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sequencing  (Solexa)

 
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    Solexa sequencing
    Sequencing, supplied by Solexa, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/transcriptome+sequencing/sequencing+transcriptome/us12553088-255-40-45
    Average 86 stars, based on 1 article reviews
    sequencing - by Bioz Stars, 2026-09
    86/100 stars

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    Related Articles

    Sequencing:

    Article Title: High-throughput deep sequencing of nucleic acids across tumors and clones within tumors
    Article Snippet: .. Sequencing methods may include, but are not limited to, high-throughput sequencing pyrosequencing, sequencing-by synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, RNA-Sew (Illumina), Digital Gene Expression (Helicos), next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Hilbery or Sanger sequencing, primer walking, sequencing using PacBio, SOLid, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and compositions for synthetic biomarkers
    Article Snippet: .. Sequencing methods may include: Next Generation sequencing, high-throughput sequencing, pyrosequencing, classic Sanger sequencing methods, sequencing-by-ligation, sequencing by synthesis, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), next generation sequencing, single molecule sequencing by synthesis (SMSS) (Helicos), Ion Torrent Sequencing Machine (Life Technologies/Thermo-Fisher), massively-parallel sequencing, clonal single molecule Array (Solexa), shotgun sequencing, Maxim-Gilbert sequencing, and primer walking. ..

    Article Title: De novo synthesized gene libraries
    Article Snippet: In some embodiments, high-throughput sequencing involves the use of technology available by 454 Lifesciences, Inc. (Branford, Conn.) such as the Pico Titer Plate device which includes a fiber optic plate that transmits chemiluninescent signal generated by the sequencing reaction to be recorded by a CCD camera in the instrument. .. In some embodiments, high-throughput sequencing is performed using Clonal Single Molecule Array (Solexa, Inc.) or sequencing-by-synthesis (SBS) utilizing reversible terminator chemistry. ..

    Article Title: Synthetic nucleic acid spike-ins
    Article Snippet: .. In some cases, high-throughput sequencing is performed using Clonal Single Molecule Array (Solexa, Inc.) or sequencing-by-synthesis (SBS) utilizing reversible terminator chemistry. ..

    Article Title: Methods and systems for detecting genetic variants
    Article Snippet: .. Sequencing methods may include, but are not limited to: high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Gilbert or Sanger sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and systems for analyzing nucleic acid molecules
    Article Snippet: .. Sequencing methods include, for example, Sanger sequencing, high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing (NGS), Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Ion Torrent, Oxford Nanopore, Roche Genia, Maxim-Gilbert sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms. ..

    Next-Generation Sequencing:

    Article Title: High-throughput deep sequencing of nucleic acids across tumors and clones within tumors
    Article Snippet: .. Sequencing methods may include, but are not limited to, high-throughput sequencing pyrosequencing, sequencing-by synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, RNA-Sew (Illumina), Digital Gene Expression (Helicos), next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Hilbery or Sanger sequencing, primer walking, sequencing using PacBio, SOLid, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and compositions for synthetic biomarkers
    Article Snippet: .. Sequencing methods may include: Next Generation sequencing, high-throughput sequencing, pyrosequencing, classic Sanger sequencing methods, sequencing-by-ligation, sequencing by synthesis, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), next generation sequencing, single molecule sequencing by synthesis (SMSS) (Helicos), Ion Torrent Sequencing Machine (Life Technologies/Thermo-Fisher), massively-parallel sequencing, clonal single molecule Array (Solexa), shotgun sequencing, Maxim-Gilbert sequencing, and primer walking. ..

    Article Title: De novo synthesized gene libraries
    Article Snippet: In some embodiments, high-throughput sequencing involves the use of technology available by 454 Lifesciences, Inc. (Branford, Conn.) such as the Pico Titer Plate device which includes a fiber optic plate that transmits chemiluninescent signal generated by the sequencing reaction to be recorded by a CCD camera in the instrument. .. In some embodiments, high-throughput sequencing is performed using Clonal Single Molecule Array (Solexa, Inc.) or sequencing-by-synthesis (SBS) utilizing reversible terminator chemistry. ..

    Article Title: Synthetic nucleic acid spike-ins
    Article Snippet: .. In some cases, high-throughput sequencing is performed using Clonal Single Molecule Array (Solexa, Inc.) or sequencing-by-synthesis (SBS) utilizing reversible terminator chemistry. ..

    Article Title: Methods and systems for detecting genetic variants
    Article Snippet: .. Sequencing methods may include, but are not limited to: high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Gilbert or Sanger sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and systems for analyzing nucleic acid molecules
    Article Snippet: .. Sequencing methods include, for example, Sanger sequencing, high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing (NGS), Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Ion Torrent, Oxford Nanopore, Roche Genia, Maxim-Gilbert sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms. ..

