single cell portal (Broad Institute Inc)
90
Structured Review
Broad Institute Inc
single cell portal
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
https://www.bioz.com/product/single-cell+spatial+transcriptomics+data/pmc11804007-87-52-59?v=Broad+Institute+Inc
Average 90 stars, based on 1 article reviews
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
https://www.bioz.com/product/single-cell+spatial+transcriptomics+data/pmc11804007-87-52-59?v=Broad+Institute+Inc
Average 90 stars, based on 1 article reviews
single cell portal - by Bioz Stars,
2026-08
90/100 stars
Images
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
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
