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Integrative analysis of single histone modifications and gene expression reveals dynamic and synergistic epigenetic regulation of pathways involved in glioblastoma pathogenesis. a Pearson correlation heatmaps of integrative analysis of ChIP Seq data for each HM and RNAseq dataset for genes only found in GIC (left) or iNSC (right) for at least one HM. RNAseq data are represented as log fold change of Differentially Expressed (DE) genes between GIC and iNSC: logFC DE > 1 and < − 1 when genes are up (red section) and downregulated (blue section) in GIC as compared to iNSC respectively (left). LogFC DE > 1 and < − 1 when genes are down and upregulated in iNSC as compared to GIC respectively (right). b Percentages of upregulated (red) and downregulated (blue) genes in iNSC as compared to GIC (top) and in GIC as compared to iNSC (bottom) for each HM based on <t>transcriptomic</t> dataset from the SYNGN cohort . Number of genes is also specified for each condition. c mRNA expression of GSC in iNSC, GIC and bulk tumour from the RNAseq dataset of the SYNGN cohort (left) and in bulk tumour and non-tumour samples from TCGA dataset . Results are expressed in log 2 (tpm) transcript per million (tpm). One-way ANOVA test. * p value < 0.05, ** p value < 0.01 and *** p value < 0.001. d Representative immunofluorescent images for GSC (green) in iNSC and GIC from patient 52. Nuclei are counterstained with DAPI. Scale bar: 50 µm. Quantification is shown as Mean Fluorescence Intensity (MFI) standardised by the number of nuclei. One-way ANOVA test. * p value < 0.05, ** p value < 0.01, *** p value < 0.001, **** p value < 0.0001. e GSC gene expression in non-tumour and bulk primary glioblastoma tumour (left panel). t-test. * p value < 0.05, ** p value < 0.01 and *** p value < 0.001. f Survival curve of glioblastoma patients with high and low expression of GSC gene (right panel). Source: TCGA Stat test: log-rank, * p value < 0.05, ** p value < 0.01 and *** p value < 0.001. g Spatial expression of GSC in glioblastoma bulk samples, analysed on Ivy –GAP . The left panel shows an example of histological anatomic structure identified in a sub-block and the right panel represents the expression of GSC in RNAseq data from anatomic structures shown as log2 normalised gene expression. Leading Edge defined as the border of the tumour, where ratio of tumour to normal cells is 1–3 / 100. Infiltrating tumour defined as the intermediate zone between leading edge and cellular tumour, where ratio of tumour to normal cells is 10–20 /100. Cellular tumour defined as tumour core, where tumour to normal cells is 100–500 / 1. One-way ANOVA test. * p value < 0.05, ** p value < 0.01 and *** p value < 0.001. h Single-cell RNAseq data showing GSC expression (left panel) in scRNAseq of glioblastoma samples in clusters defined in (right panel). Data are plotted as tSNE, with logTPM expression ranging from light orange to dark

Single Cell Portal, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Mapping chromatin remodelling in glioblastoma identifies epigenetic regulation of key molecular pathways and novel druggable targets"

Article Title: Mapping chromatin remodelling in glioblastoma identifies epigenetic regulation of key molecular pathways and novel druggable targets