    Nanopore Sequencing:

    Article Title: High-throughput deep sequencing of nucleic acids across tumors and clones within tumors
    Article Snippet: .. Sequencing methods may include, but are not limited to, high-throughput sequencing pyrosequencing, sequencing-by synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, RNA-Sew (Illumina), Digital Gene Expression (Helicos), next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Hilbery or Sanger sequencing, primer walking, sequencing using PacBio, SOLid, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and systems for detecting genetic variants
    Article Snippet: .. Sequencing methods may include, but are not limited to: high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Gilbert or Sanger sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and systems for analyzing nucleic acid molecules
    Article Snippet: .. Sequencing methods include, for example, Sanger sequencing, high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing (NGS), Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Ion Torrent, Oxford Nanopore, Roche Genia, Maxim-Gilbert sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms. ..

    Gene Expression:

    Article Title: High-throughput deep sequencing of nucleic acids across tumors and clones within tumors
    Article Snippet: .. Sequencing methods may include, but are not limited to, high-throughput sequencing pyrosequencing, sequencing-by synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, RNA-Sew (Illumina), Digital Gene Expression (Helicos), next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Hilbery or Sanger sequencing, primer walking, sequencing using PacBio, SOLid, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and compositions for synthetic biomarkers
    Article Snippet: .. Sequencing methods may include: Next Generation sequencing, high-throughput sequencing, pyrosequencing, classic Sanger sequencing methods, sequencing-by-ligation, sequencing by synthesis, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), next generation sequencing, single molecule sequencing by synthesis (SMSS) (Helicos), Ion Torrent Sequencing Machine (Life Technologies/Thermo-Fisher), massively-parallel sequencing, clonal single molecule Array (Solexa), shotgun sequencing, Maxim-Gilbert sequencing, and primer walking. ..

    Article Title: Methods and systems for detecting genetic variants
    Article Snippet: .. Sequencing methods may include, but are not limited to: high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Gilbert or Sanger sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and systems for analyzing nucleic acid molecules
    Article Snippet: .. Sequencing methods include, for example, Sanger sequencing, high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing (NGS), Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Ion Torrent, Oxford Nanopore, Roche Genia, Maxim-Gilbert sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms. ..

    Shotgun Sequencing:

    Article Title: High-throughput deep sequencing of nucleic acids across tumors and clones within tumors
    Article Snippet: .. Sequencing methods may include, but are not limited to, high-throughput sequencing pyrosequencing, sequencing-by synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, RNA-Sew (Illumina), Digital Gene Expression (Helicos), next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Hilbery or Sanger sequencing, primer walking, sequencing using PacBio, SOLid, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and compositions for synthetic biomarkers
    Article Snippet: .. Sequencing methods may include: Next Generation sequencing, high-throughput sequencing, pyrosequencing, classic Sanger sequencing methods, sequencing-by-ligation, sequencing by synthesis, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), next generation sequencing, single molecule sequencing by synthesis (SMSS) (Helicos), Ion Torrent Sequencing Machine (Life Technologies/Thermo-Fisher), massively-parallel sequencing, clonal single molecule Array (Solexa), shotgun sequencing, Maxim-Gilbert sequencing, and primer walking. ..

    Article Title: Methods and systems for detecting genetic variants
    Article Snippet: .. Sequencing methods may include, but are not limited to: high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Gilbert or Sanger sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and systems for analyzing nucleic acid molecules
    Article Snippet: .. Sequencing methods include, for example, Sanger sequencing, high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing (NGS), Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Ion Torrent, Oxford Nanopore, Roche Genia, Maxim-Gilbert sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms. ..

    Chromosome Walking:

    Article Title: High-throughput deep sequencing of nucleic acids across tumors and clones within tumors
    Article Snippet: .. Sequencing methods may include, but are not limited to, high-throughput sequencing pyrosequencing, sequencing-by synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, RNA-Sew (Illumina), Digital Gene Expression (Helicos), next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Hilbery or Sanger sequencing, primer walking, sequencing using PacBio, SOLid, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and compositions for synthetic biomarkers
    Article Snippet: .. Sequencing methods may include: Next Generation sequencing, high-throughput sequencing, pyrosequencing, classic Sanger sequencing methods, sequencing-by-ligation, sequencing by synthesis, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), next generation sequencing, single molecule sequencing by synthesis (SMSS) (Helicos), Ion Torrent Sequencing Machine (Life Technologies/Thermo-Fisher), massively-parallel sequencing, clonal single molecule Array (Solexa), shotgun sequencing, Maxim-Gilbert sequencing, and primer walking. ..

