Journal: Cell Death & Disease

Article Title: Zebularine regulates early stages of mESC differentiation: effect on cardiac commitment

doi: 10.1038/cddis.2013.88

Figure Lengend Snippet: Characterization of HS-181 cell line after treatment with zebularine. ( a ) RT-PCR of cardiac markers after treatment with zebularine. Myh7, Myh6, Actc, cTnI and Serca2 present more expression after treatment. ( b ) Immunostaining of treated cells to detect cardiac-specific proteins. Scale bars; 50 μ m. ( c ) Blots of Proteome Profiler Array and the resulting quantification histograms demonstrating inhibition of pluripotency marker expression and ( d ) increased levels of mesodermic proteins after zebularine treatment (black arrows)

Article Snippet: Protein expression profiles were assayed using the specific human pluripotent Stem Cell array kit ‘Proteome Profiler Array' (R&D Systems Europe, Abingdon, UK; ARY010) following the manufacturer's instructions.

Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing, Immunostaining, Inhibition, Marker

Journal: Nature

Article Title: High frequency of shared clonotypes in human B cell receptor repertoires

doi: 10.1038/s41586-019-0934-8

Figure Lengend Snippet: Summary of sequencing methods and cell counts

Article Snippet: , AbHelix® Human B and T Cell Profiling Assay , Full-length , 9 × 10 8 , 4.3 × 10 7 , 7.2 × 10 7 , HiSeq PE-250 , AbHelix, LLC.

Techniques: Sequencing

Journal: International Journal of Clinical Practice

Article Title: Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy

doi: 10.1155/2024/5113990

Figure Lengend Snippet: Identification of the diverse patterns based on the PANoptosis gene list. (a) A total of 226 PANoptosis-related genes belonging to necroptosis, apoptosis, and pyroptosis were collected for downstream analysis. (b) The univariate Cox regression analysis and Spearman's sum rank test were performed in the HOVON cohort, which was set as the training cohort. 28 genes with prognostic prediction were screened out with p value <0.05. (c) An interaction network of prognostic PANoptosis-related genes. (d) The 618 patients in HOVON cohort were divided into three clusters, according to the consensus clustering analysis based on the transcriptome profile of PANoptosis-related genes. (e) The KM curves showing the differential overall survival among the three subgroups. (f) A heat map showing the expression of the prognostic PANoptosis related genes in different subgroups. The two-sided p value <0.05 was considered significant for all statistical analyses and shown as ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, and ∗∗∗∗ p < 0.0001.

Article Snippet: Transcriptome data of human cancer cell lines (CCLs) were downloaded from the Broad Institute-Cancer Cell Line Encyclopedia project (CCLE, https://sites.broadinstitute.org/ccle/ ) and the CERES scores, the score to evaluate the dependency of the certain gene in the CCL, which indicated that the score was negative correlation with the possible significance of the gene in cell proliferation of the certain CCL, were downloaded from the dependency map portal (DepMap, https://depmap.org/portal/ ).

Techniques: Expressing

Journal: Nature

Article Title: High frequency of shared clonotypes in human B cell receptor repertoires