Journal: BMC Biology

doi: 10.1186/s12915-025-02127-9

Figure Legend Snippet: Integrative analysis of single histone modifications and gene expression reveals dynamic and synergistic epigenetic regulation of pathways involved in glioblastoma pathogenesis. a Pearson correlation heatmaps of integrative analysis of ChIP Seq data for each HM and RNAseq dataset for genes only found in GIC (left) or iNSC (right) for at least one HM. RNAseq data are represented as log fold change of Differentially Expressed (DE) genes between GIC and iNSC: logFC DE > 1 and < − 1 when genes are up (red section) and downregulated (blue section) in GIC as compared to iNSC respectively (left). LogFC DE > 1 and < − 1 when genes are down and upregulated in iNSC as compared to GIC respectively (right). b Percentages of upregulated (red) and downregulated (blue) genes in iNSC as compared to GIC (top) and in GIC as compared to iNSC (bottom) for each HM based on transcriptomic dataset from the SYNGN cohort . Number of genes is also specified for each condition. c mRNA expression of GSC in iNSC, GIC and bulk tumour from the RNAseq dataset of the SYNGN cohort (left) and in bulk tumour and non-tumour samples from TCGA dataset . Results are expressed in log 2 (tpm) transcript per million (tpm). One-way ANOVA test. * p value < 0.05, ** p value < 0.01 and *** p value < 0.001. d Representative immunofluorescent images for GSC (green) in iNSC and GIC from patient 52. Nuclei are counterstained with DAPI. Scale bar: 50 µm. Quantification is shown as Mean Fluorescence Intensity (MFI) standardised by the number of nuclei. One-way ANOVA test. * p value < 0.05, ** p value < 0.01, *** p value < 0.001, **** p value < 0.0001. e GSC gene expression in non-tumour and bulk primary glioblastoma tumour (left panel). t-test. * p value < 0.05, ** p value < 0.01 and *** p value < 0.001. f Survival curve of glioblastoma patients with high and low expression of GSC gene (right panel). Source: TCGA Stat test: log-rank, * p value < 0.05, ** p value < 0.01 and *** p value < 0.001. g Spatial expression of GSC in glioblastoma bulk samples, analysed on Ivy –GAP . The left panel shows an example of histological anatomic structure identified in a sub-block and the right panel represents the expression of GSC in RNAseq data from anatomic structures shown as log2 normalised gene expression. Leading Edge defined as the border of the tumour, where ratio of tumour to normal cells is 1–3 / 100. Infiltrating tumour defined as the intermediate zone between leading edge and cellular tumour, where ratio of tumour to normal cells is 10–20 /100. Cellular tumour defined as tumour core, where tumour to normal cells is 100–500 / 1. One-way ANOVA test. * p value < 0.05, ** p value < 0.01 and *** p value < 0.001. h Single-cell RNAseq data showing GSC expression (left panel) in scRNAseq of glioblastoma samples in clusters defined in (right panel). Data are plotted as tSNE, with logTPM expression ranging from light orange to dark

Techniques Used: Gene Expression, ChIP-sequencing, Expressing, Fluorescence, Blocking Assay

Comparative analysis of the functional impact of chromatin states dynamics in GIC and iNSC using automatic fragmentation analysis. a Chromatin states defined by enrichment of HM using ChromHMM . Probabilities of each HM in chromatin states are depicted as a heatmap. b Pie charts show percentages of peaks in each chromatin state in GIC (left) and iNSC (right). c Sankey diagram shows the switch of peaks from one chromatin state in iNSC to another in GIC. The thickness of the links is proportional to the number of peaks included. Flows with the highest number of peaks between two opposite state functions are highlighted in bold red (activating transition in GIC) and blue (repressing transition in GIC). d Percentages of upregulated (red) and downregulated (blue) genes in the chromatin states of interest based on transcriptomic dataset from the SYNGN Cohort . Number of genes is also specified for each condition. e Visualisation of the enriched pathways identified in GIC from genes activated in GIC as compared to iNSC and from genes inactivated in GIC as compared to iNSC. Pathways are annotated based on pathways enrichment analysis performed with Reactome and represented as circle, colours represent each histone (see legend), size of the circle is proportional to the number of genes involved in the pathway (FDR < 0.05)

Figure Legend Snippet: Comparative analysis of the functional impact of chromatin states dynamics in GIC and iNSC using automatic fragmentation analysis. a Chromatin states defined by enrichment of HM using ChromHMM . Probabilities of each HM in chromatin states are depicted as a heatmap. b Pie charts show percentages of peaks in each chromatin state in GIC (left) and iNSC (right). c Sankey diagram shows the switch of peaks from one chromatin state in iNSC to another in GIC. The thickness of the links is proportional to the number of peaks included. Flows with the highest number of peaks between two opposite state functions are highlighted in bold red (activating transition in GIC) and blue (repressing transition in GIC). d Percentages of upregulated (red) and downregulated (blue) genes in the chromatin states of interest based on transcriptomic dataset from the SYNGN Cohort . Number of genes is also specified for each condition. e Visualisation of the enriched pathways identified in GIC from genes activated in GIC as compared to iNSC and from genes inactivated in GIC as compared to iNSC. Pathways are annotated based on pathways enrichment analysis performed with Reactome and represented as circle, colours represent each histone (see legend), size of the circle is proportional to the number of genes involved in the pathway (FDR < 0.05)

