Journal: Cell Reports

Article Title: BCG Vaccination Induces Long-Term Functional Reprogramming of Human Neutrophils

doi: 10.1016/j.celrep.2020.108387

Figure Lengend Snippet:

Article Snippet: KAPA library preparation kit , Kapa Biosystems , KK8400.

Techniques: Virus, Recombinant, Protease Inhibitor, Reverse Transcription, SYBR Green Assay, Enzyme-linked Immunosorbent Assay, cDNA Synthesis, Purification, Staining, Random Hexamer, RNA HS Assay, Concentration Assay, Flow Cytometry, Software

Journal: bioRxiv

Article Title: Personalized transcriptome signatures in a cardiomyopathy stem cell biobank

doi: 10.1101/2024.05.10.593618

Figure Lengend Snippet: A. We created a biobank of stem cells from 300 donors exhibiting either HCM, DCM, LVNC, or serving as controls. iPS cells were profiled by whole genome sequencing and a subset differentiated into cardiomyocytes for additional profiling via RNA-seq, drug treatment, and microscopy-based contractility assaying. B. Plotted are the datasets which passed quality control filtering. Numbers indicate number of donors for each dataset type. The actual number of datasets is higher due to replicates. Abbreviations: hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), left ventricular noncompaction (LVNC), induced pluripotent stem cells (iPS cells), whole genome sequencing (WGS), RNA sequencing (RNA-seq), dimethyl sulfoxide (DMSO), mavacamten (myk), omecamtiv mecarbil (omec).

Article Snippet: Illumina RNA-seq libraries (TruSeq Stranded Total RNA LP Gold) were prepared on the Bravo (Agilent; 3 samples prepared manually as indicated in Table S6), pooled (Table S6), and sequenced (NovaSeq-6000, paired-end, 100bp).

Techniques: Sequencing, RNA Sequencing Assay, Microscopy

Journal: bioRxiv

Article Title: Personalized transcriptome signatures in a cardiomyopathy stem cell biobank

doi: 10.1101/2024.05.10.593618

Figure Lengend Snippet: A. Plotted is the principal component data from . PC1 for each HCM sample is shown (gray, black, blue, by HCM subgroup). PC1 is a sum of values for each edge. Also plotted is the sum of the scores for all ADCY5 edges specifically. HCM-moderate samples show ADCY5 scores increasing with PC1, while ADCY5 scores are similar across HCM-steep samples. B. ADCY5 expression is similar between control, moderate and steep samples, but ADCY5 node strength (C) is increased in HCM and DCM. D. Gene ontology analysis of genes sharing edges with ADCY5. E. Pearson correlation values between MEF2A expression and ADCY5. F. Cardiomyocytes were treated with the small molecule sarcomere activator (omecamtiv mecarbil) or inhibitor (mavacamten) at 0 hours and 24 hours, with RNA harvested at 48 hours for RNA-seq analysis. Gene ontology analysis revealed many shared drug targets. G. For the ADCY5 node, mean edge strength in the DMSO-treated control cohort was compared with the mean strength in the DMSO-treated or drug-treated disease cohort. Plotted are the difference for each edge around the node in the respective comparisons. In both cases, we see a partial correction (smaller difference vs control) with drug treatment.

Article Snippet: Illumina RNA-seq libraries (TruSeq Stranded Total RNA LP Gold) were prepared on the Bravo (Agilent; 3 samples prepared manually as indicated in Table S6), pooled (Table S6), and sequenced (NovaSeq-6000, paired-end, 100bp).

Techniques: Expressing, RNA Sequencing Assay