Journal: Cells

Article Title: Quantitative In-Depth Analysis of the Mouse Mast Cell Transcriptome Reveals Organ-Specific Mast Cell Heterogeneity

doi: 10.3390/cells9010211

Figure Lengend Snippet: Toluidine blue staining of MACS-separated peritoneal cells. MACS-separated cells were spun onto glass slides by cytospin centrifugation and were stained with toluidine blue. ( A ) the c-kit + cells from the first purification. ( B ) the Lin − /ckit + cells from the second, purer, preparation. Both were used for the transcriptome analysis.

Article Snippet: The Thermo Fisher mouse Ampliseq transcriptome analysis platform is based on the purification on a chip of the individual mRNAs (as cDNAs), which are then PCR amplified and sequenced individually.

Techniques: Staining, Centrifugation, Purification

Journal: Cells

Article Title: Quantitative In-Depth Analysis of the Mouse Mast Cell Transcriptome Reveals Organ-Specific Mast Cell Heterogeneity

doi: 10.3390/cells9010211

Figure Lengend Snippet: Transcript levels for granule proteases, cell surface receptors, and enzymes involved in the production and processing of the granule components in mouse peritoneal MCs from BALB/c mice. The number of normalized reads for the proteases is given in actual numbers (obtained from GATC biotech and SciLife Thermo Fisher Ampliseq analyses). Two independent GATC RNA seq runs were performed. For comparison, the relative levels in % to the most highly expressed transcripts (Mcpt5) are indicated in red.

Article Snippet: The Thermo Fisher mouse Ampliseq transcriptome analysis platform is based on the purification on a chip of the individual mRNAs (as cDNAs), which are then PCR amplified and sequenced individually.

Techniques: RNA Sequencing, Comparison

Journal: Cells

Article Title: Quantitative In-Depth Analysis of the Mouse Mast Cell Transcriptome Reveals Organ-Specific Mast Cell Heterogeneity

doi: 10.3390/cells9010211

Figure Lengend Snippet: Transcript levels for granule proteases, cell surface receptors, and enzymes involved in the production and processing of the granule components in mouse bone marrow-derived MCs (BMMCs; in vitro differentiated; from BALB/c mice). The number of normalized reads for the proteases is given in actual numbers (obtained from GATC biotech and SciLife Thermo Fisher Ampliseq analyses). Two different growth conditions were tested: unstimulated and stimulated by 1μg/mL of lipopolysaccharide (LPS) for 4 h. The fold increases in expression levels (for Gzm B and Gzm C) after LPS stimulation and the levels (in %) of the FcεRI alpha chain expression compared to Cpa3 are marked in red.

Article Snippet: The Thermo Fisher mouse Ampliseq transcriptome analysis platform is based on the purification on a chip of the individual mRNAs (as cDNAs), which are then PCR amplified and sequenced individually.

Techniques: In Vitro, Expressing

Journal: Cells

Article Title: Quantitative In-Depth Analysis of the Mouse Mast Cell Transcriptome Reveals Organ-Specific Mast Cell Heterogeneity

doi: 10.3390/cells9010211

Figure Lengend Snippet: Levels of major transcripts in the ears of BALB/c mice. The number of normalized reads for each of the proteases is given in actual numbers (obtained from GATC biotech and SciLife Thermo Fisher Ampliseq analyses). Two independent Ampliseq runs were performed. Note that the levels of Mcpt4 were very high in the skin compared to the peritoneal MCs.

Article Snippet: The Thermo Fisher mouse Ampliseq transcriptome analysis platform is based on the purification on a chip of the individual mRNAs (as cDNAs), which are then PCR amplified and sequenced individually.

Techniques:

Journal: Cells

Article Title: Quantitative In-Depth Analysis of the Mouse Mast Cell Transcriptome Reveals Organ-Specific Mast Cell Heterogeneity

doi: 10.3390/cells9010211

Figure Lengend Snippet: Levels of major transcripts and MC-specific transcripts in lung (BALB/c mice). The number of normalized reads for each of the different proteases is given in actual numbers (obtained from GATC biotech and SciLife Thermo Fisher Ampliseq analyses). Two independent Ampliseq runs were performed.

Article Snippet: The Thermo Fisher mouse Ampliseq transcriptome analysis platform is based on the purification on a chip of the individual mRNAs (as cDNAs), which are then PCR amplified and sequenced individually.

Techniques:

Journal: Cells

Article Title: Quantitative In-Depth Analysis of the Mouse Mast Cell Transcriptome Reveals Organ-Specific Mast Cell Heterogeneity

doi: 10.3390/cells9010211

Figure Lengend Snippet: Transcript levels for MC-related genes in rat peritoneal MCs from an earlier study using an unamplified cDNA library . The number of plaques per 100,000 clones were calculated for each of the listed transcripts. These values give an approximate value for the transcript abundance. Approximately 30% of the clones were empty indicating that the relative abundance of for example RMCP-1 was not 2.5% but closer to 3.5% of the total transcriptome.

Article Snippet: The Thermo Fisher mouse Ampliseq transcriptome analysis platform is based on the purification on a chip of the individual mRNAs (as cDNAs), which are then PCR amplified and sequenced individually.

