Journal: BMC Genomics

Article Title: Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline

doi: 10.1186/s12864-021-07390-y

Figure Lengend Snippet: Assembly and annotation metrics for all NCBI representative genome assemblies of Metarhizium species

Article Snippet: The following genomes and/or information on the genome assemblies were retrieved from NCBI’s GenBank database; Metarhizium album ARSEF 1941 (accession number: GCA_000804445.1), Metarhizium acridum CQMa 102 (accession number: GCA_000187405.1), Metarhizium anisopliae ARSEF 549 (accession number: GCA_000814975.1), Metarhizium brunneum ARSEF 3297 (accession number: GCF_000814965.1), Metarhizium guizhouense ARSEF 977 (accession number: GCA_000814955.1), Metarhizium majus ARSEF 297 (accession number: GCA_000814945.1), Metarhizium rileyi RCEF 4871 (accession number: GCA_001636745.1), Metarhizium robertsii ARSEF 23 (accession number: GCA_000187425.2), Cordyceps militaris ATCC 34164 (accession number: GCA_008080495.1), Epichloe festucae Fl1 (accession number: GCA_003814445.1), and Trichoderma reesei QM6a (accession number: GCA_002006585.1).

Techniques:

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: (A and B) MP41 (A) and MP46 (B) copy number profile established from whole-genome sequencing. Losses, gains, and normal regions are colored respectively in blue, red, and green. (C) Principal component analysis of RNA-seq of six normal choroidal melanocyte samples (blue), four preparations of MP41 UM cells (red). and three preparations of MP46 UM cells (green). (D) Hierarchical clustering of the same profiles. (E) Differential gene expression analysis of MP41 vs. NM and MP46 vs. NM to identify genes with a Log2 fold change greater than 1.5 and a p value lower than 0.05. (F) Heatmap of commonly regulated genes in MP41 vs. NM and MP46 vs. NM. (G) 50 most highly regulated pathways by reactome analysis of commonly regulated genes listed according to the significance (−log2 [p value + 1E-10]).

Article Snippet: MP41 PDX , Institut Curie , N/A.

Techniques: Sequencing, RNA Sequencing Assay, Expressing

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: Genes consistently in top 50 up- or downregulated in UM models vs. NM

Article Snippet: MP41 PDX , Institut Curie , N/A.

Techniques:

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: (A and B) Circos plot of aberrations in (A) MP41 and (B) MP46. From the central to the periphery of the circos plot: whole-genome view summarizes intra- and inter-chromosomal translocations (pink lines), copy number gains and losses are listed on the first internal layer of the circos, and SVs (insertion, deletion inversion, and duplication) are labeled as colored dots in the intermediate layer of the circos. Gene density, cytobands, and chromosomes comprise the outer layers of the circos. (C) Number of insertions, deletions, inversions, and duplications and intra- and inter-translocations are detailed for MP41 and MP46 defined by Bionano optical mapping. (D and E) Telomere and M-FISH from analysis of (D) MP41 and (E) MP46 are derived from two different FISH analyses. Upper left panels show telomere (red signal) and centromere (green signal) staining and are counter labeled with DAPI (blue). Lower left panels show M-FISH analysis. Main panels correspond to the karyotype view.

Article Snippet: MP41 PDX , Institut Curie , N/A.

Techniques: Labeling, Derivative Assay, Staining

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: (A) DNA methylation levels based on oxidative bisulfite DNA treatment followed by whole-genome sequencing are shown at CGI promoters, non-CGI promoters, non-promoters CGI, exons, introns, intergenic regions, and on repeats, in normal melanocytes, MP41, and MP46. (B) Differentially methylated regions (DMRs) as hypo- and hyper-DMRs (H− and H+) in 300-kb window in MP41 vs. NM and MP46 vs. NM. Commonly regulated DMRs correspond to DMRs identified in MP41 vs. NM and MP46 vs. NM comparisons. DMRs were considered as commonly regulated where sharing the same variation (H− or H+) and when their coordinates were identical or overlapping. (C) Percentage of CpG methylation in MP41, MP46, and NM in BAP1 locus through UCSC Genome Browser are represented in yellow, and sequencing coverages are represented in red bars. CpG island 129 overlaps the BAP1/PHF7 promoter. The blue area highlights the deletion detected in MP46. (D) IGV view of MP46 short-read sequencing (first line) and targeted ONT sequencing (second line) illustrate the boundaries of promoter/5′ UTR deletion in BAP1 and PHF7 genes.