Techniques Used: Functional Assay

Generated:

Article Title: MicroRNA signature predicts post operative atrial fibrillation after coronary artery bypass grafting
Article Snippet: .. Plot generated from the Broad Institute of MIT and Harvard’s Single Cell Portal. ( D ) Network plot displaying specific predicted small molecule drugs targeting the miRNA signature, with miRNAs represented in navy blue rhombus and small molecules in burgundy circles. ..

other:

Article Title: Truncated NTRK2 is induced in CAP1 endothelial cells during mouse lung injury-repair
Article Snippet: Processed files and metadata were downloaded from the Broad Institute Single Cell Portal for analysis on Seurat version 4.3.0.

Article Title: The differential expression of MAGI2 in glomerulopathies and its application as a molecular discriminator of podocytopathies
Article Snippet: Single-cell RNA sequencing data (raw count matrices and accompanying metadata) were downloaded from the Broad Institute Single Cell Portal (Study ID: SCP975) https://singlecell.broadinstitute.org/single_cell/study/SCP975 , which comprises murine glomerular single cell transcriptomes under control conditions and at day 1 and 5 (d1, d5) of nephrotoxic serum nephritis (NTS) as well as 7 days after Doxorubicin (20 mg/kgBW) injection.

Article Title: Choroid plexus apocrine secretion shapes CSF proteome during mouse brain development.
Article Snippet: Created with the Zylka Lab’s Single-cell transcriptomic analysis of mouse neocortical development gene-by-gene search webpage with data from Loo et al.1. https://zylkalab.org/datamousecortex (B) Violin plot of E14 Htr2c expression demonstrates high ChP Htr2c expression in mouse brain at E14.5. created with Broad Institute Single Cell Portal from Mouse E14 brain single nucleus RNA sequencing data gathered for Russell et al.2. https://singlecell.broadinstitute. org/single_cell/study/SCP2170/slide-tags-snrna-seq-on-mouse-embryonic-e14brain (C) Expression of Htr2c in E13.5, E15.5, E18.5, and P4 mouse brain shows that before E18.5, Htr2c is highly and predominantly expressed in ChP.

Article Title: Transglutaminase 2 function in glioblastoma tumor efferocytosis.
Article Snippet: Single-cell RNAseq data from Abdelfattah et al. [8] were analyzed using the Broad Institute Single Cell Portal. (https://singlecell.broadinstitute.org/single_cell).

Article Title: scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery.
Article Snippet: These individual studies were primarily sourced from Cellxgene [70] and the single-cell portal of Broad Institute [31].

Single Cell:

Article Title: Macrophages foster anti-tumor immunity by ZEB1-dependent cytotoxic T cell chemoattraction
Article Snippet: .. In ( c ) and ( d ), plots and cell type annotations were retrieved from the single cell portal from the Broad Institute using the dataset from . .. In ( c ) and ( d ), plots and cell type annotations were retrieved from the single cell portal from the Broad Institute using the dataset from .

Article Title: Macrophages foster anti-tumor immunity by ZEB1-dependent cytotoxic T cell chemoattraction.
Article Snippet: .. In (c) and (d), plots and cell type annotations were retrieved from the single cell portal from the Broad Institute using the dataset from112. .. Representative images (e) and quantification (f) of immunofluorescence staining (IF) for the number of CD68+ cells (left) per field of view and the fraction of ZEB1+ cells among CD68+ cells (right) of human colorectal cancer (CRC) with DAPI-stained nuclei.

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