Techniques: cDNA Library Assay, Clone Assay

Journal: Frontiers in Genetics

Article Title: Integrative Computational Approach Revealed Crucial Genes Associated With Different Stages of Diabetic Retinopathy

doi: 10.3389/fgene.2020.576442

Figure Lengend Snippet: Datasets and the set of comparisons.

Article Snippet: The diabetic retinopathy (DR) gene expression profiling dataset GSE60436 (platform: GPL6884 Illumina HumanWG-6 v3.0 expression BeadChip) consisted of total 9 human samples (Japanese population) out of which 3 were taken from the normal retina and 6 from the fibrovascular membrane (FVM) of proliferative diabetic retinopathy (PDR) patients.

Techniques: Clinical Proteomics

Journal: bioRxiv

Article Title: Multiomic analysis identifies suppressive myeloid cell populations in human TB granulomas

doi: 10.1101/2025.03.10.642376

Figure Lengend Snippet: Representative H&E images of granulomas from A) Case 3, B) Case 2, and C) Case 4 showing a range of granuloma morphology with D) necrotizing granulomas, E) cellular non-necrotizing granulomas, and F) small, lymphocyte rich granulomas as assessed by a pulmonary pathologist using traditional morphological annotation. Regions of interest (ROIs) ( G-K ) were selected based on morphological and fluorescence staining for DNA (blue), CD3 (green), CD68/CD163 (red), and vimentin (yellow). ROIs bordering necrotic (G) granulomas and (H) solid or cellular granulomas were selected in addition to tertiary lymphoid structures (I), lymph node (J), and uninvolved lung (K) for spatial transcriptional profiling using the human whole transcriptome probe set using GeoMx (Bruker).

Article Snippet: Due to the limited data on the functional role and significance of MDSCs in TB infected lung tissues, we used an unbiased spatial whole transcriptome analysis (WTA) platform (GeoMx, Bruker, Inc) integrated with single-cell immunophenotyping via highly multiplexed tissue cyclic immunofluorescence (CyCIF) to initiate this study of human TB.

Techniques: Fluorescence, Staining

Journal: PLoS ONE

Article Title: Subgroup-Elimination Transcriptomics Identifies Signaling Proteins that Define Subclasses of TRPV1-Positive Neurons and a Novel Paracrine Circuit

doi: 10.1371/journal.pone.0115731

Figure Lengend Snippet: (A) qPCR quantification of TRPV1 mRNA levels in samples hybridized on microarrays (n = 4, p<0.001, One-way ANOVA). (B) Relative expression levels of TRPV1 mRNA determined by microarray hybridizations (n = 4, p<0.001, One-way ANOVA with Bonferroni's multiple comparisons test). (C) Correlation matrix of the expression level of all genes (normalized fluorescence intensities) detected using micorarrays. Clustering of overall gene expression is visible between RTX and capsaicin treated samples. (D) qPCR quantification of TRPV1 mRNA levels in samples used for RNA-Seq (n = 3, p<0.001, paired two-tailed t-test). (E) Relative expression levels of TRPV1 mRNA determined by RNA-Seq (n = 3, p<0.001, One-way ANOVA). (F) Overview of the number of target transcripts identified by microarray hybridizations and RNA-Seq. Raw fluorescence intensities of microarrays were background corrected, log2 transformed, normalized, and filtered for expressed genes (Illumina detection p-value <0.01 in at least one of the samples, see sections for details). Sequencing was performed using a 5500xl SOLiD System resulting in 664 million reads in total (see sections for details). The reads were filtered to remove ribosomal RNA, tRNAs, and vector sequences. The remaining reads mapped to 16590 genes of the reference genome (rn5). Read counts were transformed to RPKM values (Reads per kilo base per million), normalized, and filtered to remove weakly expressed transcripts (RPKM>0.1). P-values of differentially expressed genes identified with both methods were adjusted for multiple testing with Benjamini and Hochberg's method, adjusted p-values <0.05 were considered significant.

Article Snippet: The selective removal of TRPV1(+) neurons as described above allowed us to perform differential transcriptome analysis with Illumina's microarray platform.

Techniques: Expressing, Microarray, Fluorescence, Gene Expression, RNA Sequencing, Two Tailed Test, Transformation Assay, Sequencing, Plasmid Preparation

Journal: PLoS ONE

Article Title: Subgroup-Elimination Transcriptomics Identifies Signaling Proteins that Define Subclasses of TRPV1-Positive Neurons and a Novel Paracrine Circuit

doi: 10.1371/journal.pone.0115731

Figure Lengend Snippet: (A) Correlation of fold-changes obtained by microarray hybridizations and RNA-Seq (Spearmans ρ = 0.66, p<0.0001). (B) qPCR validation of 14 transcripts identified as differentially expressed by microarray hybridizations or RNA-Seq. The depletion of TRPV1(+) neurons was performed with capsaicin (1 and 10 µM) for 30 min. The reduction of all target transcripts is dose-dependent.

Article Snippet: The selective removal of TRPV1(+) neurons as described above allowed us to perform differential transcriptome analysis with Illumina's microarray platform.

Techniques: Microarray, RNA Sequencing, Biomarker Discovery