEO: GSE182109 at the Gene Expression Omnibus (GEO) repository.

Techniques: Marker, Expressing

Journal: Frontiers in Immunology

Article Title: Comprehensive transcriptomic analysis reveals immune response modulation in Brontispa longissima Gestro larvae following parasitism by Asecodes hispinarum Bouček

doi: 10.3389/fimmu.2026.1823349

Figure Lengend Snippet: Length distribution of transcript sequences in the full-length transcriptome of Brontispa longissima larvae.The x-axis represents the length of the transcripts. The left y-axis corresponds to the histogram, showing the number of transcripts within each length interval along the x-axis. The right y-axis represents the cumulative distribution, indicating the number of transcripts with lengths greater than or equal to a given value on the x-axis.

Article Snippet: Samples were collected for each treatment and sent to Gene Denovo Biotechnology Co. (Guangzhou, China) for third-generation full-length transcriptome sequencing.

Techniques:

Journal: Frontiers in Immunology

Article Title: Comprehensive transcriptomic analysis reveals immune response modulation in Brontispa longissima Gestro larvae following parasitism by Asecodes hispinarum Bouček

doi: 10.3389/fimmu.2026.1823349

Figure Lengend Snippet: Functional annotation for the full-length transcriptome of B. longissima larvae. The diagram shows the overlap of transcripts annotated against four public databases: KEGG (blue), KOG (green), Nr (orange), and Swiss-Prot (pink). The numbers in each region represent the number of transcripts annotated in the corresponding database(s), with shared regions indicating transcripts annotated in multiple databases.

Article Snippet: Samples were collected for each treatment and sent to Gene Denovo Biotechnology Co. (Guangzhou, China) for third-generation full-length transcriptome sequencing.

Techniques: Functional Assay

Journal: Frontiers in Immunology

Article Title: Comprehensive transcriptomic analysis reveals immune response modulation in Brontispa longissima Gestro larvae following parasitism by Asecodes hispinarum Bouček

doi: 10.3389/fimmu.2026.1823349

Figure Lengend Snippet: Nr-annotated species distribution statistics of the full-length transcriptome of (B) longissima larvae (Top 10). The X-axis represents the top 10 annotated species, while the Y-axis indicates the number of unigenes. Anoplophora glabripennis(5411 unigenes) showed the highest homology, followed by Leptinotarsa decemlineata(1858 unigenes) and Gonioctena quinquepunctata(1648 unigenes).

Article Snippet: Samples were collected for each treatment and sent to Gene Denovo Biotechnology Co. (Guangzhou, China) for third-generation full-length transcriptome sequencing.

Techniques:

Journal: Frontiers in Immunology

Article Title: Comprehensive transcriptomic analysis reveals immune response modulation in Brontispa longissima Gestro larvae following parasitism by Asecodes hispinarum Bouček

doi: 10.3389/fimmu.2026.1823349

Figure Lengend Snippet: GO functional classification of the full-length transcriptome of (B) longissima larvae. The distribution of annotated unigenes is categorized into three main groups: Biological Process (red), Cellular Component (green), and Molecular Function (blue). The X-axis lists the specific Level 2 GO terms, and the Y-axis represents the number of genes associated with each term.

Article Snippet: Samples were collected for each treatment and sent to Gene Denovo Biotechnology Co. (Guangzhou, China) for third-generation full-length transcriptome sequencing.

Techniques: Functional Assay

Journal: Frontiers in Immunology

Article Title: Comprehensive transcriptomic analysis reveals immune response modulation in Brontispa longissima Gestro larvae following parasitism by Asecodes hispinarum Bouček

doi: 10.3389/fimmu.2026.1823349

Figure Lengend Snippet: KOG functional classification of the full-length transcriptome of (B) longissima larvae. The X-axis represents the 24 KOG categories (abbreviated from A to S), while the Y-axis indicates the number of annotated unigenes. Different colors correspond to various functional categories, with the specific class represented by each color detailed in the legend on the right. Notably, the categories “General function prediction only” (R, grey bar) and “Signal transduction mechanisms” (T, pink bar) contain the highest number of unigenes, with 2082 and 2183 respectively.

Article Snippet: Samples were collected for each treatment and sent to Gene Denovo Biotechnology Co. (Guangzhou, China) for third-generation full-length transcriptome sequencing.

Techniques: Functional Assay, Transduction