Journal: PLoS ONE

Article Title: Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454

doi: 10.1371/journal.pone.0181452

Figure Lengend Snippet: MOTU numbers at different minimum abundance thresholds of sequence reads: Comparisons of mock community analysis using (A) Illumina MiSeq and (B) Roche 454, and analyses of field-collected samples using (C) Illumina MiSeq and (D) Roche 454. A 0.05% of total reads for a single sample is indicated by dashed lines. Effects of the abundance threshold on MOTU numbers were evaluated both at a 97 and 99% similarity threshold for MOTU clustering.

Article Snippet: Major taxonomic groups can be comparatively sequenced between Roche 454 and Illumina MiSeq data.

Techniques: Sequencing

Journal: PLoS ONE

Article Title: Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454

doi: 10.1371/journal.pone.0181452

Figure Lengend Snippet: MOTU numbers were calculated at 97 and 99% similarity thresholds in metagenetic analyses using both Illumina MiSeq and Roche 454 data.

Article Snippet: Major taxonomic groups can be comparatively sequenced between Roche 454 and Illumina MiSeq data.

Techniques:

Journal: PLoS ONE

Article Title: Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454

doi: 10.1371/journal.pone.0181452

Figure Lengend Snippet: Order-level taxonomic compositions of copepods in field-collected samples between (A) species and MOTUs, and (B) biomass and sequence reads. Metagenetic analyses using both Illumina MiSeq and Roche 454 data were performed at a 97% similarity threshold.

Article Snippet: Major taxonomic groups can be comparatively sequenced between Roche 454 and Illumina MiSeq data.

Techniques: Sequencing

Journal: PLoS ONE

Article Title: Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454

doi: 10.1371/journal.pone.0181452

Figure Lengend Snippet: Family-level taxonomic compositions of calanoid copepods in field-collected samples between (A) species and MOTUs, and (B) biomass and sequence reads. Metagenetic analyses using both Illumina MiSeq and Roche 454 data were performed at a 97% similarity threshold.

Article Snippet: Major taxonomic groups can be comparatively sequenced between Roche 454 and Illumina MiSeq data.

Techniques: Sequencing

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Differentially expressed miRNAs of EVs derived from serum of patients with leukaemia before irradiation vs. healthy donors. a Volcano plot; X axis: log2 transformed fold change; Y axis: −log10 transformed p -values. b Heatmap of upregulated and c heatmap of downregulated miRNAs in EVs from serum of patients with leukaemia. d Top 10 significant Kyoto Encyclopedia of Genes and Genomes database (KEGG) pathways affected by upregulated miRNAs of patients with leukaemia vs. healthy donors, ordered from top to bottom by p value, with the most significant pathway on the top. e Top 10 significant KEGG pathways affected by downregulated miRNAs of patients with leukaemia vs. healthy donors, ordered from top to bottom by p -value

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques: Derivative Assay, Irradiation, Transformation Assay

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Significantly up- ( n = 23) and downregulated ( n = 16) miRNAs in EVs from serum of patients with leukaemia vs. healthy volunteers

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques:

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Differentially expressed miRNAs of EVs derived from serum of patients with leukaemia after whole-body irradiation vs. before irradiation. a Volcano plot, b heatmap of upregulated and c heatmap of downregulated miRNAs in EVs from serum of patients with leukaemia after and before irradiation. d Top 10 KEGG pathways affected by upregulated miRNAs or e downregulated miRNAs from irradiated vs. non-irradiated patients with leukaemia

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques: Derivative Assay, Irradiation

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Significantly up- ( n = 11) and downregulated ( n = 15) miRNAs in EVs from serum of patients with leukaemia after irradiation

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques:

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Venn diagram analyses (program InteractiVenn, www.interactivenn.net ) of ( a ) upregulated or ( b ) downregulated miRNAs in AML, ALL and combined (AML+ALL = leukaemia) patients and of miRNAs ( c ) upregulated and ( d ) downregulated following TBI in AML, ALL and combined cohort patients (leukaemia)

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques:

Journal: bioRxiv

Article Title: Comparative Transcriptomic and Metabolomic Analyses in Response to Cold in Tartary Buckwheat ( Fagopyrum tataricum )

doi: 10.1101/278432

Figure Lengend Snippet: (A) Heatmap analysis of the phenylpropanoid biosynthetic genes in tartary buckwheat plants in response to cold. The response of the phenylpropanoid biosynthetic genes was obtained from RNA-sequencing analysis. The log 2 fold change values for each time point were calculated. Scales indicate the color assigned to each log2 fold change. (B) QRT-PCR analysis of the phenylpropanoid biosynthetic genes in tartary buckwheat plants in response to cold. Six-day-old light-grown plants were treated at 4°C for varying periods of time (hour), and total RNA isolated was subjected to quantitative RT-PCR. Relative fold changes were plotted after normalization to histone H3. Mean values and SE from triplicate biological experiments are plotted. Asterisks indicate significant differences compared with the plant at 0 h using Student’s t test (*P < 0.05; **P < 0.01). PAL, phenylalanine ammonia-lyase; C4H, cinnamate 4-hydroxylase; 4CL, 4-coumarate-CoA ligase; OMT, O-methyltransferase; HCT, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase; CHS, chalcone synthase; CHI, chalcone isomerase; CHIL, chalcone isomerase like; F3H, flavanone-3-hydroxylase; F3’H, flavonoid-3’-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol reductase; ANS, anthocyanin synthase.

Article Snippet: Our Illumina RNA sequencing data for Fagopyrum tataricum have been deposited in the NCBI Short Read Archive database under accession number SRP132029.

Techniques: RNA Sequencing Assay, Quantitative RT-PCR, Isolation