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eqtl mapping procedures  (Metabrain Research)

 
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    Metabrain Research eqtl mapping procedures
    (A) Spearman correlations between the 5 predicted cell count proportions. Lower triangle is within cortex samples, upper triangle is within cerebellum samples. (B) Predicted cell type proportions (x-axis) compared to cell type proportions measured using immunohistochemistry (IHC; y-axis) for 42 ROSMAP samples. Values in the plot are Pearson correlation coefficients. Cell count predictions for most cell types closely approximates actual IHC cell counts, although neurons are underestimated. (C) Number of cell type interacting eQTLs for Cortex-EUR deconvoluted cell types. The majority of interactions are with neurons and oligodendrocytes. Notably, most interactions are unique for one cell type in 90% of the cases. ( D, E, F ) Replication of cell type interacting eQTLs for STMN4 ( D ), FAM221A ( E ) and SLC25A27 ( F ), consisting of the scatterplot of the interaction <t>eQTL</t> <t>in</t> <t>MetaBrain</t> Cortex-EUR bulk RNA-seq (left) and a forest plot for the eQTL effect in the ROSMAP snRNA-seq data (right). Scatterplot: the x-axis shows the estimated cell type proportion, the y-axis shows the gene expression, each dot represents a sample. Colors indicate SNP genotype, with yellow being the minor allele. Values under the alleles are Spearman correlation coefficients. Forest plot: Spearman coefficients with effect direction relative to the minor allele when replicating the eQTL effect in ROSMAP single nucleus data (n=38). Error bars indicate 95% confidence interval. Each row denotes a cell type specific dataset: excitatory neurons (EX), oligodendrocytes (OLI), inhibitory neurons (IN), astrocytes (AST), oligodendrocyte precursor cells (OPC), microglia (MIC), pericytes (PER) and endothelial cells (END). Cell types highlighted in bold reflect the equivalent to the cell type used in the interaction eQTL.
    Eqtl Mapping Procedures, supplied by Metabrain Research, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/eqtl+mapping+procedures/bio_rxiv__2021__03__01__433439-55-4-9?v=Metabrain+Research
    Average 90 stars, based on 1 article reviews
    eqtl mapping procedures - by Bioz Stars, 2026-07
    90/100 stars

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    1) Product Images from "Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases"

    Article Title: Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases

    Journal: bioRxiv

    doi: 10.1101/2021.03.01.433439

    (A) Spearman correlations between the 5 predicted cell count proportions. Lower triangle is within cortex samples, upper triangle is within cerebellum samples. (B) Predicted cell type proportions (x-axis) compared to cell type proportions measured using immunohistochemistry (IHC; y-axis) for 42 ROSMAP samples. Values in the plot are Pearson correlation coefficients. Cell count predictions for most cell types closely approximates actual IHC cell counts, although neurons are underestimated. (C) Number of cell type interacting eQTLs for Cortex-EUR deconvoluted cell types. The majority of interactions are with neurons and oligodendrocytes. Notably, most interactions are unique for one cell type in 90% of the cases. ( D, E, F ) Replication of cell type interacting eQTLs for STMN4 ( D ), FAM221A ( E ) and SLC25A27 ( F ), consisting of the scatterplot of the interaction eQTL in MetaBrain Cortex-EUR bulk RNA-seq (left) and a forest plot for the eQTL effect in the ROSMAP snRNA-seq data (right). Scatterplot: the x-axis shows the estimated cell type proportion, the y-axis shows the gene expression, each dot represents a sample. Colors indicate SNP genotype, with yellow being the minor allele. Values under the alleles are Spearman correlation coefficients. Forest plot: Spearman coefficients with effect direction relative to the minor allele when replicating the eQTL effect in ROSMAP single nucleus data (n=38). Error bars indicate 95% confidence interval. Each row denotes a cell type specific dataset: excitatory neurons (EX), oligodendrocytes (OLI), inhibitory neurons (IN), astrocytes (AST), oligodendrocyte precursor cells (OPC), microglia (MIC), pericytes (PER) and endothelial cells (END). Cell types highlighted in bold reflect the equivalent to the cell type used in the interaction eQTL.
    Figure Legend Snippet: (A) Spearman correlations between the 5 predicted cell count proportions. Lower triangle is within cortex samples, upper triangle is within cerebellum samples. (B) Predicted cell type proportions (x-axis) compared to cell type proportions measured using immunohistochemistry (IHC; y-axis) for 42 ROSMAP samples. Values in the plot are Pearson correlation coefficients. Cell count predictions for most cell types closely approximates actual IHC cell counts, although neurons are underestimated. (C) Number of cell type interacting eQTLs for Cortex-EUR deconvoluted cell types. The majority of interactions are with neurons and oligodendrocytes. Notably, most interactions are unique for one cell type in 90% of the cases. ( D, E, F ) Replication of cell type interacting eQTLs for STMN4 ( D ), FAM221A ( E ) and SLC25A27 ( F ), consisting of the scatterplot of the interaction eQTL in MetaBrain Cortex-EUR bulk RNA-seq (left) and a forest plot for the eQTL effect in the ROSMAP snRNA-seq data (right). Scatterplot: the x-axis shows the estimated cell type proportion, the y-axis shows the gene expression, each dot represents a sample. Colors indicate SNP genotype, with yellow being the minor allele. Values under the alleles are Spearman correlation coefficients. Forest plot: Spearman coefficients with effect direction relative to the minor allele when replicating the eQTL effect in ROSMAP single nucleus data (n=38). Error bars indicate 95% confidence interval. Each row denotes a cell type specific dataset: excitatory neurons (EX), oligodendrocytes (OLI), inhibitory neurons (IN), astrocytes (AST), oligodendrocyte precursor cells (OPC), microglia (MIC), pericytes (PER) and endothelial cells (END). Cell types highlighted in bold reflect the equivalent to the cell type used in the interaction eQTL.