    Article Title: Methods and systems for detecting genetic variants
    Article Snippet: .. Sequencing methods may include, but are not limited to: high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Gilbert or Sanger sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and systems for analyzing nucleic acid molecules
    Article Snippet: .. Sequencing methods include, for example, Sanger sequencing, high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing (NGS), Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Ion Torrent, Oxford Nanopore, Roche Genia, Maxim-Gilbert sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms. ..

    other:

    Article Title: High-throughput single-nuclei and single-cell libraries and methods of making and of using
    Article Snippet: For example, the different nucleotides present in a sequencing reagent can have different labels and they can be distinguished using appropriate optics as exemplified by the sequencing methods developed by Solexa (now Illumina, Inc.).

    Article Title: Early detection of drug-resistant mycobacterium tuberculosis
    Article Snippet: For example, the different nucleotides present in a sequencing reagent can have different labels and they can be distinguished using appropriate optics as exemplified by the sequencing methods developed by Solexa (now Illumina, Inc.).

    RNA sequencing:

    Article Title: Methods and compositions for synthetic biomarkers
    Article Snippet: .. Sequencing methods may include: Next Generation sequencing, high-throughput sequencing, pyrosequencing, classic Sanger sequencing methods, sequencing-by-ligation, sequencing by synthesis, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), next generation sequencing, single molecule sequencing by synthesis (SMSS) (Helicos), Ion Torrent Sequencing Machine (Life Technologies/Thermo-Fisher), massively-parallel sequencing, clonal single molecule Array (Solexa), shotgun sequencing, Maxim-Gilbert sequencing, and primer walking. ..

    Article Title: Methods and systems for detecting genetic variants
    Article Snippet: .. Sequencing methods may include, but are not limited to: high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Gilbert or Sanger sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms and any other sequencing methods known in the art. ..

    Article Title: Methods and systems for analyzing nucleic acid molecules
    Article Snippet: .. Sequencing methods include, for example, Sanger sequencing, high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing (NGS), Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Ion Torrent, Oxford Nanopore, Roche Genia, Maxim-Gilbert sequencing, primer walking, sequencing using PacBio, SOLID, Ion Torrent, or Nanopore platforms. ..



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    86
    Novogene eukaryotic transcriptome sequencing
    Transcriptomic profiling of the pretreatment biopsy sample. RNA-seq was used to obtain <t>gene</t> <t>expression</t> <t>profiles</t> of tumor samples. A global embedding of cancer types was calculated by transforming these gene expression profiles using PCA, followed by a t-SNE transformation to obtain a 2-dimensional approximate “map” of transcriptional similarity. The new patient sample is projected onto a pre-calculated PCA embedding space based on historical samples analyzed at Caris. Its proximity to other samples on the map reflects shared transcriptional programs with these samples. Only the immediate neighborhoods of samples should be considered for further interpretation since t-SNE embeddings do not preserve similarity correlations over long distances. Each point on the t-SNE map represents a different sample. The target symbol represents the present patient’s pretreatment biopsy sample. PCA, principal component analysis; t-SNE, t-stochastic neighbor embedding.
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    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.

    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

    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.

    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

    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.

    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

    (A) Heatmap of DEG cluster analysis for DT and CK transcriptomes. The black dendrogram shows hierarchical clustering of samples and genes with similar expression patterns. The color scale represents normalized gene expression levels (yellow/orange = high expression, blue = low expression), demonstrating clear separation between CK and DT groups. (B) Volcano plot of differentially expressed genes. Orange dots indicate up-regulated genes (log 2 FC > 1, p < 0.05), blue dots indicate down-regulated genes (log 2 FC < −1, p < 0.05), and gray dots indicate non-significant genes.

    Journal: PeerJ

    Article Title: A cellular view of drought adaptation in sugarcane: multi-omics integration reveals a quadruple module network linking water regulation, oxidative defense, cell wall remodeling, and cell cycle regulation

    doi: 10.7717/peerj.21396

    Figure Lengend Snippet: (A) Heatmap of DEG cluster analysis for DT and CK transcriptomes. The black dendrogram shows hierarchical clustering of samples and genes with similar expression patterns. The color scale represents normalized gene expression levels (yellow/orange = high expression, blue = low expression), demonstrating clear separation between CK and DT groups. (B) Volcano plot of differentially expressed genes. Orange dots indicate up-regulated genes (log 2 FC > 1, p < 0.05), blue dots indicate down-regulated genes (log 2 FC < −1, p < 0.05), and gray dots indicate non-significant genes.