doi: 10.1038/s41586-019-0934-8

Figure Lengend Snippet: Summary of sequencing methods and cell counts

Article Snippet: Subject Immune Repertoire Assay Target Number PBMCs Processed Number B Cells Studied Number T Cells Studied NGS Platform Sequencing Vendor HIP1 Adaptive ImmmunoSEQ® Human TCRa/b Kit HCDR3 4 × 10 7 -- 1.3 × 10 7 NextSeq SR-150 VANTAGE Clontech SMARTer® Human TCR Profiling Kit Full-length 1 × 10 7 -- 4 × 10 6 MiSeq PE-300 VANTAGE NEB AbSeq® Human B and T Cell Profiling Kit Full-length 1 × 10 7 4.5 × 10 5 2 × 10 6 MiSeq PE-300 VANTAGE AbHelix® Human B and T-Cell Profiling Assay Full-length 9 × 10 8 3.6 × 10 7 6 × 10 7 HiSeq PE-250 AbHelix, LLC Crowe Laboratory B Cell Profiling Assay CDR1-FR4 4 × 10 8 2.7 × 10 7 -- HiSeq PE-250 HudsonAlpha HIP2 Adaptive ImmmunoSEQ® Human TCRa/b Kit HCDR3 7.9 × 10 8 -- 1.8 × 10 7 NextSeq SR-150 VANTAGE Crowe Laboratory B Cell MAF Profiling Assay CDR1-FR4 2.9 × 10 8 2.1 × 10 7 -- HiSeq PE-250 VANTAGE AbHelix® Human B and T Cell Profiling Assay Full-length 9 × 10 8 4.3 × 10 7 7.2 × 10 7 HiSeq PE-250 AbHelix, LLC Crowe Laboratory B Cell Profiling Assay CDR1-FR4 4 × 10 8 2.7 × 10 7 -- HiSeq PE-250 HudsonAlpha Adaptive ImmmunoSEQ® Human BCR Kit HCDR3 6 × 10 9 1.9 × 10 7 -- HiSeq SR-150 Adaptive HIP3 Adaptive ImmmunoSEQ® Human TCRa/b Kit HCDR3 8.1 × 10 8 -- 1.8 × 10 7 NextSeq SR-150 VANTAGE AbHelix® Human B and T Cell Profiling Assay Full-length 9 × 10 8 4.3 × 10 7 7.2 × 10 7 HiSeq PE-250 AbHelix, LLC Crowe Laboratory B Cell Profiling Assay CDR1-FR4 4 × 10 8 2.7 × 10 7 -- HiSeq PE-250 HudsonAlpha CORD1 Crowe Laboratory B Cell MAF Profiling Assay CDR1-FR4 1.4 × 10 7 3.5 × 10 5 -- MiSeq PE-250 VANTAGE CORD2 Crowe Laboratory B Cell MAF Profiling Assay CDR1-FR4 7.5 × 10 6 6.1 × 10 5 -- MiSeq PE-250 VANTAGE CORD3 Crowe Laboratory B Cell MAF Profiling Assay CDR1-FR4 1.3 × 10 7 9.8 × 10 5 -- MiSeq PE-250 VANTAGE Open in a separate window Summary of sequencing methods and cell counts Extended Data Table 3.

Techniques: Sequencing

Journal: NPJ Breast Cancer

Article Title: Immunologically “cold” triple negative breast cancers engraft at a higher rate in patient derived xenografts

doi: 10.1038/s41523-022-00476-0

Figure Lengend Snippet: a Bulk expression of immune genes in TCGA TNBC. Heatmap of the bulk expression of immune gene markers in hot and cold TNBC TCGA tumors (red bars and blue bars respectively). b Immune proportions in TCGA TNBC. Proportions of M2 macrophages (top left), T-regs (top right), M1 macrophages (bottom left), and non-T-reg CD4 T-cells (bottom right) in hot and cold TCGA TNBC tumors (red bars and blue bars respectively). T-tests were used to investigate the differences between hot and cold TNBC samples, and enter lines in the boxplots indicate the median. The bounds of the box indicate the first to third quartile values, while the bounds of the lower and upper whiskers indicate the smallest observation greater than or equal to the first quartile −1.5 times the inter-quartile range and the largest observation smaller or equal to the third quartile +1.5 times the inter-quartile range respectively. c Matching the PDX cancer cell profiles to the deconvoluted TCGA cancer cell profiles. 94% of the PDX models match the cold cancer cell profile. The histogram shows the frequency of the ratios of each model’s correlation the cold cancer cell profile vs the hot cancer cell profile. The bars in red (left) indicate that the hot cancer cell profile was the best match, while the bars in blue (right) indicate that the cold cancer cell profile was the best match. d Bulk expression of immune genes in patient tumors. Heatmap of bulk expression of immune cell markers in the HCI tumors that did not engraft in PDXs vs those that did (blue and red bars respectively). e Immune proportions in patient tumors. Proportions of M2 macrophages (top left), T-regs (top right), M1 macrophages (bottom left), and non-T-reg CD4 T-cells (bottom right) in hot and cold TCGA TNBC tumors (red bars and blue bars respectively). T-tests were used to investigate the differences between TNBCs that engrafted in murine models and those that did not. Center lines in the boxplots indicate the median, and the bounds of the box indicate the first to third quartile values. The bounds of the lower and upper whiskers indicate the smallest observation greater than or equal to the first quartile −1.5 times the inter-quartile range and the largest observation smaller or equal to the third quartile +1.5 times the inter-quartile range respectively. f Immune State. M2 macrophages release exosomes that include miR-29a-3p and miR-21-5p that reprogram T-cells to T-regs. Conversely, Tregs then release interleukins including IL-10, IL-4 and IL-13 that then reprogram M1 to M2 macrophages. The presence of T-regs and M2 macrophages leads to a cancer promoting tumor state.

Article Snippet: The human cancer cell profiles of these PDXs were isolated by Xenome , and the PDX cancer cell profiles were correlated to the deconvoluted cold and hot primary TCGA TNBC profiles.

Techniques: Expressing