Journal: Communications Biology

Article Title: Single-cell and spatial architecture of primary liver cancer

doi: 10.1038/s42003-023-05455-0

Figure Lengend Snippet: a Experimental workflow using scRNA-seq, multi-omics and ST, validated by RNAscope ISH and mIHC. b Demographic and clinical characteristics of 9 donors and related sample collection of tumor, peritumor, lymph node and peripheral blood (P121-P127 for scRNA-seq and multi-omics, and P128-P129 for ST). c UMAP distribution of single cells from 7 donors’ perioperative samples (P121-P127). d UMAP distribution of ST spots from 2 donors (P128-P129). e UMAP distribution of cell populations (247,515 cells from 22 peri-operative samples). T, T cells; NK, natural killer cells; B, B cells; myeloid, myeloid cells; endothelial, endothelial cells; fibroblast, fibroblast cells or hepatic stellate cells; M1, M2, M3, supra-clusters related to malignant cells. f UMAP distribution based on tumor type, cell cycle phase, tissue type. It shows an equilibrium distribution that was not affected by these factors. g UMAP distribution based on canonical marker gene of supra-clusters. h Bar plots of supra-clusters based on tissue type, patient, tumor type, cell cycle phase and cell number. ST, spatial transcriptomics; UMAP, uniform manifold approximation and projection; G1, gap 1 Phase; S, synthesis phase; G2M, gap 2 and mitotic phase. Mix, mixed and unassigned cells or clusters.

Article Snippet: To expand the borders of the molecular architecture of PLC, bulk tissue multi-omics were performed on 15 matched solid tissues (P121-P127), ranging from genome to metabolome: assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) and reduced representation bisulfite sequencing (RRBS) in epigenomics, whole-exome sequencing (WES) in genomics, whole RNA-seq in transcriptomics, isobaric tandem mass tags (TMT)-based global proteomics, and LC-MS in metabolomics (Fig. ).

Techniques: Biomarker Discovery, RNAscope, Marker

Journal: Cancer research

Article Title: Integrative genomic analysis predicts causative cis-regulatory mechanisms of the breast cancer-associated genetic variant rs4415084

doi: 10.1158/0008-5472.CAN-17-3486

Figure Lengend Snippet: (a) Schematic representation of the integrated analysis workflow for identifying (causative SNP, TF, target gene) triplets. For inferring target genes (left part), eQTL analysis and a modified version of allele-specific expression analysis using the TCGA data are combined. For identifying causative SNPs and corresponding TFs (right part), epigenetics information, motif analysis and TF-target expression correlation analysis are used to filter the list of candidate causative variants. ChIP-seq data, allele-specific binding events and 3D chromatin interaction data are analysed when available. SNP: single-nucleotide polymorphism; eQTL: expression quantitative trait loci; LCASE: local chromosome allele-specific expression; LD: linkage disequilibrium; DHS: DNase I hypersensitive sites; TF: transcription factor; ASB: allele-specific binding; ChIA-PET: Chromatin Interaction Analysis by Paired-End Tag Sequencing; Hi-C: High-throughput chromosome conformation capture. (b) Visual illustration of the genomic analysis pipeline. Candidate SNPs are selected among the SNPs in strong LD with a GWAS SNP (yellow block) by overlapping with DHS (top track). The entire analysis is restricted to the topologically associated domain (TAD) containing the GWAS SNP.

Article Snippet: In the second approach of analysing differential k -mer enrichment (with k = L ), we tested for a difference in the occurrence frequencies of x and x a between TF ChIP-seq peaks and control regions sampled from breast cancer cell line DHS (Chi-squared test).

Techniques: Modification, Expressing, ChIP-sequencing, Binding Assay, ChIA Pet Assay, Paired-end Tag, Sequencing, Hi-C, High Throughput Screening Assay, Blocking Assay

Journal: Nature reviews. Neuroscience

Article Title: The Molecular Biology of FMRP: New Insights into Fragile X Syndrome

doi: 10.1038/s41583-021-00432-0

Figure Lengend Snippet: High throughput identification of FMRP targeted mRNAs

Article Snippet: Tran 2019 ( 43 ) , Human , postmortem adult human frontal cortex , Anti-FMRP pAb (MBL, RN016P), CLIP-seq , 4895 , binds to A-to-I edited site; predominantly 3’UTR , ACUG , , Synaptic functions, (focus was editing in autism, not FMRP targets).

Techniques: High Throughput Screening Assay, Binding Assay, Sequencing, Transmission Assay, Activity Assay, Membrane, Transfection, FLAG-tag, Modification