Article Snippet: MP41 PDX , Institut Curie , N/A.

Techniques: DNA Methylation Assay, Sequencing, Methylation, CpG Methylation Assay

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: (A) Contacts maps derived from in situ Hi-C at the whole genome level for NM, MP41, and MP46. (B) Histogram of compartment changes in NM, MP41, and MP46. A and B compartments identified at 250-kb resolution. (C) Localization of inactivated (ABB) and activated (BAA) compartment in MP41 and MP46 vs. NM on a whole-genome view. (D) Integration of compartment changes and gene expression among NM, MP41, and MP46. (E and F) Number (E) and size (F) of TADs in NM, MP41, and MP46.

Article Snippet: MP41 PDX , Institut Curie , N/A.

Techniques: Derivative Assay, In Situ, Hi-C, Expressing

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: (A) Gene expression of PRAME and its neighbors as BMS1P20, ZNF280B, and ZNF280A upstream genes and POM121LP downstream. RNA-seq data of NM, MP41, and MP46 replicates (FPKM). (B) UCSC Genome Browser view (hg19) of percentage of DNA methylation (golden bars). (C) DNA contacts maps of NM, MP41, and MP46 at 5-kb resolution in PRAME TAD (blue square). (D) UCSC Genome Browser view of the PRAME locus showing DNA methylation, RNA-seq (log2), H2AUb, H3K4me3, H3K27me3, H3K27Ac, CTCF, and RefSeq genes. (E) H3K27Ac marks and HiC interaction of PRAME promoter with potential distal enhancer E1. HiC interactions anchored in E1 (left) and E2 (right) quantified in boxes under genomic locus.

Article Snippet: MP41 PDX , Institut Curie , N/A.

Techniques: Expressing, RNA Sequencing Assay, DNA Methylation Assay

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: MP41 PDX , Institut Curie , N/A.

Techniques: Isolation, HD Assay, Sequencing, Software

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: (A and B) MP41 (A) and MP46 (B) copy number profile established from whole-genome sequencing. Losses, gains, and normal regions are colored respectively in blue, red, and green. (C) Principal component analysis of RNA-seq of six normal choroidal melanocyte samples (blue), four preparations of MP41 UM cells (red). and three preparations of MP46 UM cells (green). (D) Hierarchical clustering of the same profiles. (E) Differential gene expression analysis of MP41 vs. NM and MP46 vs. NM to identify genes with a Log2 fold change greater than 1.5 and a p value lower than 0.05. (F) Heatmap of commonly regulated genes in MP41 vs. NM and MP46 vs. NM. (G) 50 most highly regulated pathways by reactome analysis of commonly regulated genes listed according to the significance (−log2 [p value + 1E-10]).

Article Snippet: MP41 cell line , Institut Curie, and ATCC , CRL-3297.

Techniques: Sequencing, RNA Sequencing Assay, Expressing

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: Genes consistently in top 50 up- or downregulated in UM models vs. NM

Article Snippet: MP41 cell line , Institut Curie, and ATCC , CRL-3297.

