mace kit  (GenXPro)

Journal: Cell Death & Disease

Article Title: NGS-based transcriptome profiling reveals biomarkers for companion diagnostics of the TGF-β receptor blocker galunisertib in HCC

doi: 10.1038/cddis.2017.44

Figure Lengend Snippet: NGS data in HLF cell line from MACE and validation by qRT-PCR. Three replicates were performed for each condition. ( a ) Clustered heat map of normalized sequence counts of the genes with the highest expression as determined by MACE. ( b ) Transcriptional response of selected potential biomarkers to both TGF- β 1 and galunisertib (gal). ( c ) Comparison of mRNA expression measurement results obtained with either qRT-PCR or MACE. For each gene, the change of expression level is calculated by fold change. ( d ) Expression of mRNA of target genes in comparison with their expression levels in control samples as measured by qRT-PCR. For each gene, the change of expression (−ΔΔCt) is calculated by – (delta Ct target–delta Ct control) and for MACE data the log 2 fold change is used)

Article Snippet: Preparation and next-generation sequencing (NGS) of MACE libraries were performed using the MACE kit (GenXPro GmbH, Frankfurt, Germany) according to the manual provided with the kit and essentially as described.

Techniques: Next-Generation Sequencing, Quantitative RT-PCR, Sequencing, Expressing

Journal: Cardiovascular Research

Article Title: Cardiac SARS-CoV-2 infection is associated with pro-inflammatory transcriptomic alterations within the heart

doi: 10.1093/cvr/cvab322

Figure Lengend Snippet: Cardiac SARS-CoV-2 infection was not associated with increased immune cell infiltration. ( A ) The previously published ‘Heart Cell Atlas’ 14 served as single-cell RNA-sequencing dataset to generate a signature matrix using CibersortX from left ventricular tissue originated cells. Digital cytometry was performed, applying the generated signature matrix to our MACE-RNA-seq data by CibersortX. Cell fractions were estimated for each individual case. Comparing the immune cell fractions between cases with ( n = 10) and without ( n = 10) cardiac infection, no significant differences were determined using Mann–Whitney U test. Cell fractions are depicted as Tukey-style box plots with median and inter-quartile range without outliers. ( B ) The number of positively stained immune cells per mm 2 is displayed. Cases without cardiac infections ( n = 46) are depicted in white, whereas cases with cardiac infection ( n = 41) are depicted in red. The patient groups were compared using Mann–Whitney U test revealing no significant differences. Data are depicted as Tukey-style box plots with median and inter-quartile range without outliers. Representative staining of immune cells in cardiac tissue is displayed. On the left panel, the CD45R0 staining for Case 65, quantified as 15.1 cells per mm 2 , is shown. The middle panel depicts the CD3 staining for Case 21 (7.4 cells/mm 2 ). For Case 47, the CD68 staining is shown on the right panel (14.7 cells/mm 2 ). Magnifications are displayed below for each case.

Article Snippet: The RNA samples were processed using the MACE-Kit v.2 according to the manufacturer’s protocol (GenXPro GmbH, Germany).

Techniques: Infection, RNA Sequencing Assay, Cytometry, Generated, MANN-WHITNEY, Staining

Journal: Cardiovascular Research

Article Title: Cardiac SARS-CoV-2 infection is associated with pro-inflammatory transcriptomic alterations within the heart

doi: 10.1093/cvr/cvab322

Figure Lengend Snippet: Presence of SARS-CoV-2 in cardiac left ventricular tissue of fatal COVID-19 cases. ( A ) Presence of SARS-CoV-2 RNA was examined in the cardiac tissue of 95 SARS-CoV-2-positive deceased. Virus load in 1 µg RNA was quantified by reverse transcription followed by quantitative polymerase chain reaction (RT–PCR). Despite the SARS-CoV-2 diagnosis, 46 out of 95 cases revealed no SARS-CoV-2 in the cardiac tissue. A copy number > 1000 copies per µg RNA in the heart was deemed as clinically relevant and was detected in 41 cases, while 8 cases did not exceed the relevant number and were therefore excluded from further analyses. Cases without cardiac infection are depicted in white, whereas cases with cardiac infection are depicted in red. The median copy number (cn) per µg RNA was 7952 (IQR: 2507–32 005). Virus load for each case individually is plotted as heatmap in Supplementary material online, Figure S1A . MACE-RNA-seq identified 19 differentially expressed genes (DEGs) comparing cardiac tissue with ( n = 10) and without ( n = 10) cardiac infection. ( B ) In situ hybridization was used to visualize SARS-CoV-2 RNA on tissue specimens. Hybridized probes are specific either for the plus strand representing the viral genome or the minus strand representing the intermediate strand for replication. Representative images of Case 08 are displayed. Negative and positive controls for chromogenic in situ hybridization are shown in Supplementary material online, Figure S2 .

Article Snippet: The RNA samples were processed using the MACE-Kit v.2 according to the manufacturer’s protocol (GenXPro GmbH, Germany).

Techniques: Real-time Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Infection, RNA Sequencing Assay, In Situ Hybridization, Chromogenic In Situ Hybridization

Journal: Cardiovascular Research

Article Title: Cardiac SARS-CoV-2 infection is associated with pro-inflammatory transcriptomic alterations within the heart

doi: 10.1093/cvr/cvab322

Figure Lengend Snippet: Identification of 19 differentially expressed genes (DEGs). Gene expression was analysed by MACE-RNA-seq in 10 cases with and 10 cases without cardiac infection. Downregulated genes in SARS-CoV-2-infected cardiac tissue are depicted in blue, while red highlights upregulated genes. FDR-adjusted P -value ( q -value) revealed 19 DEGs. ( A ) Fold change and P -value are displayed in the volcano plot to visualize significant differences in gene expression; 11 upregulated and 8 downregulated DEGs were identified. Gene symbols and full names are displayed in ( C ) according to here depicted numbers. DEGs were calculated using DESeq2. ( B ) In the profile plot, fold change and average of normalized counts per 1 million reads are displayed. Red and blue colours highlight genes with P -value

Article Snippet: The RNA samples were processed using the MACE-Kit v.2 according to the manufacturer’s protocol (GenXPro GmbH, Germany).

Techniques: Expressing, RNA Sequencing Assay, Infection

Journal: Frontiers in Plant Science

Article Title: A variable gene family encoding nodule-specific cysteine-rich peptides in pea (Pisum sativum L.)

doi: 10.3389/fpls.2022.884726

Figure Lengend Snippet: (A) Cluster analysis of P. sativum NCR genes on the basis of the expression pattern change at the different stages of symbiosis. MACE sequencing data of wild-type line SGE at 12, 21, and 28 dpi. (B) Cluster analysis of P. sativum NCR genes on the basis of the expression pattern change at the different stages of nodule development. RNA sequencing data of wild-type line SGE in early II nodule zone and late II and III nodule zones. All log2(CPM) expression values were transformed into z -score to build heatmaps.

Article Snippet: The 3′ MACE sequencing libraries were prepared from RNA samples using a 3′ MACE kit (GenXPro GmbH, Frankfurt am Main, Germany) and sequenced on Illumina HiSeq 2500 at GenXPro GmbH (Frankfurt am Main, Germany).

Techniques: Expressing, Sequencing, RNA Sequencing Assay, Transformation Assay