    Techniques Used: Cell Counting, Immunohistochemistry, RNA Sequencing, Gene Expression


    Figure Legend Snippet:

    Techniques Used:



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    eqtl mapping procedures  (Metabrain Research)
    90
    Metabrain Research eqtl mapping procedures
    (A) Spearman correlations between the 5 predicted cell count proportions. Lower triangle is within cortex samples, upper triangle is within cerebellum samples. (B) Predicted cell type proportions (x-axis) compared to cell type proportions measured using immunohistochemistry (IHC; y-axis) for 42 ROSMAP samples. Values in the plot are Pearson correlation coefficients. Cell count predictions for most cell types closely approximates actual IHC cell counts, although neurons are underestimated. (C) Number of cell type interacting eQTLs for Cortex-EUR deconvoluted cell types. The majority of interactions are with neurons and oligodendrocytes. Notably, most interactions are unique for one cell type in 90% of the cases. ( D, E, F ) Replication of cell type interacting eQTLs for STMN4 ( D ), FAM221A ( E ) and SLC25A27 ( F ), consisting of the scatterplot of the interaction <t>eQTL</t> <t>in</t> <t>MetaBrain</t> Cortex-EUR bulk RNA-seq (left) and a forest plot for the eQTL effect in the ROSMAP snRNA-seq data (right). Scatterplot: the x-axis shows the estimated cell type proportion, the y-axis shows the gene expression, each dot represents a sample. Colors indicate SNP genotype, with yellow being the minor allele. Values under the alleles are Spearman correlation coefficients. Forest plot: Spearman coefficients with effect direction relative to the minor allele when replicating the eQTL effect in ROSMAP single nucleus data (n=38). Error bars indicate 95% confidence interval. Each row denotes a cell type specific dataset: excitatory neurons (EX), oligodendrocytes (OLI), inhibitory neurons (IN), astrocytes (AST), oligodendrocyte precursor cells (OPC), microglia (MIC), pericytes (PER) and endothelial cells (END). Cell types highlighted in bold reflect the equivalent to the cell type used in the interaction eQTL.
    Eqtl Mapping Procedures, supplied by Metabrain Research, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/eqtl+mapping+procedures/bio_rxiv__2021__03__01__433439-55-4-9?v=Metabrain+Research
    Average 90 stars, based on 1 article reviews
    eqtl mapping procedures - by Bioz Stars, 2026-07
    90/100 stars
    		  Buy from Supplier