Techniques:

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: (A and B) Circos plot of aberrations in (A) MP41 and (B) MP46. From the central to the periphery of the circos plot: whole-genome view summarizes intra- and inter-chromosomal translocations (pink lines), copy number gains and losses are listed on the first internal layer of the circos, and SVs (insertion, deletion inversion, and duplication) are labeled as colored dots in the intermediate layer of the circos. Gene density, cytobands, and chromosomes comprise the outer layers of the circos. (C) Number of insertions, deletions, inversions, and duplications and intra- and inter-translocations are detailed for MP41 and MP46 defined by Bionano optical mapping. (D and E) Telomere and M-FISH from analysis of (D) MP41 and (E) MP46 are derived from two different FISH analyses. Upper left panels show telomere (red signal) and centromere (green signal) staining and are counter labeled with DAPI (blue). Lower left panels show M-FISH analysis. Main panels correspond to the karyotype view.

Article Snippet: MP41 cell line , Institut Curie, and ATCC , CRL-3297.

Techniques: Labeling, Derivative Assay, Staining

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: (A) DNA methylation levels based on oxidative bisulfite DNA treatment followed by whole-genome sequencing are shown at CGI promoters, non-CGI promoters, non-promoters CGI, exons, introns, intergenic regions, and on repeats, in normal melanocytes, MP41, and MP46. (B) Differentially methylated regions (DMRs) as hypo- and hyper-DMRs (H− and H+) in 300-kb window in MP41 vs. NM and MP46 vs. NM. Commonly regulated DMRs correspond to DMRs identified in MP41 vs. NM and MP46 vs. NM comparisons. DMRs were considered as commonly regulated where sharing the same variation (H− or H+) and when their coordinates were identical or overlapping. (C) Percentage of CpG methylation in MP41, MP46, and NM in BAP1 locus through UCSC Genome Browser are represented in yellow, and sequencing coverages are represented in red bars. CpG island 129 overlaps the BAP1/PHF7 promoter. The blue area highlights the deletion detected in MP46. (D) IGV view of MP46 short-read sequencing (first line) and targeted ONT sequencing (second line) illustrate the boundaries of promoter/5′ UTR deletion in BAP1 and PHF7 genes.

Article Snippet: MP41 cell line , Institut Curie, and ATCC , CRL-3297.

Techniques: DNA Methylation Assay, Sequencing, Methylation, CpG Methylation Assay

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: (A) Contacts maps derived from in situ Hi-C at the whole genome level for NM, MP41, and MP46. (B) Histogram of compartment changes in NM, MP41, and MP46. A and B compartments identified at 250-kb resolution. (C) Localization of inactivated (ABB) and activated (BAA) compartment in MP41 and MP46 vs. NM on a whole-genome view. (D) Integration of compartment changes and gene expression among NM, MP41, and MP46. (E and F) Number (E) and size (F) of TADs in NM, MP41, and MP46.

Article Snippet: MP41 cell line , Institut Curie, and ATCC , CRL-3297.

Techniques: Derivative Assay, In Situ, Hi-C, Expressing

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: (A) Gene expression of PRAME and its neighbors as BMS1P20, ZNF280B, and ZNF280A upstream genes and POM121LP downstream. RNA-seq data of NM, MP41, and MP46 replicates (FPKM). (B) UCSC Genome Browser view (hg19) of percentage of DNA methylation (golden bars). (C) DNA contacts maps of NM, MP41, and MP46 at 5-kb resolution in PRAME TAD (blue square). (D) UCSC Genome Browser view of the PRAME locus showing DNA methylation, RNA-seq (log2), H2AUb, H3K4me3, H3K27me3, H3K27Ac, CTCF, and RefSeq genes. (E) H3K27Ac marks and HiC interaction of PRAME promoter with potential distal enhancer E1. HiC interactions anchored in E1 (left) and E2 (right) quantified in boxes under genomic locus.

Article Snippet: MP41 cell line , Institut Curie, and ATCC , CRL-3297.

Techniques: Expressing, RNA Sequencing Assay, DNA Methylation Assay

Journal: Cell reports

Article Title: Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

doi: 10.1016/j.celrep.2023.113132

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: MP41 cell line , Institut Curie, and ATCC , CRL-3297.

Techniques: Isolation, HD Assay, Sequencing, Software