    Article Snippet: The transcriptome sequences and annotation information of Saccharum spp. suspension cells under drought stress determined in this study have been uploaded to the National Center for Biotechnology Information ( PRJNA1403770 ) for access by relevant researchers.

    Techniques: Expressing, Gene Expression

    (A) The abscissa indicates the selected DEGs related to drought stress in sugarcane, and the ordinate indicates the log 2 fold change of gene expression measured by RNA-seq (orange bars) and RT-qPCR (blue bars). The column height represents the differential expression multiple, and the smaller the height difference between orange and blue bars, the more consistent the expression trend between the two methods. (B) Correlation analysis of log 2 fold change values from RNA-seq ( x -axis) and RT-qPCR ( y -axis). Each blue square represents one DEG. The linear regression equation and R 2 value ( R 2 = 0.97581) indicate a high positive correlation between the two techniques, verifying the reliability of the transcriptome sequencing data.

    Journal: PeerJ

    Article Title: A cellular view of drought adaptation in sugarcane: multi-omics integration reveals a quadruple module network linking water regulation, oxidative defense, cell wall remodeling, and cell cycle regulation

    doi: 10.7717/peerj.21396

    Figure Lengend Snippet: (A) The abscissa indicates the selected DEGs related to drought stress in sugarcane, and the ordinate indicates the log 2 fold change of gene expression measured by RNA-seq (orange bars) and RT-qPCR (blue bars). The column height represents the differential expression multiple, and the smaller the height difference between orange and blue bars, the more consistent the expression trend between the two methods. (B) Correlation analysis of log 2 fold change values from RNA-seq ( x -axis) and RT-qPCR ( y -axis). Each blue square represents one DEG. The linear regression equation and R 2 value ( R 2 = 0.97581) indicate a high positive correlation between the two techniques, verifying the reliability of the transcriptome sequencing data.

    Article Snippet: The transcriptome sequences and annotation information of Saccharum spp. suspension cells under drought stress determined in this study have been uploaded to the National Center for Biotechnology Information ( PRJNA1403770 ) for access by relevant researchers.

    Techniques: Gene Expression, RNA Sequencing, Quantitative RT-PCR, Quantitative Proteomics, Expressing, Sequencing

    Transcriptomic profiling of the pretreatment biopsy sample. RNA-seq was used to obtain gene expression profiles of tumor samples. A global embedding of cancer types was calculated by transforming these gene expression profiles using PCA, followed by a t-SNE transformation to obtain a 2-dimensional approximate “map” of transcriptional similarity. The new patient sample is projected onto a pre-calculated PCA embedding space based on historical samples analyzed at Caris. Its proximity to other samples on the map reflects shared transcriptional programs with these samples. Only the immediate neighborhoods of samples should be considered for further interpretation since t-SNE embeddings do not preserve similarity correlations over long distances. Each point on the t-SNE map represents a different sample. The target symbol represents the present patient’s pretreatment biopsy sample. PCA, principal component analysis; t-SNE, t-stochastic neighbor embedding.

    Journal: Therapeutic Advances in Medical Oncology

    Article Title: Lineage infidelity in FH-deficient RCC with secondary somatic alterations: a case report and implications for diagnosis and treatment

    doi: 10.1177/17588359261456676

    Figure Lengend Snippet: Transcriptomic profiling of the pretreatment biopsy sample. RNA-seq was used to obtain gene expression profiles of tumor samples. A global embedding of cancer types was calculated by transforming these gene expression profiles using PCA, followed by a t-SNE transformation to obtain a 2-dimensional approximate “map” of transcriptional similarity. The new patient sample is projected onto a pre-calculated PCA embedding space based on historical samples analyzed at Caris. Its proximity to other samples on the map reflects shared transcriptional programs with these samples. Only the immediate neighborhoods of samples should be considered for further interpretation since t-SNE embeddings do not preserve similarity correlations over long distances. Each point on the t-SNE map represents a different sample. The target symbol represents the present patient’s pretreatment biopsy sample. PCA, principal component analysis; t-SNE, t-stochastic neighbor embedding.

    Article Snippet: To confirm the diagnosis, molecular testing (next-generation sequencing (NGS); whole exome and whole transcriptome sequencing, Caris Life Sciences (Irving, Texas, United States)) revealed an S419P mutation in the FH gene, along with pathogenic mutations in KMT2A , NF2 , and TP53 , discussed in greater detail below.

    Techniques: RNA Sequencing, Gene Expression, Transformation Assay