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    (A) Spearman correlations between the 5 predicted cell count proportions. Lower triangle is within cortex samples, upper triangle is within cerebellum samples. (B) Predicted cell type proportions (x-axis) compared to cell type proportions measured using immunohistochemistry (IHC; y-axis) for 42 ROSMAP samples. Values in the plot are Pearson correlation coefficients. Cell count predictions for most cell types closely approximates actual IHC cell counts, although neurons are underestimated. (C) Number of cell type interacting eQTLs for Cortex-EUR deconvoluted cell types. The majority of interactions are with neurons and oligodendrocytes. Notably, most interactions are unique for one cell type in 90% of the cases. ( D, E, F ) Replication of cell type interacting eQTLs for STMN4 ( D ), FAM221A ( E ) and SLC25A27 ( F ), consisting of the scatterplot of the interaction eQTL in MetaBrain Cortex-EUR bulk RNA-seq (left) and a forest plot for the eQTL effect in the ROSMAP snRNA-seq data (right). Scatterplot: the x-axis shows the estimated cell type proportion, the y-axis shows the gene expression, each dot represents a sample. Colors indicate SNP genotype, with yellow being the minor allele. Values under the alleles are Spearman correlation coefficients. Forest plot: Spearman coefficients with effect direction relative to the minor allele when replicating the eQTL effect in ROSMAP single nucleus data (n=38). Error bars indicate 95% confidence interval. Each row denotes a cell type specific dataset: excitatory neurons (EX), oligodendrocytes (OLI), inhibitory neurons (IN), astrocytes (AST), oligodendrocyte precursor cells (OPC), microglia (MIC), pericytes (PER) and endothelial cells (END). Cell types highlighted in bold reflect the equivalent to the cell type used in the interaction eQTL.

    Journal: bioRxiv

    Article Title: Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases

    doi: 10.1101/2021.03.01.433439

    Figure Lengend Snippet: (A) Spearman correlations between the 5 predicted cell count proportions. Lower triangle is within cortex samples, upper triangle is within cerebellum samples. (B) Predicted cell type proportions (x-axis) compared to cell type proportions measured using immunohistochemistry (IHC; y-axis) for 42 ROSMAP samples. Values in the plot are Pearson correlation coefficients. Cell count predictions for most cell types closely approximates actual IHC cell counts, although neurons are underestimated. (C) Number of cell type interacting eQTLs for Cortex-EUR deconvoluted cell types. The majority of interactions are with neurons and oligodendrocytes. Notably, most interactions are unique for one cell type in 90% of the cases. ( D, E, F ) Replication of cell type interacting eQTLs for STMN4 ( D ), FAM221A ( E ) and SLC25A27 ( F ), consisting of the scatterplot of the interaction eQTL in MetaBrain Cortex-EUR bulk RNA-seq (left) and a forest plot for the eQTL effect in the ROSMAP snRNA-seq data (right). Scatterplot: the x-axis shows the estimated cell type proportion, the y-axis shows the gene expression, each dot represents a sample. Colors indicate SNP genotype, with yellow being the minor allele. Values under the alleles are Spearman correlation coefficients. Forest plot: Spearman coefficients with effect direction relative to the minor allele when replicating the eQTL effect in ROSMAP single nucleus data (n=38). Error bars indicate 95% confidence interval. Each row denotes a cell type specific dataset: excitatory neurons (EX), oligodendrocytes (OLI), inhibitory neurons (IN), astrocytes (AST), oligodendrocyte precursor cells (OPC), microglia (MIC), pericytes (PER) and endothelial cells (END). Cell types highlighted in bold reflect the equivalent to the cell type used in the interaction eQTL.

    Article Snippet: Since the procedures for eQTL mapping were identical between MetaBrain and eQTLGen, our results highlight the relevance of tissue-specific eQTL mapping to accurately assess the directionality of eQTLs, which can elucidate eQTLs with opposite allelic effects .

    Techniques: Cell Counting, Immunohistochemistry, RNA Sequencing, Gene Expression

    Journal: bioRxiv

    Article Title: Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases

    doi: 10.1101/2021.03.01.433439

    Figure Lengend Snippet:

    Article Snippet: Since the procedures for eQTL mapping were identical between MetaBrain and eQTLGen, our results highlight the relevance of tissue-specific eQTL mapping to accurately assess the directionality of eQTLs, which can elucidate eQTLs with opposite allelic effects .

    Techniques: