Structured Review

Agilent technologies rrna
To produce stable isotope-labeled internal standards (SILIS), Escherichia coli ( E. coli ) or Saccharomyces cerevisiae ( S. cerevisiae ) were cultured in isotope labeled media using nutrients with the highest isotope-purity possible. The total RNA was isolated and then separated into transfer RNA (tRNA) or large/ribosomal RNA through size exclusion chromatography. (* indicates 5.8 and 5S <t>rRNA</t> and # phenol) The different RNAs were enzymatically digested into nucleosides and analyzed by liquid chromatography–mass spectrometry (LC–MS/MS).
Rrna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 19376 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/rrna/product/Agilent technologies
Average 93 stars, based on 19376 article reviews
Price from $9.99 to $1999.99
rrna - by Bioz Stars, 2020-07
93/100 stars

Images

1) Product Images from "Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis"

Article Title: Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis

Journal: Genes

doi: 10.3390/genes10010026

To produce stable isotope-labeled internal standards (SILIS), Escherichia coli ( E. coli ) or Saccharomyces cerevisiae ( S. cerevisiae ) were cultured in isotope labeled media using nutrients with the highest isotope-purity possible. The total RNA was isolated and then separated into transfer RNA (tRNA) or large/ribosomal RNA through size exclusion chromatography. (* indicates 5.8 and 5S rRNA and # phenol) The different RNAs were enzymatically digested into nucleosides and analyzed by liquid chromatography–mass spectrometry (LC–MS/MS).
Figure Legend Snippet: To produce stable isotope-labeled internal standards (SILIS), Escherichia coli ( E. coli ) or Saccharomyces cerevisiae ( S. cerevisiae ) were cultured in isotope labeled media using nutrients with the highest isotope-purity possible. The total RNA was isolated and then separated into transfer RNA (tRNA) or large/ribosomal RNA through size exclusion chromatography. (* indicates 5.8 and 5S rRNA and # phenol) The different RNAs were enzymatically digested into nucleosides and analyzed by liquid chromatography–mass spectrometry (LC–MS/MS).

Techniques Used: Labeling, Cell Culture, Isolation, Size-exclusion Chromatography, Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy

2) Product Images from "Intratumoural Heterogeneity Underlies Distinct Therapy Responses and Treatment Resistance in Glioblastoma"

Article Title: Intratumoural Heterogeneity Underlies Distinct Therapy Responses and Treatment Resistance in Glioblastoma

Journal: Cancers

doi: 10.3390/cancers11020190

Comprehensive genomic analyses of single-cell clones. ( A ) Genomic proportion of copy number alteration. For clonal samples B–F, > 84% of their genome is between copy number 3 and 4 (ranging from 84.82% to 85.9%, shown as dark grey bars) as compared to ≤3% for the other samples. This global whole genome duplication typically affected both alleles, preserving heterozygosity in these samples. ( B ) Number of somatic structural variants identified per sample with the type indicated by colours. ( C ) Hierarchical clustering of somatic substitution variant allele frequencies across tumour and clonal samples. The absence of a variant in the normal control cortex sample is demonstrated by a variant allele frequency of zero (dark blue). ( D ) Hierarchical clustering of Log2-normalised and gene-scaled RNA seq gene expression of genes with most variable expression as identified as contributing to the first principle component. Positive values indicate a sample with the highest expression and negative values with the lowest expression. ( E ) Hierarchical clustering of 1000 most variable β-values from DNA methylation sequencing data. Β-value of 1 indicates completely methylated and 0 unmethylated CpGs.
Figure Legend Snippet: Comprehensive genomic analyses of single-cell clones. ( A ) Genomic proportion of copy number alteration. For clonal samples B–F, > 84% of their genome is between copy number 3 and 4 (ranging from 84.82% to 85.9%, shown as dark grey bars) as compared to ≤3% for the other samples. This global whole genome duplication typically affected both alleles, preserving heterozygosity in these samples. ( B ) Number of somatic structural variants identified per sample with the type indicated by colours. ( C ) Hierarchical clustering of somatic substitution variant allele frequencies across tumour and clonal samples. The absence of a variant in the normal control cortex sample is demonstrated by a variant allele frequency of zero (dark blue). ( D ) Hierarchical clustering of Log2-normalised and gene-scaled RNA seq gene expression of genes with most variable expression as identified as contributing to the first principle component. Positive values indicate a sample with the highest expression and negative values with the lowest expression. ( E ) Hierarchical clustering of 1000 most variable β-values from DNA methylation sequencing data. Β-value of 1 indicates completely methylated and 0 unmethylated CpGs.

Techniques Used: Clone Assay, Preserving, Variant Assay, RNA Sequencing Assay, Expressing, DNA Methylation Assay, Sequencing, Methylation

3) Product Images from "Biobanking: Objectives, Requirements, and Future Challenges—Experiences from the Munich Vascular Biobank"

Article Title: Biobanking: Objectives, Requirements, and Future Challenges—Experiences from the Munich Vascular Biobank

Journal: Journal of Clinical Medicine

doi: 10.3390/jcm8020251

Evaluation of the extent of RNA fragmentation from FFPE tissue samples measuring the area under the curve from Agilent Bioanalyzer. Two values were defined: maximal RNA length and the 50% RNA length calculated as a 50% reduction of the area under the curve. RIN: RNA integrity number; FFPE: formalin-fixed paraffin-embedded specimens. nt: number of nucleotides; FU: fluorescence unit.
Figure Legend Snippet: Evaluation of the extent of RNA fragmentation from FFPE tissue samples measuring the area under the curve from Agilent Bioanalyzer. Two values were defined: maximal RNA length and the 50% RNA length calculated as a 50% reduction of the area under the curve. RIN: RNA integrity number; FFPE: formalin-fixed paraffin-embedded specimens. nt: number of nucleotides; FU: fluorescence unit.

Techniques Used: Formalin-fixed Paraffin-Embedded, Fluorescence

( A ) Measurement of RNA integrity number (RIN) in FFPE vascular tissue samples using Agilent Bioanalyzer between 2009 and 2018 ( n = 5 for each group and year). ( B ) Evaluation of the length of the RNA fragments, as described in Figure 3 . No significant differences were observed between the study years over time.
Figure Legend Snippet: ( A ) Measurement of RNA integrity number (RIN) in FFPE vascular tissue samples using Agilent Bioanalyzer between 2009 and 2018 ( n = 5 for each group and year). ( B ) Evaluation of the length of the RNA fragments, as described in Figure 3 . No significant differences were observed between the study years over time.

Techniques Used: Formalin-fixed Paraffin-Embedded

4) Product Images from "Global Assessment of Antrodia cinnamomea-Induced MicroRNA Alterations in Hepatocarcinoma Cells"

Article Title: Global Assessment of Antrodia cinnamomea-Induced MicroRNA Alterations in Hepatocarcinoma Cells

Journal: PLoS ONE

doi: 10.1371/journal.pone.0082751

MicroRNA analysis workflow. Both experimental and control cells were treated, or untreated (control, DMSO alone was added), with 500 µg/ml AcFBE (experimental) for 2 or 4 hours. MicroRNAs were extracted, sequenced, and compared. Both cross-time and cross-experiment analyses were performed to test the reliability and AcFBE effect, respectively. The same experiments were repeated once to ensure reliability. Messenger RNA transcriptomes were also prepared for further understanding of the nature of miRNA fluctuation.
Figure Legend Snippet: MicroRNA analysis workflow. Both experimental and control cells were treated, or untreated (control, DMSO alone was added), with 500 µg/ml AcFBE (experimental) for 2 or 4 hours. MicroRNAs were extracted, sequenced, and compared. Both cross-time and cross-experiment analyses were performed to test the reliability and AcFBE effect, respectively. The same experiments were repeated once to ensure reliability. Messenger RNA transcriptomes were also prepared for further understanding of the nature of miRNA fluctuation.

Techniques Used:

Transcriptome analyses of SK-HEP-1 liver cancer cells treated or untreated with AcFBE. All transcriptomes were analyzed with RNA-Seq approach. The expression level of an mRNA is represented as FPKM (fragments per kilo base of exon per million fragments mapped). ( A ) Scatter plots reveal a linear correlation in mRNA expression between AcFBE-untreated SK-HEP-1 samples (2U vs. 4U) and also between AcFBE-treated SK-HEP-1 samples (2T vs. 4T). The correlation coefficient (R) and P-value of each library were calculated using Student's t-test. The profile of treated sample seems to be less scattered than the untreated sample.( B ) Box plots show the expression distribution and median (inside parenthesis) for each transcriptome library.
Figure Legend Snippet: Transcriptome analyses of SK-HEP-1 liver cancer cells treated or untreated with AcFBE. All transcriptomes were analyzed with RNA-Seq approach. The expression level of an mRNA is represented as FPKM (fragments per kilo base of exon per million fragments mapped). ( A ) Scatter plots reveal a linear correlation in mRNA expression between AcFBE-untreated SK-HEP-1 samples (2U vs. 4U) and also between AcFBE-treated SK-HEP-1 samples (2T vs. 4T). The correlation coefficient (R) and P-value of each library were calculated using Student's t-test. The profile of treated sample seems to be less scattered than the untreated sample.( B ) Box plots show the expression distribution and median (inside parenthesis) for each transcriptome library.

Techniques Used: RNA Sequencing Assay, Expressing

5) Product Images from "Comparison of target labeling methods for use with Affymetrix GeneChips"

Article Title: Comparison of target labeling methods for use with Affymetrix GeneChips

Journal: BMC Biotechnology

doi: 10.1186/1472-6750-7-24

Overlaid Bioanalyzer electropherograms for fragmented labeled cRNA targets showing the size distribution of fragmented target. One-Cycle replicates (blue and green); Superscript replicates (orange and black); BioArray replicates (pink and turquoise). RNA ladder in red showing the lower alignment marker and the 200 and 500 base markers.
Figure Legend Snippet: Overlaid Bioanalyzer electropherograms for fragmented labeled cRNA targets showing the size distribution of fragmented target. One-Cycle replicates (blue and green); Superscript replicates (orange and black); BioArray replicates (pink and turquoise). RNA ladder in red showing the lower alignment marker and the 200 and 500 base markers.

Techniques Used: Labeling, Marker

Overlaid electropherograms from the analysis of unfragmented biotinylated cRNA products from the IVT reactions of the 3 different labeling kits by the Agilent 2100 Bioanalyzer. The replicate reactions from donor A are shown for each kit: One-Cycle data represented as blue and green line; BioArray as black and orange and Superscript by the pink and turquoise lines. 1 μl of the final volume (One-Cycle = 21 μl; BioArray = 60 μl; Superscript = 100 μl) of purified IVT reaction is loaded. The RNA ladder (peaks represented in red) contains a mixture of RNAs of known concentration and size (50 (lower marker) 200, 500, 1,000, 2,000, 4,000, and 6,000 bases from left to right).
Figure Legend Snippet: Overlaid electropherograms from the analysis of unfragmented biotinylated cRNA products from the IVT reactions of the 3 different labeling kits by the Agilent 2100 Bioanalyzer. The replicate reactions from donor A are shown for each kit: One-Cycle data represented as blue and green line; BioArray as black and orange and Superscript by the pink and turquoise lines. 1 μl of the final volume (One-Cycle = 21 μl; BioArray = 60 μl; Superscript = 100 μl) of purified IVT reaction is loaded. The RNA ladder (peaks represented in red) contains a mixture of RNAs of known concentration and size (50 (lower marker) 200, 500, 1,000, 2,000, 4,000, and 6,000 bases from left to right).

Techniques Used: Labeling, Purification, Concentration Assay, Marker

6) Product Images from "Mutation of EMG1 causing Bowen–Conradi syndrome results in reduced cell proliferation rates concomitant with G2/M arrest and 18S rRNA processing delay"

Article Title: Mutation of EMG1 causing Bowen–Conradi syndrome results in reduced cell proliferation rates concomitant with G2/M arrest and 18S rRNA processing delay

Journal: BBA Clinical

doi: 10.1016/j.bbacli.2014.05.002

Ribosomal RNA processing is delayed in BCS patient cells. (A) In fibroblasts, nascent rRNA was metabolically labeled using (methyl- 3 H) methionine for 30 min, and RNA was isolated at twenty minute intervals to follow the processing rate of the large 45S rRNA precursor to the mature 18S (arrowhead) and 28S species (arrow). Equal counts were separated on a 0.7% agarose gel, and transferred to a positively-charged nylon membrane. The membrane was exposed to a phosphor storage screen, which was scanned using a phosphorimager. The precursor 45S rRNA, the 28S and 18S mature species, and the intermediates are indicated on the left side of the diagram. A representative image of three independent experiments is shown. (B, C) The intensity of each band in (A) was quantified using Image Lab software. The graphs indicate the mean density in arbitrary units of the 18S (B) and 28S rRNA (C) bands at each time point, and the error bars represent standard deviation. For this experiment, the average of three control cell lines and two BCS cell lines are shown. The 18S rRNA level was significantly reduced in BCS cells at the 20 minute time point (*p = 0.0287). (D) A representative image of an rRNA processing experiment in lymphoblasts. The experiment was performed essentially as in (A), except the rRNA was labeled with 32 P i for a twenty minute pulse. Following gel electrophoresis to separate the RNA species, the gel was dried and directly exposed to a phosphor storage screen. (E) and (F) show the intensity of each band. The 18S rRNA was significantly reduced in BCS cells at the 40 minute time point (*p = 0.0292).
Figure Legend Snippet: Ribosomal RNA processing is delayed in BCS patient cells. (A) In fibroblasts, nascent rRNA was metabolically labeled using (methyl- 3 H) methionine for 30 min, and RNA was isolated at twenty minute intervals to follow the processing rate of the large 45S rRNA precursor to the mature 18S (arrowhead) and 28S species (arrow). Equal counts were separated on a 0.7% agarose gel, and transferred to a positively-charged nylon membrane. The membrane was exposed to a phosphor storage screen, which was scanned using a phosphorimager. The precursor 45S rRNA, the 28S and 18S mature species, and the intermediates are indicated on the left side of the diagram. A representative image of three independent experiments is shown. (B, C) The intensity of each band in (A) was quantified using Image Lab software. The graphs indicate the mean density in arbitrary units of the 18S (B) and 28S rRNA (C) bands at each time point, and the error bars represent standard deviation. For this experiment, the average of three control cell lines and two BCS cell lines are shown. The 18S rRNA level was significantly reduced in BCS cells at the 20 minute time point (*p = 0.0287). (D) A representative image of an rRNA processing experiment in lymphoblasts. The experiment was performed essentially as in (A), except the rRNA was labeled with 32 P i for a twenty minute pulse. Following gel electrophoresis to separate the RNA species, the gel was dried and directly exposed to a phosphor storage screen. (E) and (F) show the intensity of each band. The 18S rRNA was significantly reduced in BCS cells at the 40 minute time point (*p = 0.0292).

Techniques Used: Metabolic Labelling, Labeling, Isolation, Agarose Gel Electrophoresis, Software, Standard Deviation, Nucleic Acid Electrophoresis

Ribosomal RNA levels at steady-state are normal in BCS patient cells. (A, B) Total RNA was isolated from unaffected control and BCS-affected lymphoblasts (A) and fibroblasts (B), and separated by capillary chromatography using the 6000 RNA Nano kit in an Agilent Bioanalyzer. The resulting electropherograms show the 18S and 28S peaks, as well as a smaller peak which encompasses the 5S, 5.8S, and tRNA. (C, D) 28S/18S ratios for lymphoblasts (C) and fibroblasts (D). The area of each peak was calculated by the Agilent software, and the ratios of 28S to 18S rRNA were calculated. The mean of three individual experiments, performed in triplicate, and SEM are shown. No significant difference was found between the control and BCS patient cells.
Figure Legend Snippet: Ribosomal RNA levels at steady-state are normal in BCS patient cells. (A, B) Total RNA was isolated from unaffected control and BCS-affected lymphoblasts (A) and fibroblasts (B), and separated by capillary chromatography using the 6000 RNA Nano kit in an Agilent Bioanalyzer. The resulting electropherograms show the 18S and 28S peaks, as well as a smaller peak which encompasses the 5S, 5.8S, and tRNA. (C, D) 28S/18S ratios for lymphoblasts (C) and fibroblasts (D). The area of each peak was calculated by the Agilent software, and the ratios of 28S to 18S rRNA were calculated. The mean of three individual experiments, performed in triplicate, and SEM are shown. No significant difference was found between the control and BCS patient cells.

Techniques Used: Isolation, Chromatography, Software

7) Product Images from "MiRNAs and piRNAs from bone marrow mesenchymal stem cell extracellular vesicles induce cell survival and inhibit cell differentiation of cord blood hematopoietic stem cells: a new insight in transplantation"

Article Title: MiRNAs and piRNAs from bone marrow mesenchymal stem cell extracellular vesicles induce cell survival and inhibit cell differentiation of cord blood hematopoietic stem cells: a new insight in transplantation

Journal: Oncotarget

doi: 10.18632/oncotarget.6791

Bioanalyzer profile and small RNA sequencing of BM-MSC derived EVs Representative bioanalyzer profile of the RNAs contained in BM-MSC ( A ) and in BM-MSC-EVs ( B ). The electropherograms show the size distribution in nucleotides (nt) and fluorescence intensity (FU) of total RNA. The short peak at 25 nt is an internal standard. In BM-MSC the most dominant peaks are the 18S and 28S ribosomal RNA, whereas in EVs is the small RNAs peak respect to the absent rRNA peaks. ( C ) Representative bioanalyzer profile of small RNAs performed on EVs derived from BM-MSC showing an enrichment of small RNAs of the size of miRNAs in respect to the cells of origin. Three different samples of cells and EVs were analyzed. ( D ) Pie-charts showing the percentage of small RNA species identified in BM-MSC-EVs by small RNA sequencing. ( E ) Mature miRNA list obtained by sequencing BM-MSC-EVs small RNA content. The 87 microRNAs, obtained by miRanalyzer, were subdivided in quartiles on the base of readCount numbers and the most representative (1st quartile) were used in the integrated analysis with gene expression profile. ( F ) piRNA list obtained by sequencing BM-MSC-EVs small RNA content with readCount more than five.
Figure Legend Snippet: Bioanalyzer profile and small RNA sequencing of BM-MSC derived EVs Representative bioanalyzer profile of the RNAs contained in BM-MSC ( A ) and in BM-MSC-EVs ( B ). The electropherograms show the size distribution in nucleotides (nt) and fluorescence intensity (FU) of total RNA. The short peak at 25 nt is an internal standard. In BM-MSC the most dominant peaks are the 18S and 28S ribosomal RNA, whereas in EVs is the small RNAs peak respect to the absent rRNA peaks. ( C ) Representative bioanalyzer profile of small RNAs performed on EVs derived from BM-MSC showing an enrichment of small RNAs of the size of miRNAs in respect to the cells of origin. Three different samples of cells and EVs were analyzed. ( D ) Pie-charts showing the percentage of small RNA species identified in BM-MSC-EVs by small RNA sequencing. ( E ) Mature miRNA list obtained by sequencing BM-MSC-EVs small RNA content. The 87 microRNAs, obtained by miRanalyzer, were subdivided in quartiles on the base of readCount numbers and the most representative (1st quartile) were used in the integrated analysis with gene expression profile. ( F ) piRNA list obtained by sequencing BM-MSC-EVs small RNA content with readCount more than five.

Techniques Used: RNA Sequencing Assay, Derivative Assay, Fluorescence, Sequencing, Expressing

8) Product Images from "Long-term storage of blood RNA collected in RNA stabilizing Tempus tubes in a large biobank – evaluation of RNA quality and stability"

Article Title: Long-term storage of blood RNA collected in RNA stabilizing Tempus tubes in a large biobank – evaluation of RNA quality and stability

Journal: BMC Research Notes

doi: 10.1186/1756-0500-7-633

Long-term storage effects on RNA integrity. RIN values for RNA samples isolated from Tempus tubes stored at –80°C until analyzed by Agilent 2100 Bioanalyzer. RIN values for adult blood samples (n = 15 Tempus tubes/year) and RIN values for cord blood samples (n = 6 Tempus tubes/year). Bars represent means ± SE. The average RIN values for adult and cord blood samples were 7.6 ± 0.5 and 7.7 ± 0.7, respectively, and no significant long-term storage related effects on RNA integrity were observed.
Figure Legend Snippet: Long-term storage effects on RNA integrity. RIN values for RNA samples isolated from Tempus tubes stored at –80°C until analyzed by Agilent 2100 Bioanalyzer. RIN values for adult blood samples (n = 15 Tempus tubes/year) and RIN values for cord blood samples (n = 6 Tempus tubes/year). Bars represent means ± SE. The average RIN values for adult and cord blood samples were 7.6 ± 0.5 and 7.7 ± 0.7, respectively, and no significant long-term storage related effects on RNA integrity were observed.

Techniques Used: Isolation

9) Product Images from "High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis"

Article Title: High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis

Journal: Arthritis Research & Therapy

doi:

Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .
Figure Legend Snippet: Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Derivative Assay

10) Product Images from "Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis"

Article Title: Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis

Journal: Genes

doi: 10.3390/genes10010026

To produce stable isotope-labeled internal standards (SILIS), Escherichia coli ( E. coli ) or Saccharomyces cerevisiae ( S. cerevisiae ) were cultured in isotope labeled media using nutrients with the highest isotope-purity possible. The total RNA was isolated and then separated into transfer RNA (tRNA) or large/ribosomal RNA through size exclusion chromatography. (* indicates 5.8 and 5S rRNA and # phenol) The different RNAs were enzymatically digested into nucleosides and analyzed by liquid chromatography–mass spectrometry (LC–MS/MS).
Figure Legend Snippet: To produce stable isotope-labeled internal standards (SILIS), Escherichia coli ( E. coli ) or Saccharomyces cerevisiae ( S. cerevisiae ) were cultured in isotope labeled media using nutrients with the highest isotope-purity possible. The total RNA was isolated and then separated into transfer RNA (tRNA) or large/ribosomal RNA through size exclusion chromatography. (* indicates 5.8 and 5S rRNA and # phenol) The different RNAs were enzymatically digested into nucleosides and analyzed by liquid chromatography–mass spectrometry (LC–MS/MS).

Techniques Used: Labeling, Cell Culture, Isolation, Size-exclusion Chromatography, Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy

11) Product Images from "MicroRNA in exosomes isolated directly from the liver circulation in patients with metastatic uveal melanoma"

Article Title: MicroRNA in exosomes isolated directly from the liver circulation in patients with metastatic uveal melanoma

Journal: BMC Cancer

doi: 10.1186/1471-2407-14-962

RNA profile of liver perfusate exosomes. (A) A representative Bioanalyzer electropherogram of liver perfusate exosomes, showing a classical exosomal RNA profile, lacking the ribosomal 18S and 28S subunits, and enriched in lower molecular weight RNAs. (B) Cluster analysis of the miRNAs found in exosomes from patients and cell lines, showing a clear similarity between the patients. (C) A close-up of a specific portion of the cluster analysis, highlighting three miRNA clusters. Cluster 3 shows miRNAs that are more associated with patients than control cell lines. Abbreviations: P1-9 = Patient 1 to 9, C1-3 = Cluster 1 to 3, NI = Not identified.
Figure Legend Snippet: RNA profile of liver perfusate exosomes. (A) A representative Bioanalyzer electropherogram of liver perfusate exosomes, showing a classical exosomal RNA profile, lacking the ribosomal 18S and 28S subunits, and enriched in lower molecular weight RNAs. (B) Cluster analysis of the miRNAs found in exosomes from patients and cell lines, showing a clear similarity between the patients. (C) A close-up of a specific portion of the cluster analysis, highlighting three miRNA clusters. Cluster 3 shows miRNAs that are more associated with patients than control cell lines. Abbreviations: P1-9 = Patient 1 to 9, C1-3 = Cluster 1 to 3, NI = Not identified.

Techniques Used: Molecular Weight

12) Product Images from "Stage-Regulated GFP Expression in Trypanosoma cruzi: Applications from Host-Parasite Interactions to Drug Screening"

Article Title: Stage-Regulated GFP Expression in Trypanosoma cruzi: Applications from Host-Parasite Interactions to Drug Screening

Journal: PLoS ONE

doi: 10.1371/journal.pone.0067441

Integration of the green fluorescent protein (GFP) gene following parasite transfection. (A) Schematic representation of the pBEX/GFP construct. The expression vector has the Trypanosoma cruzi 18S ribosomal sequences flanking the intergenic regions between the alpha and beta tubulin genes that provides the spliced leader and polyadenylation sites for the GFP mRNA and the neomycin resistance gene (NeoR) used as a selectable marker. (B and C) Southern-blot analyses of transfected parasites. High-molecular weight DNA, isolated from wild-type (WT) epimastigotes of T. cruzi Dm28c (B1 and C1) and Dm28c transfected (T) with pBEX/GFP (fluorescent epimastigotes) (B2 and C2) were separated by PFGE and stained with ethidium bromide. The bands were transferred to nylon membranes and hybridized with [ 32 P]-labeled probes corresponding to the 24S alpha rDNA (B3 and B4), 18S rDNA (C3 and C4) and GFP (B5, B6, C5 and C6) sequences. (D) Total RNA was isolated from wild-type epimastigotes and pBEX fluorescent epimastigotes and analyzed with an Agilent 2100 Bioanalyzer; data are displayed as a densitometry plot (gel-like image). In this analysis, the fluorescent parasites display a rRNA band pattern (D3) similar to that of the wild-type parasites (D2), suggesting that the mobility shift of the 1.4 Mbp chromosome did not affect the production of functional rRNA molecules. D1 = molecular weight marker.
Figure Legend Snippet: Integration of the green fluorescent protein (GFP) gene following parasite transfection. (A) Schematic representation of the pBEX/GFP construct. The expression vector has the Trypanosoma cruzi 18S ribosomal sequences flanking the intergenic regions between the alpha and beta tubulin genes that provides the spliced leader and polyadenylation sites for the GFP mRNA and the neomycin resistance gene (NeoR) used as a selectable marker. (B and C) Southern-blot analyses of transfected parasites. High-molecular weight DNA, isolated from wild-type (WT) epimastigotes of T. cruzi Dm28c (B1 and C1) and Dm28c transfected (T) with pBEX/GFP (fluorescent epimastigotes) (B2 and C2) were separated by PFGE and stained with ethidium bromide. The bands were transferred to nylon membranes and hybridized with [ 32 P]-labeled probes corresponding to the 24S alpha rDNA (B3 and B4), 18S rDNA (C3 and C4) and GFP (B5, B6, C5 and C6) sequences. (D) Total RNA was isolated from wild-type epimastigotes and pBEX fluorescent epimastigotes and analyzed with an Agilent 2100 Bioanalyzer; data are displayed as a densitometry plot (gel-like image). In this analysis, the fluorescent parasites display a rRNA band pattern (D3) similar to that of the wild-type parasites (D2), suggesting that the mobility shift of the 1.4 Mbp chromosome did not affect the production of functional rRNA molecules. D1 = molecular weight marker.

Techniques Used: Transfection, Construct, Expressing, Plasmid Preparation, Marker, Southern Blot, Molecular Weight, Isolation, Staining, Labeling, Mobility Shift, Functional Assay

13) Product Images from "A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis"

Article Title: A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis

Journal: Scientific Data

doi: 10.1038/sdata.2016.103

High quality RNA was extracted from a single cornea, and was sufficient for whole transcriptome analysis. All CHIPs passed the initial quality checks. ( a ) RNA purity as determined by Nanodrop 2000, ( b ) is the gel size separation of the 18S and 28S subunits shown as distinct bands, and S, integration number. Results in b were obtained using RNA 6000 pico kit following the eukaryote total RNA Pico assay. ( c ) Boxplot of four of Affymetrix Spike-In controls, lys-M, phe-M, thr-M and dap-M illustrating the range of signal (log2) over the experiment as well as quality control of the arrays technical run. ( d ) Illustrates the Pearsson Correlation for all samples after DABG correction and RMA normalization (figure constructed using R/Bioconducter and package pheatmap). ( e , f ) Boxplot showing raw log 2 Probe Cell Intensities, before ( e ) and after the DABG correction and RMA normalized log 2 Expression Signal ( f ) for all samples.
Figure Legend Snippet: High quality RNA was extracted from a single cornea, and was sufficient for whole transcriptome analysis. All CHIPs passed the initial quality checks. ( a ) RNA purity as determined by Nanodrop 2000, ( b ) is the gel size separation of the 18S and 28S subunits shown as distinct bands, and S, integration number. Results in b were obtained using RNA 6000 pico kit following the eukaryote total RNA Pico assay. ( c ) Boxplot of four of Affymetrix Spike-In controls, lys-M, phe-M, thr-M and dap-M illustrating the range of signal (log2) over the experiment as well as quality control of the arrays technical run. ( d ) Illustrates the Pearsson Correlation for all samples after DABG correction and RMA normalization (figure constructed using R/Bioconducter and package pheatmap). ( e , f ) Boxplot showing raw log 2 Probe Cell Intensities, before ( e ) and after the DABG correction and RMA normalized log 2 Expression Signal ( f ) for all samples.

Techniques Used: Construct, Expressing

14) Product Images from "Steps to achieve quantitative measurements of microRNA using two step droplet digital PCR"

Article Title: Steps to achieve quantitative measurements of microRNA using two step droplet digital PCR

Journal: PLoS ONE

doi: 10.1371/journal.pone.0188085

Quantitative miRNA measurements in THP-1 cells. Total RNA was extracted from macrophage derived THP-1 cells and was (A) analyzed for integrity, purity, and concentration using the chip-based automated electrophoresis system. (B) Total RNA was reverse transcribed by cDNA synthesis kit “A”, “B”, or “C” and specific miRNA targets were measured using ddPCR. (C) Each kit, “A” (×), “B” (+), and”C” (ӿ), was used to make cDNA and total number of targets were counted via ddPCR. Average NTC and NEC were similarly measured for each experiment. For all targets, cel-miR-238 (gray), cel-miR-39 (orange), hsa-miR-223 (brown), and hsa-miR-155 (red), fraction positive targets per droplet were calculated by subtracting NEC and NTC positive and applying Poisson distribution. Predicted 10 4 miRNA copies/μL for cel-miR-238 (gray square), cel-miR-39 (orange square), and hsa-miR-223 (brown square) was calculated using pre-existing power curve values ( Table 6 ). For each respective kit, a new power curve was developed using experimental versus predicted cel-mir-238, cel-miR-39, and hsa-miR-223 concentration ( Table 7 ). This new power curve was applied to respective, endogenously measured, experimental hsa-miR-155 λ’ to generate predicted hsa-miR-155 (red circle) copies/μL. The standard uncertainty is shown on the graph for hsa-miR-155 for each respective point (dark red line). For visualization purposes, data is either graphed on one chart or separated out based on cDNA synthesis kit. New power models are calculated only for individual cDNA synthesis kits and both equation and correlation coefficient are interlayered. Graphs are single representations of repeated biological trials. Microsoft Excel was used to calculate and graph data.
Figure Legend Snippet: Quantitative miRNA measurements in THP-1 cells. Total RNA was extracted from macrophage derived THP-1 cells and was (A) analyzed for integrity, purity, and concentration using the chip-based automated electrophoresis system. (B) Total RNA was reverse transcribed by cDNA synthesis kit “A”, “B”, or “C” and specific miRNA targets were measured using ddPCR. (C) Each kit, “A” (×), “B” (+), and”C” (ӿ), was used to make cDNA and total number of targets were counted via ddPCR. Average NTC and NEC were similarly measured for each experiment. For all targets, cel-miR-238 (gray), cel-miR-39 (orange), hsa-miR-223 (brown), and hsa-miR-155 (red), fraction positive targets per droplet were calculated by subtracting NEC and NTC positive and applying Poisson distribution. Predicted 10 4 miRNA copies/μL for cel-miR-238 (gray square), cel-miR-39 (orange square), and hsa-miR-223 (brown square) was calculated using pre-existing power curve values ( Table 6 ). For each respective kit, a new power curve was developed using experimental versus predicted cel-mir-238, cel-miR-39, and hsa-miR-223 concentration ( Table 7 ). This new power curve was applied to respective, endogenously measured, experimental hsa-miR-155 λ’ to generate predicted hsa-miR-155 (red circle) copies/μL. The standard uncertainty is shown on the graph for hsa-miR-155 for each respective point (dark red line). For visualization purposes, data is either graphed on one chart or separated out based on cDNA synthesis kit. New power models are calculated only for individual cDNA synthesis kits and both equation and correlation coefficient are interlayered. Graphs are single representations of repeated biological trials. Microsoft Excel was used to calculate and graph data.

Techniques Used: Derivative Assay, Concentration Assay, Chromatin Immunoprecipitation, Electrophoresis

Procedure for analyzing microRNA (miRNA) in a clinical sample. (A) Prepare samples either by isolating total RNA from cells or acquiring synthetic miRNA oligonucleotides. miRNA spike-in controls are added at different points within the RNA extraction process to control for loss of material associated with different steps. (B) cDNA is synthesized using miRNA-specific cDNA synthesis kits. The kits contain reagents that will add adaptor sequences onto the target miRNA so that primers and probes can respectively bind either during cDNA synthesis or during PCR steps. All cDNA synthesis kits show signs of non-specific cDNA products so it is recommended to create one reaction without RNA template (NTC) and one reaction without enzymes (NEC) for each round of cDNA synthesis. (C) Droplet digital PCR (ddPCR) is done by taking the cDNA synthesized from miRNA template and creating water-in-oil droplets that each contain zero to a few target sequences. The cDNA template might need to be diluted to obtain the optimal number of targets per droplet. Results are reported as florescence intensity. Either the user or the instrument software can define a threshold. Droplets that fluoresce at an amplitude higher than the defined threshold will be positive for target sequence and those below threshold are negative for target sequence [ 16 ]. (D) Average fraction positive droplet in both the NTC and NEC are subtracted from sample of interest and Poisson distribution can be applied to the remaining fraction negative total droplets. The resultant is the targets per droplet (λ’) and can then be manipulated to give targets per microliter, copies of cDNA per microliter, copies of miRNA per microliter, and concentration. By performing a titration of synthetic miRNA oligonucleotide with a known concentration, one can create a power model that defines how much miRNA input corresponds to a miRNA value following ddPCR. This model will account for any loss assumed in both cDNA synthesis and ddPCR steps. (E) A clinical sample is processed using spike-in controls and validated endogenous miRNA measurements that have been titrated previously. A 96-well plate for a sample contains primers and probes to measure sample-specific values for spike-in controls and validated endogenous. These experimental values are inserted into the power model developed during miRNA titration and converted to predicted values. Graphing experimental targets per droplet (λ’) versus predicted miRNA copies/μL of validated spike-in or endogenous miRNA generates a new power curve that can be applied to all remaining sample targets of interest. These resultants are finite miRNA copy number. Values can be extrapolated to concentration or measurement per cell number using the Avogadro constant or previously measured cell number. Results can be used for clinical diagnosis, prognosis, or treatment purposes.
Figure Legend Snippet: Procedure for analyzing microRNA (miRNA) in a clinical sample. (A) Prepare samples either by isolating total RNA from cells or acquiring synthetic miRNA oligonucleotides. miRNA spike-in controls are added at different points within the RNA extraction process to control for loss of material associated with different steps. (B) cDNA is synthesized using miRNA-specific cDNA synthesis kits. The kits contain reagents that will add adaptor sequences onto the target miRNA so that primers and probes can respectively bind either during cDNA synthesis or during PCR steps. All cDNA synthesis kits show signs of non-specific cDNA products so it is recommended to create one reaction without RNA template (NTC) and one reaction without enzymes (NEC) for each round of cDNA synthesis. (C) Droplet digital PCR (ddPCR) is done by taking the cDNA synthesized from miRNA template and creating water-in-oil droplets that each contain zero to a few target sequences. The cDNA template might need to be diluted to obtain the optimal number of targets per droplet. Results are reported as florescence intensity. Either the user or the instrument software can define a threshold. Droplets that fluoresce at an amplitude higher than the defined threshold will be positive for target sequence and those below threshold are negative for target sequence [ 16 ]. (D) Average fraction positive droplet in both the NTC and NEC are subtracted from sample of interest and Poisson distribution can be applied to the remaining fraction negative total droplets. The resultant is the targets per droplet (λ’) and can then be manipulated to give targets per microliter, copies of cDNA per microliter, copies of miRNA per microliter, and concentration. By performing a titration of synthetic miRNA oligonucleotide with a known concentration, one can create a power model that defines how much miRNA input corresponds to a miRNA value following ddPCR. This model will account for any loss assumed in both cDNA synthesis and ddPCR steps. (E) A clinical sample is processed using spike-in controls and validated endogenous miRNA measurements that have been titrated previously. A 96-well plate for a sample contains primers and probes to measure sample-specific values for spike-in controls and validated endogenous. These experimental values are inserted into the power model developed during miRNA titration and converted to predicted values. Graphing experimental targets per droplet (λ’) versus predicted miRNA copies/μL of validated spike-in or endogenous miRNA generates a new power curve that can be applied to all remaining sample targets of interest. These resultants are finite miRNA copy number. Values can be extrapolated to concentration or measurement per cell number using the Avogadro constant or previously measured cell number. Results can be used for clinical diagnosis, prognosis, or treatment purposes.

Techniques Used: RNA Extraction, Synthesized, Polymerase Chain Reaction, Digital PCR, Software, Sequencing, Concentration Assay, Titration

15) Product Images from "Levels of sdRNAs in cytoplasm and their association with ribosomes are dependent upon stress conditions but independent from snoRNA expression"

Article Title: Levels of sdRNAs in cytoplasm and their association with ribosomes are dependent upon stress conditions but independent from snoRNA expression

Journal: Scientific Reports

doi: 10.1038/s41598-019-54924-2

RNA length composition of the P100 (ribosome-enriched pellet) and S100 (ribosome-depleted supernatant) fractions derived from the lysates of native and stressed cells. RNA was isolated with TRI Reagent and subjected to Agilent RNA 6000 Nano assay. The bands corresponding to ribosomal RNAs (18 S rRNA of ~2000 bp and 26 S rRNA of ~3,800 bp) are visible in P100 fraction. Low molecular weight RNAs, up to 200 bp are mostly present in S100 fraction.
Figure Legend Snippet: RNA length composition of the P100 (ribosome-enriched pellet) and S100 (ribosome-depleted supernatant) fractions derived from the lysates of native and stressed cells. RNA was isolated with TRI Reagent and subjected to Agilent RNA 6000 Nano assay. The bands corresponding to ribosomal RNAs (18 S rRNA of ~2000 bp and 26 S rRNA of ~3,800 bp) are visible in P100 fraction. Low molecular weight RNAs, up to 200 bp are mostly present in S100 fraction.

Techniques Used: Derivative Assay, Isolation, Molecular Weight

Differential accumulation of snoRNAs and sdRNAs in S30, S100 and P100 fractions. Values are means of replicates that are fully presented in Figs. 2 , 5 and 7 .
Figure Legend Snippet: Differential accumulation of snoRNAs and sdRNAs in S30, S100 and P100 fractions. Values are means of replicates that are fully presented in Figs. 2 , 5 and 7 .

Techniques Used:

16) Product Images from "METHOD FOR MICRORNA ISOLATION FROM CLINICAL SERUM SAMPLES"

Article Title: METHOD FOR MICRORNA ISOLATION FROM CLINICAL SERUM SAMPLES

Journal: Analytical biochemistry

doi: 10.1016/j.ab.2012.09.007

RNA quality A: Left . Fluorescence intensity of small RNA fractions at different sizes. Two dash-lines (10–150 nt) indicate the size range for small RNA measurement. The lower marker peak centered at 4 nt is partially shown. Right. Gel electrophoresis analysis of small RNA fractions on an Agilent small RNA chip. Gel images demonstrate small RNA profiles of RNA samples isolated by Qiagen, Ambion and Norgen kits. The “Gel Enhanced View” function of Bioanalyzer was turned on to show low abundant RNA species. It is a representation of three repeat extractions. B: Percentage of microRNA in small RNA fractions. Small RNA and microRNA were defined as RNA species in size between 10 nt and 150 nt, and between 14 nt and 29 nt, respectively. The quantification of each RNA species was performed using a Bioanalyzer. A student t-test was performed to evaluate statistical significance. The percentage was an average of three repeat extractions.
Figure Legend Snippet: RNA quality A: Left . Fluorescence intensity of small RNA fractions at different sizes. Two dash-lines (10–150 nt) indicate the size range for small RNA measurement. The lower marker peak centered at 4 nt is partially shown. Right. Gel electrophoresis analysis of small RNA fractions on an Agilent small RNA chip. Gel images demonstrate small RNA profiles of RNA samples isolated by Qiagen, Ambion and Norgen kits. The “Gel Enhanced View” function of Bioanalyzer was turned on to show low abundant RNA species. It is a representation of three repeat extractions. B: Percentage of microRNA in small RNA fractions. Small RNA and microRNA were defined as RNA species in size between 10 nt and 150 nt, and between 14 nt and 29 nt, respectively. The quantification of each RNA species was performed using a Bioanalyzer. A student t-test was performed to evaluate statistical significance. The percentage was an average of three repeat extractions.

Techniques Used: Fluorescence, Marker, Nucleic Acid Electrophoresis, Chromatin Immunoprecipitation, Isolation

17) Product Images from "Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling"

Article Title: Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling

Journal: BMC Genomics

doi: 10.1186/1471-2164-5-9

Effect of aRNA purity and labelled-aRNA purification . (A) Graph showing coupling efficiency (C) and 320/650 (B) values for six MCF-7 aRNA samples with different 260/280 ratios. (B) Agilent Bioanalyzer pattern of MCF-7 Cy5-labelled target using an aRNA with 260/280 ratio of 1.6. Sharp spikes represent uncoupled Cy5 dye. (C) Same as B for aRNA with 260/280 ratio of 2 and coupling efficiency near 1. (D) NanoDrop ® ND-1000 Spectrophotometer absorptions at 320 and 650 nm wavelengths of a MCF-7 Cy5-labelled target. 320/650 ratio-0.6. (E) Same as in d (different sample). 320/650 ratio-0.09. (F) Recovery rates (R) and coupling efficiencies (C) for different labelled-aRNA purification methods. Data is presented for MCF-7 cell line and measurements represent an average of three separate reactions. Li-ETOH – LiCl-ethanol; PCI – phenol/chloroform/isoamyl alcohol.
Figure Legend Snippet: Effect of aRNA purity and labelled-aRNA purification . (A) Graph showing coupling efficiency (C) and 320/650 (B) values for six MCF-7 aRNA samples with different 260/280 ratios. (B) Agilent Bioanalyzer pattern of MCF-7 Cy5-labelled target using an aRNA with 260/280 ratio of 1.6. Sharp spikes represent uncoupled Cy5 dye. (C) Same as B for aRNA with 260/280 ratio of 2 and coupling efficiency near 1. (D) NanoDrop ® ND-1000 Spectrophotometer absorptions at 320 and 650 nm wavelengths of a MCF-7 Cy5-labelled target. 320/650 ratio-0.6. (E) Same as in d (different sample). 320/650 ratio-0.09. (F) Recovery rates (R) and coupling efficiencies (C) for different labelled-aRNA purification methods. Data is presented for MCF-7 cell line and measurements represent an average of three separate reactions. Li-ETOH – LiCl-ethanol; PCI – phenol/chloroform/isoamyl alcohol.

Techniques Used: Purification, Spectrophotometry

Effect of genomic DNA contamination in total RNA . (A) 1% agarose gel of purified MCF-7 total RNA samples. L-1 kb ladder (Invitrogen); Col. – column purified RNA; D20 – DNase treated/PCI extracted (RNA concentration – 20 μg/100 μl); D5 – DNase treated/PCI extracted (RNA concentration – 5 μg/100 μl); LiCl – DNase treated/Lithium Chloride purified. (B) Agilent Bioanalyzer image of MCF-7 total RNA sample purified using column method. Arrow pointing at shoulder after 28S band indicating genomic DNA carry over. (C) 1% agarose/formamide denaturing gel of MCF-7 aRNA. L1 – 6000 RNA ladder (Ambion); L2-1 Kb ladder (Invitrogen). (D) Absorption at 260 nm of nucleic acid products derived from the 4 total RNA purification methods. 2 μg of total RNA from each of the five cell lines was amplified with and without reverse transcriptase being added to the cDNA synthesis reaction (with RT and no RT respectively). C – column; Li – LiCl precipitation; D5/D20 – as in A. Cell lines included MCF-7, ZR-75-1-1, OCUB-M, Cal51, and HCT-1187.
Figure Legend Snippet: Effect of genomic DNA contamination in total RNA . (A) 1% agarose gel of purified MCF-7 total RNA samples. L-1 kb ladder (Invitrogen); Col. – column purified RNA; D20 – DNase treated/PCI extracted (RNA concentration – 20 μg/100 μl); D5 – DNase treated/PCI extracted (RNA concentration – 5 μg/100 μl); LiCl – DNase treated/Lithium Chloride purified. (B) Agilent Bioanalyzer image of MCF-7 total RNA sample purified using column method. Arrow pointing at shoulder after 28S band indicating genomic DNA carry over. (C) 1% agarose/formamide denaturing gel of MCF-7 aRNA. L1 – 6000 RNA ladder (Ambion); L2-1 Kb ladder (Invitrogen). (D) Absorption at 260 nm of nucleic acid products derived from the 4 total RNA purification methods. 2 μg of total RNA from each of the five cell lines was amplified with and without reverse transcriptase being added to the cDNA synthesis reaction (with RT and no RT respectively). C – column; Li – LiCl precipitation; D5/D20 – as in A. Cell lines included MCF-7, ZR-75-1-1, OCUB-M, Cal51, and HCT-1187.

Techniques Used: Agarose Gel Electrophoresis, Purification, Concentration Assay, Derivative Assay, Amplification

Analysis of aRNA purification . (A) Amplified RNA yields and 260/280 ratios with 4 methods of purification. Col – column; PCI – phenol/chlorform/isoamyl alchohol; LiCl – 2.5 M LiCl; G-P – guanidinium-phenol. (B) 1% denaturing agarose/formamide gel of MCF-7 aRNA purified using column (C) Agilent Bioanalyzer analysis of aRNA (from MCF-7) purified by G-P. 6000 nano marker from Ambion (blue) superimposed on the RNA trace. (D) Plot of aRNA yield in μg for different starting total RNA quantities. C1 – OCUB-M with Col.; L1 – OCUB-M with LiCl; G1 – OCUB-M with G-P; C2 – MCF-7 with Col.; L2 – MCF-7 with LiCl; G2 – MCF-7 with G-P.
Figure Legend Snippet: Analysis of aRNA purification . (A) Amplified RNA yields and 260/280 ratios with 4 methods of purification. Col – column; PCI – phenol/chlorform/isoamyl alchohol; LiCl – 2.5 M LiCl; G-P – guanidinium-phenol. (B) 1% denaturing agarose/formamide gel of MCF-7 aRNA purified using column (C) Agilent Bioanalyzer analysis of aRNA (from MCF-7) purified by G-P. 6000 nano marker from Ambion (blue) superimposed on the RNA trace. (D) Plot of aRNA yield in μg for different starting total RNA quantities. C1 – OCUB-M with Col.; L1 – OCUB-M with LiCl; G1 – OCUB-M with G-P; C2 – MCF-7 with Col.; L2 – MCF-7 with LiCl; G2 – MCF-7 with G-P.

Techniques Used: Purification, Amplification, Marker

18) Product Images from "Limited predictability of postmortem human brain tissue quality by RNA integrity numbers"

Article Title: Limited predictability of postmortem human brain tissue quality by RNA integrity numbers

Journal: Journal of neurochemistry

doi: 10.1111/jnc.13637

RNA and cDNA analysis by Agilent 2100. Representative electropherogram and electrophoresis assays from 10 RNA and corresponding cDNA measurements used in qRT-PCR analysis. Numbers indicate brain sample identification numbers.
Figure Legend Snippet: RNA and cDNA analysis by Agilent 2100. Representative electropherogram and electrophoresis assays from 10 RNA and corresponding cDNA measurements used in qRT-PCR analysis. Numbers indicate brain sample identification numbers.

Techniques Used: Electrophoresis, Quantitative RT-PCR

19) Product Images from "Necrotizing enterocolitis is associated with acute brain responses in preterm pigs"

Article Title: Necrotizing enterocolitis is associated with acute brain responses in preterm pigs

Journal: Journal of Neuroinflammation

doi: 10.1186/s12974-018-1201-x

Hippocampal transcriptome in pigs with or without NEC. a Venn diagram indicates the number of hippocampal DEGs that were specifically related to Si-NEC (25 genes) and Co-NEC (10 genes), and two genes that were shared for both groups ( HBB and TMEM167 ). These NEC-related DEGs are listed, including the genes further validated by qPCR in a larger cohort (highlighted in light brown, n = 9–16). b Volcano plots of RNA-seq hippocampal gene expression are shown as a scatter-plot of log 2 changes in expression of NEC-affected pigs versus No NEC pigs plotted against the negative log of the q value ( n = 5–6 per group). The genes up- or downregulated with FDR-adjusted statistical q value
Figure Legend Snippet: Hippocampal transcriptome in pigs with or without NEC. a Venn diagram indicates the number of hippocampal DEGs that were specifically related to Si-NEC (25 genes) and Co-NEC (10 genes), and two genes that were shared for both groups ( HBB and TMEM167 ). These NEC-related DEGs are listed, including the genes further validated by qPCR in a larger cohort (highlighted in light brown, n = 9–16). b Volcano plots of RNA-seq hippocampal gene expression are shown as a scatter-plot of log 2 changes in expression of NEC-affected pigs versus No NEC pigs plotted against the negative log of the q value ( n = 5–6 per group). The genes up- or downregulated with FDR-adjusted statistical q value

Techniques Used: Real-time Polymerase Chain Reaction, RNA Sequencing Assay, Expressing

20) Product Images from "Nucleolin facilitates nuclear retention of an ultraconserved region containing TRA2β4 and accelerates colon cancer cell growth"

Article Title: Nucleolin facilitates nuclear retention of an ultraconserved region containing TRA2β4 and accelerates colon cancer cell growth

Journal: Oncotarget

doi: 10.18632/oncotarget.25510

Nucleolin is essential for nuclear localization of TRA2β4 ( A ) After transfection with the truncated nucleolin, the subcellular localization was measured by Western blotting. FLAG signals were quantified by densitometry. ( B ) After NMD was inhibited with cycloheximide treatment (100 μg/mL), the amounts of TRA2β4 and TRA2β1 mRNAs in the cytoplasmic or nuclear fraction were analyzed by qPCR. ( C ) Purities of the extracted nuclear and cytoplasmic fractions were confirmed by Western blotting using antibodies for cytosolic (α-tubulin) or nuclear proteins (hnRNP C1/C2) and by RT-PCR using primers targeting GAPDH pre-mRNA as a nuclear marker. ( D ) After a 24-h transfection of full-length or ΔGAR nucleolin, subcellular localization of TRA2β4 (green) and nucleolin (red) was examined by RNA-fluorescence in situ hybridization (RNA-FISH) using a probe that specifically hybridized to exon 2 (313-588 nt) and anti-FLAG antibody. Nucleoli were counterstained with TO-PRO-3. Scale bars, 5 μM.
Figure Legend Snippet: Nucleolin is essential for nuclear localization of TRA2β4 ( A ) After transfection with the truncated nucleolin, the subcellular localization was measured by Western blotting. FLAG signals were quantified by densitometry. ( B ) After NMD was inhibited with cycloheximide treatment (100 μg/mL), the amounts of TRA2β4 and TRA2β1 mRNAs in the cytoplasmic or nuclear fraction were analyzed by qPCR. ( C ) Purities of the extracted nuclear and cytoplasmic fractions were confirmed by Western blotting using antibodies for cytosolic (α-tubulin) or nuclear proteins (hnRNP C1/C2) and by RT-PCR using primers targeting GAPDH pre-mRNA as a nuclear marker. ( D ) After a 24-h transfection of full-length or ΔGAR nucleolin, subcellular localization of TRA2β4 (green) and nucleolin (red) was examined by RNA-fluorescence in situ hybridization (RNA-FISH) using a probe that specifically hybridized to exon 2 (313-588 nt) and anti-FLAG antibody. Nucleoli were counterstained with TO-PRO-3. Scale bars, 5 μM.

Techniques Used: Transfection, Western Blot, Real-time Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Marker, Fluorescence, In Situ Hybridization, Fluorescence In Situ Hybridization

Nucleolin regulates TRA2β4 expression in colon and breast cancer cells ( A ) Microarray analysis showed that NCL siRNA #1-treated cells differentially expressed 2,493 genes (≥ 1.5-fold), compared with control siRNA-treated cells. TRA2β4 -silenced cells altered the expression of 3,044 genes (≥ 1.5-fold). A total of 630 genes were commonly changed in the same direction between TRA2β4- and nucleolin-silenced cells. ( B ) Commonly regulated 630 genes were subjected to Ingenuity Pathway Analysis (QIAGEN Bioinformatics) to identify biologically relevant functions. ( C ) Using colon adenocarcinoma TissueScan Tissue qPCR arrays (HCRT103, OriGene), NCL and ACTB mRNAs were measured by qPCR. ACTB mRNA was used as an endogenous quality control. * Significantly different by paired Student's t -test ( p
Figure Legend Snippet: Nucleolin regulates TRA2β4 expression in colon and breast cancer cells ( A ) Microarray analysis showed that NCL siRNA #1-treated cells differentially expressed 2,493 genes (≥ 1.5-fold), compared with control siRNA-treated cells. TRA2β4 -silenced cells altered the expression of 3,044 genes (≥ 1.5-fold). A total of 630 genes were commonly changed in the same direction between TRA2β4- and nucleolin-silenced cells. ( B ) Commonly regulated 630 genes were subjected to Ingenuity Pathway Analysis (QIAGEN Bioinformatics) to identify biologically relevant functions. ( C ) Using colon adenocarcinoma TissueScan Tissue qPCR arrays (HCRT103, OriGene), NCL and ACTB mRNAs were measured by qPCR. ACTB mRNA was used as an endogenous quality control. * Significantly different by paired Student's t -test ( p

Techniques Used: Expressing, Microarray, Real-time Polymerase Chain Reaction

21) Product Images from "Blood Transcriptional Signatures for Disease Progression in a Rat Model of Osteoarthritis"

Article Title: Blood Transcriptional Signatures for Disease Progression in a Rat Model of Osteoarthritis

Journal: International Journal of Genomics

doi: 10.1155/2017/1746426

Gene expression patterns in blood associated with OA progression in the rat model of the knee joint arthritis. Hierarchical clustering of MIA-induced transcriptional alterations in whole blood. Microarray results are shown as a heat map and include 41 transcripts with significantly different levels of transcript abundance. Colored rectangles represent transcript abundance 2, 14, 21, and 28 days after the intra-articular injection of the MIA of the gene labeled on the right. The intensity of the color is proportional to the standardized values (between −3 and 3) from each microarray, as indicated on the bar below the heat map image. Hierarchical clustering was performed with the dChip software using Euclidean distance and average linkage method. Major MIA-induced gene transcription patterns are arbitrarily described as A–C. The regulated genes from gene clusters A–C were labeled on the right.
Figure Legend Snippet: Gene expression patterns in blood associated with OA progression in the rat model of the knee joint arthritis. Hierarchical clustering of MIA-induced transcriptional alterations in whole blood. Microarray results are shown as a heat map and include 41 transcripts with significantly different levels of transcript abundance. Colored rectangles represent transcript abundance 2, 14, 21, and 28 days after the intra-articular injection of the MIA of the gene labeled on the right. The intensity of the color is proportional to the standardized values (between −3 and 3) from each microarray, as indicated on the bar below the heat map image. Hierarchical clustering was performed with the dChip software using Euclidean distance and average linkage method. Major MIA-induced gene transcription patterns are arbitrarily described as A–C. The regulated genes from gene clusters A–C were labeled on the right.

Techniques Used: Expressing, Microarray, Injection, Labeling, Software

Gene expression profiles of three genes regulated in both animal model and human blood samples. (a) Clustering of the OA patients based on the expression of three genes commonly regulated in the blood of rats and humans. mRNA abundance levels measured by the microarrays were obtained from the GARP study [ 11 ]. The dataset consists of blood gene expression profiles of 106 OA patients and 33 controls (OA samples were indicated by green while controls by violet colors). The intensity of the color is proportional to the standardized values (between −3 and 3) from each microarray, as indicated on the bar below the heat map image. Hierarchical clustering was performed with the dChip software using correlation distance metric and centroid linkage method. (b) Time course of gene expression alterations in rat blood of the selected genes. The profiles of individual animals are presented ( n = 5).
Figure Legend Snippet: Gene expression profiles of three genes regulated in both animal model and human blood samples. (a) Clustering of the OA patients based on the expression of three genes commonly regulated in the blood of rats and humans. mRNA abundance levels measured by the microarrays were obtained from the GARP study [ 11 ]. The dataset consists of blood gene expression profiles of 106 OA patients and 33 controls (OA samples were indicated by green while controls by violet colors). The intensity of the color is proportional to the standardized values (between −3 and 3) from each microarray, as indicated on the bar below the heat map image. Hierarchical clustering was performed with the dChip software using correlation distance metric and centroid linkage method. (b) Time course of gene expression alterations in rat blood of the selected genes. The profiles of individual animals are presented ( n = 5).

Techniques Used: Expressing, Animal Model, Microarray, Software

22) Product Images from "Quantification of Small Non-Coding RNAs Allows an Accurate Comparison of miRNA Expression Profiles"

Article Title: Quantification of Small Non-Coding RNAs Allows an Accurate Comparison of miRNA Expression Profiles

Journal: Journal of Biomedicine and Biotechnology

doi: 10.1155/2009/659028

Agilent 2100 Bioanalyzer electropherogram profiles of total RNA samples (HeLa cells) extracted with TRIzol reagent (green), MirVana kit (blue), and RNEasy kit (red). Inbox: magnification of small RNA profiles for the three samples (between 23 and 29 seconds).
Figure Legend Snippet: Agilent 2100 Bioanalyzer electropherogram profiles of total RNA samples (HeLa cells) extracted with TRIzol reagent (green), MirVana kit (blue), and RNEasy kit (red). Inbox: magnification of small RNA profiles for the three samples (between 23 and 29 seconds).

Techniques Used:

(a) Gel electrophoresis (polyacrylamide 15% stained with ethidium bromide) of LMW RNA samples (LCL) extracted with TRIzol reagent (lane 1), RNEasy kit (lane 2), and small RNA fraction enriched with MirVana kit (lane 3). LMW profile obtained with MirVana kit extraction is similar to that obtained with TRIzol reagent which is not shown for clarity. (b) Agilent 2100 Bioanalyzer electropherogram profile of LMW RNAs (LCL) extracted with TRIzol (black) superimposed on 5.8S (red), 5S (green), and tRNA (blue) bands eluted from polyacrylamide gel. (c) Lymphoblastoid (LCL) LMW RNA profile obtained after plotting the exported raw data from Agilent electropherogram ( ) together with the PeakFit fitted curve (solid line) and the component peak functions. Seven peaks below the LMW RNA profile were fitted by the software ( r 2 = 0.998693).
Figure Legend Snippet: (a) Gel electrophoresis (polyacrylamide 15% stained with ethidium bromide) of LMW RNA samples (LCL) extracted with TRIzol reagent (lane 1), RNEasy kit (lane 2), and small RNA fraction enriched with MirVana kit (lane 3). LMW profile obtained with MirVana kit extraction is similar to that obtained with TRIzol reagent which is not shown for clarity. (b) Agilent 2100 Bioanalyzer electropherogram profile of LMW RNAs (LCL) extracted with TRIzol (black) superimposed on 5.8S (red), 5S (green), and tRNA (blue) bands eluted from polyacrylamide gel. (c) Lymphoblastoid (LCL) LMW RNA profile obtained after plotting the exported raw data from Agilent electropherogram ( ) together with the PeakFit fitted curve (solid line) and the component peak functions. Seven peaks below the LMW RNA profile were fitted by the software ( r 2 = 0.998693).

Techniques Used: Nucleic Acid Electrophoresis, Staining, Software

23) Product Images from "Total RNA Isolation from Separately Established Monolayer and Hydrogel Cultures of Human Glioblastoma Cell Line"

Article Title: Total RNA Isolation from Separately Established Monolayer and Hydrogel Cultures of Human Glioblastoma Cell Line

Journal: Bio-protocol

doi: 10.21769/BioProtoc.3305

Electropherograms showing the quality of total RNA extracted from monolayer and hydrogel cultures. The total RNA was extracted from monolayer and hydrogel cultures of astrocytoma cell line, CCF-STTG1. One microliter of total RNA per sample was analyzed using Agilent Bioanalyzer. A. RNA isolated from CCF-STTG1 cells using TRIzol (Top panel) and cell recovery solution (Bottom panel). B. RNA extracted from HCC70 (breast cancer cell line) cells used as control to show that cell recovery solution works well for HCC70 cells, but not for CCFSTTG1 cells. a: 18s peak, b: 28s peak.
Figure Legend Snippet: Electropherograms showing the quality of total RNA extracted from monolayer and hydrogel cultures. The total RNA was extracted from monolayer and hydrogel cultures of astrocytoma cell line, CCF-STTG1. One microliter of total RNA per sample was analyzed using Agilent Bioanalyzer. A. RNA isolated from CCF-STTG1 cells using TRIzol (Top panel) and cell recovery solution (Bottom panel). B. RNA extracted from HCC70 (breast cancer cell line) cells used as control to show that cell recovery solution works well for HCC70 cells, but not for CCFSTTG1 cells. a: 18s peak, b: 28s peak.

Techniques Used: Isolation

24) Product Images from "Age-dependent increase in miRNA-34a expression in the posterior pole of the mouse eye"

Article Title: Age-dependent increase in miRNA-34a expression in the posterior pole of the mouse eye

Journal: Molecular Vision

doi:

Real-time PCR (RT-PCR) results for the expression of miR-34a in the aging posterior mouse eye. RT–PCR of the retina ( A ) and RPE/choroid ( B ) of isolated miRNA samples at 4, 18, 24, and 32 months of age. There were three samples (n=3) for each of the four time points, for a total of twelve animals (n=12). miRNA samples from each animal tissue at each time point were run in triplicate, resulting in each time point representing an average of nine data values. Data were normalized to a geometric mean of three control small RNAs (U6, sno-202, and sno-135) and calibrated to the 4-month-old sample. The y-axis represents the fold change compared to the 4-month-old sample. * denotes statistically significant differences (p
Figure Legend Snippet: Real-time PCR (RT-PCR) results for the expression of miR-34a in the aging posterior mouse eye. RT–PCR of the retina ( A ) and RPE/choroid ( B ) of isolated miRNA samples at 4, 18, 24, and 32 months of age. There were three samples (n=3) for each of the four time points, for a total of twelve animals (n=12). miRNA samples from each animal tissue at each time point were run in triplicate, resulting in each time point representing an average of nine data values. Data were normalized to a geometric mean of three control small RNAs (U6, sno-202, and sno-135) and calibrated to the 4-month-old sample. The y-axis represents the fold change compared to the 4-month-old sample. * denotes statistically significant differences (p

Techniques Used: Real-time Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Expressing, Isolation

25) Product Images from "Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research"

Article Title: Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research

Journal: Scientific Reports

doi: 10.1038/s41598-019-56509-5

RNA quality of cultivated tissue slices. RNA quality was determined by a Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies) and revealed good quality before the DNase digestion was performed ( a ). After the DNase digestion, the RNA quality was strongly reduced ( b ). The left graphs show untreated peritumoral brain tissue, the right graphs the corresponding GBM tissue.
Figure Legend Snippet: RNA quality of cultivated tissue slices. RNA quality was determined by a Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies) and revealed good quality before the DNase digestion was performed ( a ). After the DNase digestion, the RNA quality was strongly reduced ( b ). The left graphs show untreated peritumoral brain tissue, the right graphs the corresponding GBM tissue.

Techniques Used:

26) Product Images from "Focused Microarray Analysis of Peripheral Mononuclear Blood Cells from Churg-Strauss Syndrome Patients"

Article Title: Focused Microarray Analysis of Peripheral Mononuclear Blood Cells from Churg-Strauss Syndrome Patients

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

doi: 10.1093/dnares/dsm035

Expression profiles of PREP genes in CSS patient PBMCs. Agilent's whole human genome DNA microarray was employed for this analysis. ( A ) Presentation of mosaic tiles for the 33 and 3 PREP genes whose expressions are up-regulated ( > 1.2-fold change) or down-regulated (
Figure Legend Snippet: Expression profiles of PREP genes in CSS patient PBMCs. Agilent's whole human genome DNA microarray was employed for this analysis. ( A ) Presentation of mosaic tiles for the 33 and 3 PREP genes whose expressions are up-regulated ( > 1.2-fold change) or down-regulated (

Techniques Used: Expressing, Microarray

27) Product Images from "Identification of an optimal method for extracting RNA from human skin biopsy, using domestic pig as a model system"

Article Title: Identification of an optimal method for extracting RNA from human skin biopsy, using domestic pig as a model system

Journal: Scientific Reports

doi: 10.1038/s41598-019-56579-5

RNA quality values from human skin derived RNA samples. ( A ) RNA Integrity Numbers (RIN) obtained by applying the Agilent 2100 Bioanalyzer and RNA 6000 Nano kit. ( B ) The RNA absorbance spectrum measured with NanoDrop spectrophotometer.
Figure Legend Snippet: RNA quality values from human skin derived RNA samples. ( A ) RNA Integrity Numbers (RIN) obtained by applying the Agilent 2100 Bioanalyzer and RNA 6000 Nano kit. ( B ) The RNA absorbance spectrum measured with NanoDrop spectrophotometer.

Techniques Used: Derivative Assay, Spectrophotometry

28) Product Images from "Small RNAs in metastatic and non-metastatic oral squamous cell carcinoma"

Article Title: Small RNAs in metastatic and non-metastatic oral squamous cell carcinoma

Journal: BMC Medical Genomics

doi: 10.1186/s12920-015-0102-4

PCA plot depicting global small RNA expression in OSCC samples. For the clusterization of clinical samples based on the expression levels of small RNAs other that miRNAs we used Principal Components Analysis (PCA). All annotated molecules were included in this analysis. Results show that samples are very homogeneous concerning the expression of these small RNA molecules
Figure Legend Snippet: PCA plot depicting global small RNA expression in OSCC samples. For the clusterization of clinical samples based on the expression levels of small RNAs other that miRNAs we used Principal Components Analysis (PCA). All annotated molecules were included in this analysis. Results show that samples are very homogeneous concerning the expression of these small RNA molecules

Techniques Used: RNA Expression, Expressing

Expression levels of RNU48 and U6 in miRNA samples and total RNA samples used as input for the sequencing protocol. a : Expression levels of RNU48; b : Expression levels of U6.
Figure Legend Snippet: Expression levels of RNU48 and U6 in miRNA samples and total RNA samples used as input for the sequencing protocol. a : Expression levels of RNU48; b : Expression levels of U6.

Techniques Used: Expressing, Sequencing

PCA plot depicting global miRNA RNA expression in OSCC samples
Figure Legend Snippet: PCA plot depicting global miRNA RNA expression in OSCC samples

Techniques Used: RNA Expression

29) Product Images from "Why Does Insect RNA Look Degraded?"

Article Title: Why Does Insect RNA Look Degraded?

Journal: Journal of Insect Science

doi: 10.1673/031.010.14119

Electrophoretic profiles and virtual gels of Apis mellifera RNA. (A) A. mellifera brain RNA profile after heat-denaturation of two minutes at 70° C. (B) A. mellifera brain RNA profile without prior heat-denaturation. The main constituents of peaks are given: yellow denotes 18S; blue, 5.8S; and red, α and β fragments of 28S rRNA. Colored areas under the curve are only illustrative and not quantitative. High quality figures are available online.
Figure Legend Snippet: Electrophoretic profiles and virtual gels of Apis mellifera RNA. (A) A. mellifera brain RNA profile after heat-denaturation of two minutes at 70° C. (B) A. mellifera brain RNA profile without prior heat-denaturation. The main constituents of peaks are given: yellow denotes 18S; blue, 5.8S; and red, α and β fragments of 28S rRNA. Colored areas under the curve are only illustrative and not quantitative. High quality figures are available online.

Techniques Used:

30) Product Images from "Metabolic labeling of RNA using multiple ribonucleoside analogs enables simultaneous evaluation of transcription and degradation rates"

Article Title: Metabolic labeling of RNA using multiple ribonucleoside analogs enables simultaneous evaluation of transcription and degradation rates

Journal: bioRxiv

doi: 10.1101/2020.03.06.980250

Effect of transcription and degradation rates on behavior of gene expression ( A ) Comparison of ratios of transcription and degradation rates, with expression levels. X- and Y-axes indicate the ratio of transcription and degradation rates ( k s / k d ) and the expression level calculated based on the sequencing of Alkyl-RNAs (total RNA-seq reads with/without T > C conversion), respectively. Black solid line is the regression line based on log-transformed values. ( B ) Simulations of expression time series of genes imitating the characteristics of Class I (fast transcription and fast degradation), Class II (fast transcription and slow degradation), Class III (slow transcription and fast degradation), and Class IV (slow transcription and slow degradation). In each simulation, the transcription rates doubled at 0 min (red dotted line). ( C ) Time constants of expression of genes exhibiting various transcription and degradation rates. X- and Y-axes indicate transcription rate ( k s ) and degradation rate ( k d ). Colors indicate the time constants ( τ ). ( D and E ) GSEA of degradation rate ( D ) and transcription rate ( E ) showing enrichment of “estrogen response (early)” and “estrogen response (late).” NES, normalized enrichment score. ( F ) Comparison of degradation rates ( k d ) and time constants ( τ ). X- and Y-axes indicate the degradation rate and time constants, respectively. Red dashed line is a regression line based on log-transformed values. ( G ) Comparison of transcription rates ( k s ) and time constants ( τ ). X- and Y-axes indicate the transcription rate and time constants, respectively. Red dashed line is a regression line based on log-transformed values.
Figure Legend Snippet: Effect of transcription and degradation rates on behavior of gene expression ( A ) Comparison of ratios of transcription and degradation rates, with expression levels. X- and Y-axes indicate the ratio of transcription and degradation rates ( k s / k d ) and the expression level calculated based on the sequencing of Alkyl-RNAs (total RNA-seq reads with/without T > C conversion), respectively. Black solid line is the regression line based on log-transformed values. ( B ) Simulations of expression time series of genes imitating the characteristics of Class I (fast transcription and fast degradation), Class II (fast transcription and slow degradation), Class III (slow transcription and fast degradation), and Class IV (slow transcription and slow degradation). In each simulation, the transcription rates doubled at 0 min (red dotted line). ( C ) Time constants of expression of genes exhibiting various transcription and degradation rates. X- and Y-axes indicate transcription rate ( k s ) and degradation rate ( k d ). Colors indicate the time constants ( τ ). ( D and E ) GSEA of degradation rate ( D ) and transcription rate ( E ) showing enrichment of “estrogen response (early)” and “estrogen response (late).” NES, normalized enrichment score. ( F ) Comparison of degradation rates ( k d ) and time constants ( τ ). X- and Y-axes indicate the degradation rate and time constants, respectively. Red dashed line is a regression line based on log-transformed values. ( G ) Comparison of transcription rates ( k s ) and time constants ( τ ). X- and Y-axes indicate the transcription rate and time constants, respectively. Red dashed line is a regression line based on log-transformed values.

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

31) Product Images from "Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format"

Article Title: Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format

Journal: Plant Methods

doi: 10.1186/1746-4811-7-40

Lysed samples can be stored for 6 months . RNA was extracted using the automated HTP procedure from lysed seedlings in RA1 buffer immediately (fresh, n = 96) or after being frozen at -20°C for 2 days (n = 96) or 6 months (n = 96). Data are presented as: A. The mean RNA concentration (ng/μl) per well of a 96 well plate ± SD. B. NanoDrop spectrometry scans of three representative samples. C. Electropherograms from bioanalyzer analysis of the same three representative samples.
Figure Legend Snippet: Lysed samples can be stored for 6 months . RNA was extracted using the automated HTP procedure from lysed seedlings in RA1 buffer immediately (fresh, n = 96) or after being frozen at -20°C for 2 days (n = 96) or 6 months (n = 96). Data are presented as: A. The mean RNA concentration (ng/μl) per well of a 96 well plate ± SD. B. NanoDrop spectrometry scans of three representative samples. C. Electropherograms from bioanalyzer analysis of the same three representative samples.

Techniques Used: Concentration Assay

Assessment of quality of HTP purified RNA . The quality of the total RNA purified using the HTP RNA extraction procedure was analysed by UV spectrometry using a NanoDrop (A) and an Agilent Bioanalyzer (B, C) which demonstrated the consistent quality of the RNA. A: Measured A 260/280 ratios for the four samples shown were 2.05, 2.07, 2.03 and 2.02 while the corresponding figures for the A 260/230 ratios were 1.63, 1.39, 1.12 and 1.44. B: Representative electropherograms and C: corresponding digital electrophoresis gels images show clear sharp ribosomal RNA peaks/bands typical of high quality Arabidopsis RNA. In addition to the cytoplasmic 25S and 18S rRNA peaks, other peaks corresponding to 23S and 16S rRNA from chloroplasts and 5S and small rRNA are evident.
Figure Legend Snippet: Assessment of quality of HTP purified RNA . The quality of the total RNA purified using the HTP RNA extraction procedure was analysed by UV spectrometry using a NanoDrop (A) and an Agilent Bioanalyzer (B, C) which demonstrated the consistent quality of the RNA. A: Measured A 260/280 ratios for the four samples shown were 2.05, 2.07, 2.03 and 2.02 while the corresponding figures for the A 260/230 ratios were 1.63, 1.39, 1.12 and 1.44. B: Representative electropherograms and C: corresponding digital electrophoresis gels images show clear sharp ribosomal RNA peaks/bands typical of high quality Arabidopsis RNA. In addition to the cytoplasmic 25S and 18S rRNA peaks, other peaks corresponding to 23S and 16S rRNA from chloroplasts and 5S and small rRNA are evident.

Techniques Used: Purification, RNA Extraction, Electrophoresis

32) Product Images from "Probing Oral Microbial Functionality - Expression of spxB in Plaque Samples"

Article Title: Probing Oral Microbial Functionality - Expression of spxB in Plaque Samples

Journal: PLoS ONE

doi: 10.1371/journal.pone.0086685

RNA integrity and concentration. A) Gel-eletrophoretic separation of isolated total RNA after DNase digest and clean-up on 1% agarose. B) Gel images of RNA samples generated by the Agilent Bioanalyzer using RNA 6000 Nano Lab Chip. C) RNA concentration and RIN as determined by the Agilent Bioanalyzer. RIN = RNA Integrity Number; L = RNA Ladder. Green line in Figure 4B: Bioanalyzer internal marker.
Figure Legend Snippet: RNA integrity and concentration. A) Gel-eletrophoretic separation of isolated total RNA after DNase digest and clean-up on 1% agarose. B) Gel images of RNA samples generated by the Agilent Bioanalyzer using RNA 6000 Nano Lab Chip. C) RNA concentration and RIN as determined by the Agilent Bioanalyzer. RIN = RNA Integrity Number; L = RNA Ladder. Green line in Figure 4B: Bioanalyzer internal marker.

Techniques Used: Concentration Assay, Isolation, Generated, Chromatin Immunoprecipitation, Marker

33) Product Images from "Comparison of target labeling methods for use with Affymetrix GeneChips"

Article Title: Comparison of target labeling methods for use with Affymetrix GeneChips

Journal: BMC Biotechnology

doi: 10.1186/1472-6750-7-24

Overlaid electropherograms from the analysis of unfragmented biotinylated cRNA products from the IVT reactions of the 3 different labeling kits by the Agilent 2100 Bioanalyzer. The replicate reactions from donor A are shown for each kit: One-Cycle data represented as blue and green line; BioArray as black and orange and Superscript by the pink and turquoise lines. 1 μl of the final volume (One-Cycle = 21 μl; BioArray = 60 μl; Superscript = 100 μl) of purified IVT reaction is loaded. The RNA ladder (peaks represented in red) contains a mixture of RNAs of known concentration and size (50 (lower marker) 200, 500, 1,000, 2,000, 4,000, and 6,000 bases from left to right).
Figure Legend Snippet: Overlaid electropherograms from the analysis of unfragmented biotinylated cRNA products from the IVT reactions of the 3 different labeling kits by the Agilent 2100 Bioanalyzer. The replicate reactions from donor A are shown for each kit: One-Cycle data represented as blue and green line; BioArray as black and orange and Superscript by the pink and turquoise lines. 1 μl of the final volume (One-Cycle = 21 μl; BioArray = 60 μl; Superscript = 100 μl) of purified IVT reaction is loaded. The RNA ladder (peaks represented in red) contains a mixture of RNAs of known concentration and size (50 (lower marker) 200, 500, 1,000, 2,000, 4,000, and 6,000 bases from left to right).

Techniques Used: Labeling, Purification, Concentration Assay, Marker

34) Product Images from "Intelectin 3 is dispensable for resistance against a mycobacterial infection in zebrafish (Danio rerio)"

Article Title: Intelectin 3 is dispensable for resistance against a mycobacterial infection in zebrafish (Danio rerio)

Journal: Scientific Reports

doi: 10.1038/s41598-018-37678-1

Zebrafish intelectin genes are differentially expressed upon M. marinum infection. ( A ) A genome-wide gene expression microarray was conducted in adult WT AB zebrafish injected with M. marinum (20 CFU; SD 6 CFU) (n = 2) or PBS (n = 3). Average numerical results (log2) for each probe in both infected fish (y-axis) and PBS controls (x-axis) are shown. Up- and down-regulated transcripts (log2 fold change \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$|3|$$\end{document} | 3 | ) in the organ blocks are shown in grey, and the common immunological genes are annotated. Two itln3 probes as well as itln2 and itln2-like probes are highlighted. ( B – E ) The expression of zebrafish itln genes ( itln1 , itln2 , itln2-like and itln3 ) was measured with qPCR in the organ blocks of the M. marinum infected (6 CFU; SD 3 CFU) and PBS injected adult WT e46 zebrafish at 1 (n = 12 and n = 4, respectively) and 6 dpi (n = 12 and n = 8, respectively) as well as 4 (n = 12 and n = 11, respectively) and 9 wpi (n = 12 and n = 10, respectively). ( F – I ) The expression of itln1 , itln2 , itln2-like and itln3 was determined with qPCR in the M. marinum (39 CFU; SD 47 CFU) infected WT AB embryos (n = 5 at all timepoints) and in PBS injected controls (n = 5 at all timepoints) at 1–7 dpi. Note the different scales of the y axes in B-I. Gene expressions were normalized to eef1a1l1 expression and target genes were run once in the qPCR analyses. A two-tailed Mann-Whitney test was used in the statistical comparison of differences in B–I.
Figure Legend Snippet: Zebrafish intelectin genes are differentially expressed upon M. marinum infection. ( A ) A genome-wide gene expression microarray was conducted in adult WT AB zebrafish injected with M. marinum (20 CFU; SD 6 CFU) (n = 2) or PBS (n = 3). Average numerical results (log2) for each probe in both infected fish (y-axis) and PBS controls (x-axis) are shown. Up- and down-regulated transcripts (log2 fold change \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$|3|$$\end{document} | 3 | ) in the organ blocks are shown in grey, and the common immunological genes are annotated. Two itln3 probes as well as itln2 and itln2-like probes are highlighted. ( B – E ) The expression of zebrafish itln genes ( itln1 , itln2 , itln2-like and itln3 ) was measured with qPCR in the organ blocks of the M. marinum infected (6 CFU; SD 3 CFU) and PBS injected adult WT e46 zebrafish at 1 (n = 12 and n = 4, respectively) and 6 dpi (n = 12 and n = 8, respectively) as well as 4 (n = 12 and n = 11, respectively) and 9 wpi (n = 12 and n = 10, respectively). ( F – I ) The expression of itln1 , itln2 , itln2-like and itln3 was determined with qPCR in the M. marinum (39 CFU; SD 47 CFU) infected WT AB embryos (n = 5 at all timepoints) and in PBS injected controls (n = 5 at all timepoints) at 1–7 dpi. Note the different scales of the y axes in B-I. Gene expressions were normalized to eef1a1l1 expression and target genes were run once in the qPCR analyses. A two-tailed Mann-Whitney test was used in the statistical comparison of differences in B–I.

Techniques Used: Infection, Genome Wide, Expressing, Microarray, Injection, Fluorescence In Situ Hybridization, Real-time Polymerase Chain Reaction, Two Tailed Test, MANN-WHITNEY

35) Product Images from "The expression profile of human peripheral blood mononuclear cell miRNA is altered by antibody-dependent enhancement of infection with dengue virus serotype 3"

Article Title: The expression profile of human peripheral blood mononuclear cell miRNA is altered by antibody-dependent enhancement of infection with dengue virus serotype 3

Journal: Virology Journal

doi: 10.1186/s12985-018-0963-1

a , Analysis of GO functional enrichment of target genes of differentially expressed miRNA during infection between DENV-3 and DENV-3-ADE. b , Pathways predicted to be induced by differentially expressed miRNA during the DENV-3 infection. Enrichment score is presented as the negative log 10 of the P value (-log 10 P) and is plotted on the x-axis
Figure Legend Snippet: a , Analysis of GO functional enrichment of target genes of differentially expressed miRNA during infection between DENV-3 and DENV-3-ADE. b , Pathways predicted to be induced by differentially expressed miRNA during the DENV-3 infection. Enrichment score is presented as the negative log 10 of the P value (-log 10 P) and is plotted on the x-axis

Techniques Used: Functional Assay, Infection

Global analysis of differentially expressed miRNAs. a Hierarchical cluster of differentially expressed miRNAs during the DENV-3 and ADE infections at 8 h and 24 h relative to control samples. Significance was determined using a fold-change threshold of at least 2 and a P value cutoff of 0.05, numbers with s0 denote normal controls. b Venn diagram of all differentially expressed miRNAs in all samples. Different colors represent different experimental groups as indicated and the numbers 1, 2, 4, 5, 7 and 26 show the differentially expressed miRNAs that were significantly changed during infection with DENV-3 and ADE
Figure Legend Snippet: Global analysis of differentially expressed miRNAs. a Hierarchical cluster of differentially expressed miRNAs during the DENV-3 and ADE infections at 8 h and 24 h relative to control samples. Significance was determined using a fold-change threshold of at least 2 and a P value cutoff of 0.05, numbers with s0 denote normal controls. b Venn diagram of all differentially expressed miRNAs in all samples. Different colors represent different experimental groups as indicated and the numbers 1, 2, 4, 5, 7 and 26 show the differentially expressed miRNAs that were significantly changed during infection with DENV-3 and ADE

Techniques Used: Infection

36) Product Images from "Long-term storage of blood RNA collected in RNA stabilizing Tempus tubes in a large biobank – evaluation of RNA quality and stability"

Article Title: Long-term storage of blood RNA collected in RNA stabilizing Tempus tubes in a large biobank – evaluation of RNA quality and stability

Journal: BMC Research Notes

doi: 10.1186/1756-0500-7-633

Long-term storage effects on RNA integrity. RIN values for RNA samples isolated from Tempus tubes stored at –80°C until analyzed by Agilent 2100 Bioanalyzer. RIN values for adult blood samples (n = 15 Tempus tubes/year) and RIN values for cord blood samples (n = 6 Tempus tubes/year). Bars represent means ± SE. The average RIN values for adult and cord blood samples were 7.6 ± 0.5 and 7.7 ± 0.7, respectively, and no significant long-term storage related effects on RNA integrity were observed.
Figure Legend Snippet: Long-term storage effects on RNA integrity. RIN values for RNA samples isolated from Tempus tubes stored at –80°C until analyzed by Agilent 2100 Bioanalyzer. RIN values for adult blood samples (n = 15 Tempus tubes/year) and RIN values for cord blood samples (n = 6 Tempus tubes/year). Bars represent means ± SE. The average RIN values for adult and cord blood samples were 7.6 ± 0.5 and 7.7 ± 0.7, respectively, and no significant long-term storage related effects on RNA integrity were observed.

Techniques Used: Isolation

37) Product Images from "Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development"

Article Title: Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/ers076

Small RNAs (sRNAs) concentration in total RNA in the control and low relative humidity (LRH) treatment. (A) Fragment of a bioanalyser gel image for small RNAs in equalized total RNA in an example control and an example LRH sample, showing the increase under LRH in the 19–25 nt range. The ladder (double-stranded sRNAs) is from the same gel; the vertical line indicates lanes not shown. (B) The percentage increase in [sRNAs] under LRH compared with the control within RNA size class (data are means for n =6).
Figure Legend Snippet: Small RNAs (sRNAs) concentration in total RNA in the control and low relative humidity (LRH) treatment. (A) Fragment of a bioanalyser gel image for small RNAs in equalized total RNA in an example control and an example LRH sample, showing the increase under LRH in the 19–25 nt range. The ladder (double-stranded sRNAs) is from the same gel; the vertical line indicates lanes not shown. (B) The percentage increase in [sRNAs] under LRH compared with the control within RNA size class (data are means for n =6).

Techniques Used: Concentration Assay

Small RNAs (sRNAs) concentration and stomatal index in plants mutant for components of the RNA-directed DNA methylation (RdDM) pathway in the control and low relative humidity treatment (LRH). (A) Fragment of a bioanalyser gel image for small (6–150 nt) RNAs in 200 ng equalized total RNA in sample control and sample LRH-grown ago 4-1 , rdr6 , dcl3-1 , and rdr2 plants. (B) Mean (±SE) stomatal index (stomata as a percentage of epidermal cells) of mature leaves of siRNA mutants rdr2 , dcl3 , and rdr6 in the control (solid bar) and under LRH treatment (open bar).
Figure Legend Snippet: Small RNAs (sRNAs) concentration and stomatal index in plants mutant for components of the RNA-directed DNA methylation (RdDM) pathway in the control and low relative humidity treatment (LRH). (A) Fragment of a bioanalyser gel image for small (6–150 nt) RNAs in 200 ng equalized total RNA in sample control and sample LRH-grown ago 4-1 , rdr6 , dcl3-1 , and rdr2 plants. (B) Mean (±SE) stomatal index (stomata as a percentage of epidermal cells) of mature leaves of siRNA mutants rdr2 , dcl3 , and rdr6 in the control (solid bar) and under LRH treatment (open bar).

Techniques Used: Concentration Assay, Mutagenesis, DNA Methylation Assay

38) Product Images from "Gene expression profiling of microglia infected by a highly neurovirulent murine leukemia virus: implications for neuropathogenesis"

Article Title: Gene expression profiling of microglia infected by a highly neurovirulent murine leukemia virus: implications for neuropathogenesis

Journal: Retrovirology

doi: 10.1186/1742-4690-3-26

Taqman real-time RT-PCR validation assessment of microglial genes identified in Fr57E versus FrCasE gene arrays . Panel A shows qRT-PCR analysis of RNA from two independent microglial culture experiments assaying three separate cultures in triplicate for SIGIRR, exosome component 4 (Exosc4), and Riken cDNA 1810008K03 gene (ChaC). These cultures were distinct from those used for microarray analysis. Panel B shows qRT-PCR analysis of SIGIRR RNA obtained from microglia isolated from the brains of virus-infected and uninfected mice. FrCasE- infected (black); F43- infected (gray); mock-infected (white)
Figure Legend Snippet: Taqman real-time RT-PCR validation assessment of microglial genes identified in Fr57E versus FrCasE gene arrays . Panel A shows qRT-PCR analysis of RNA from two independent microglial culture experiments assaying three separate cultures in triplicate for SIGIRR, exosome component 4 (Exosc4), and Riken cDNA 1810008K03 gene (ChaC). These cultures were distinct from those used for microarray analysis. Panel B shows qRT-PCR analysis of SIGIRR RNA obtained from microglia isolated from the brains of virus-infected and uninfected mice. FrCasE- infected (black); F43- infected (gray); mock-infected (white)

Techniques Used: Quantitative RT-PCR, Microarray, Isolation, Infection, Mouse Assay

39) Product Images from "Adipose-Derived Stem Cells Induce Angiogenesis via Microvesicle Transport of miRNA-31"

Article Title: Adipose-Derived Stem Cells Induce Angiogenesis via Microvesicle Transport of miRNA-31

Journal: Stem Cells Translational Medicine

doi: 10.5966/sctm.2015-0177

Analysis of RNA extracted from ASC-released MVs. (A): Small RNA (fewer than 200 nucleotides) and large RNA extracted from ASCs and ASC-released MVs were quantified ( n = 3– 4). Total RNA was set to 100%. (B): Equal amounts of total RNA from ASCs and MVs were analyzed using Bioanalyzer (Agilent Technologies). 18S and 28S indicated the ribosomal RNA. (C): Small RNA from MVs was analyzed using Bioanalyzer. (D): An electropherogram of the lane MV on (C) . (E): Reverse-transcriptase-polymerase chain reaction analysis of miRNA for small RNA extracted from MV-P. The level of miRNA in MV was set to 1 (dashed line). U6 was used as an internal control. n = 4. ∗, p
Figure Legend Snippet: Analysis of RNA extracted from ASC-released MVs. (A): Small RNA (fewer than 200 nucleotides) and large RNA extracted from ASCs and ASC-released MVs were quantified ( n = 3– 4). Total RNA was set to 100%. (B): Equal amounts of total RNA from ASCs and MVs were analyzed using Bioanalyzer (Agilent Technologies). 18S and 28S indicated the ribosomal RNA. (C): Small RNA from MVs was analyzed using Bioanalyzer. (D): An electropherogram of the lane MV on (C) . (E): Reverse-transcriptase-polymerase chain reaction analysis of miRNA for small RNA extracted from MV-P. The level of miRNA in MV was set to 1 (dashed line). U6 was used as an internal control. n = 4. ∗, p

Techniques Used: Polymerase Chain Reaction

40) Product Images from "Adipose-Derived Stem Cells Induce Angiogenesis via Microvesicle Transport of miRNA-31"

Article Title: Adipose-Derived Stem Cells Induce Angiogenesis via Microvesicle Transport of miRNA-31

Journal: Stem Cells Translational Medicine

doi: 10.5966/sctm.2015-0177

Induction of migration and tube formation of HUVECs by CdM from adipose-derived stem cells (ASCs). ASCs were incubated in endothelial basal medium/1% fetal bovine serum (FBS) for 2 days in the absence (A, B) or presence (C, D) of GW4869, an MV-formation inhibitor. CdM was collected and used to treat HUVECs. Cell migration (A, C) and tube formation (B, D) assays for treated HUVECs were performed. The endothelial basal medium/1% FBS without cells was incubated in parallel and was used as a control. The CdM with removal of MVs via ultracentrifugation was used as CdM-MV free. Representative images of cell migration and tube formation are displayed. Scale bar = 200 µm. ( A–D): n = 4. ∗, p
Figure Legend Snippet: Induction of migration and tube formation of HUVECs by CdM from adipose-derived stem cells (ASCs). ASCs were incubated in endothelial basal medium/1% fetal bovine serum (FBS) for 2 days in the absence (A, B) or presence (C, D) of GW4869, an MV-formation inhibitor. CdM was collected and used to treat HUVECs. Cell migration (A, C) and tube formation (B, D) assays for treated HUVECs were performed. The endothelial basal medium/1% FBS without cells was incubated in parallel and was used as a control. The CdM with removal of MVs via ultracentrifugation was used as CdM-MV free. Representative images of cell migration and tube formation are displayed. Scale bar = 200 µm. ( A–D): n = 4. ∗, p

Techniques Used: Migration, Derivative Assay, Incubation

miR-31 contributes to the proangiogenesis induced by MV-P in vitro. (A–C): Adipose-derived stem cells (ASCs) were transduced with lentiviral ZipmiR-31 to silence miR-31. ZipmiR-Cont was used as a control. MVs and MV-P were obtained from the transduced ASCs and were used to treat HUVECs. The miR-31 content in HUVECs (A) , and the cell migration (B) and tube formation (C) of HUVECs were determined. (D): HUVECs were transfected with commercial pre-miR-31. A pre-miR-Cont was used as a control. The tube formation of HUVECs was measured 48 hours after transfection. (A–D): n = 4–5. ∗, p
Figure Legend Snippet: miR-31 contributes to the proangiogenesis induced by MV-P in vitro. (A–C): Adipose-derived stem cells (ASCs) were transduced with lentiviral ZipmiR-31 to silence miR-31. ZipmiR-Cont was used as a control. MVs and MV-P were obtained from the transduced ASCs and were used to treat HUVECs. The miR-31 content in HUVECs (A) , and the cell migration (B) and tube formation (C) of HUVECs were determined. (D): HUVECs were transfected with commercial pre-miR-31. A pre-miR-Cont was used as a control. The tube formation of HUVECs was measured 48 hours after transfection. (A–D): n = 4–5. ∗, p

Techniques Used: In Vitro, Derivative Assay, Transduction, Migration, Transfection

miR-31 contributes to the proangiogenesis induced by MV-P ex vivo and in vivo. Adipose-derived stem cells (ASCs) were transduced with lentiviral ZipmiR-31 to silence miR-31. ASCs untransduced (control) or transduced with a ZipmiR-Cont were used as controls. MV and MV-P were obtained from these ASCs. (A): Mouse aortic rings were collected and treated with various MVs, as indicated, for 5 days ( n = 8). Representative images (upper panel) and a statistical analysis of the outgrowth area of aortic rings (lower panel) for each treatment condition are displayed. The outgrowth area of aortic rings treated with MV from untransduced cells was set to 1. Scale bar = 100 µm. (B): PBS, MV, or MV-P was mixed with Matrigel and injected subcutaneously into the flanks of the nude mice. The Matrigel plugs were harvested 2 weeks postimplantation ( n = 6). Upper panel: Representative pictures of the plugs are exhibited. Scale bar = 5 mm. Middle panel: The sections of the plugs were subject to immunohistochemistry analysis for CD31, an endothelial cell marker, and counterstained with DAPI. Scale bar = 100 µm. Lower panel: Quantification of the CD31-positive area was performed. The positive area in the slide from the plugs containing PBS was set to 1. ∗, p
Figure Legend Snippet: miR-31 contributes to the proangiogenesis induced by MV-P ex vivo and in vivo. Adipose-derived stem cells (ASCs) were transduced with lentiviral ZipmiR-31 to silence miR-31. ASCs untransduced (control) or transduced with a ZipmiR-Cont were used as controls. MV and MV-P were obtained from these ASCs. (A): Mouse aortic rings were collected and treated with various MVs, as indicated, for 5 days ( n = 8). Representative images (upper panel) and a statistical analysis of the outgrowth area of aortic rings (lower panel) for each treatment condition are displayed. The outgrowth area of aortic rings treated with MV from untransduced cells was set to 1. Scale bar = 100 µm. (B): PBS, MV, or MV-P was mixed with Matrigel and injected subcutaneously into the flanks of the nude mice. The Matrigel plugs were harvested 2 weeks postimplantation ( n = 6). Upper panel: Representative pictures of the plugs are exhibited. Scale bar = 5 mm. Middle panel: The sections of the plugs were subject to immunohistochemistry analysis for CD31, an endothelial cell marker, and counterstained with DAPI. Scale bar = 100 µm. Lower panel: Quantification of the CD31-positive area was performed. The positive area in the slide from the plugs containing PBS was set to 1. ∗, p

Techniques Used: Ex Vivo, In Vivo, Derivative Assay, Transduction, Injection, Mouse Assay, Immunohistochemistry, Marker

Analysis of RNA extracted from ASC-released MVs. (A): Small RNA (fewer than 200 nucleotides) and large RNA extracted from ASCs and ASC-released MVs were quantified ( n = 3– 4). Total RNA was set to 100%. (B): Equal amounts of total RNA from ASCs and MVs were analyzed using Bioanalyzer (Agilent Technologies). 18S and 28S indicated the ribosomal RNA. (C): Small RNA from MVs was analyzed using Bioanalyzer. (D): An electropherogram of the lane MV on (C) . (E): Reverse-transcriptase-polymerase chain reaction analysis of miRNA for small RNA extracted from MV-P. The level of miRNA in MV was set to 1 (dashed line). U6 was used as an internal control. n = 4. ∗, p
Figure Legend Snippet: Analysis of RNA extracted from ASC-released MVs. (A): Small RNA (fewer than 200 nucleotides) and large RNA extracted from ASCs and ASC-released MVs were quantified ( n = 3– 4). Total RNA was set to 100%. (B): Equal amounts of total RNA from ASCs and MVs were analyzed using Bioanalyzer (Agilent Technologies). 18S and 28S indicated the ribosomal RNA. (C): Small RNA from MVs was analyzed using Bioanalyzer. (D): An electropherogram of the lane MV on (C) . (E): Reverse-transcriptase-polymerase chain reaction analysis of miRNA for small RNA extracted from MV-P. The level of miRNA in MV was set to 1 (dashed line). U6 was used as an internal control. n = 4. ∗, p

Techniques Used: Polymerase Chain Reaction

Induction of migration and tube formation of HUVECs by MVs from adipose-derived stem cells (ASCs). (A): Conditioned medium was subjected to standard serial centrifugation for MV isolation. The isolated pellet was examined with scanning electron microscopy (scale bar = 1 µm). (B): ASCs were maintained in growth medium or preconditioned with endothelial differentiation medium for 4 days. After washing, the ASCs were then incubated for 2 days in endothelial basal medium/1% FBS with or without the presence of GW4869. Western blot analysis of the MVs was performed with Alix, an MV marker. Each lane represented an MV lysate from 3 × 10 6 cells. (C): The protein content of MVs and MV-P from ASCs were determined. (D–F): HUVECs were treated with 30 µg/ml (protein concentration) MV or MV-P. HUVECs in fresh endothelial basal medium/1% FBS was used as a control. Cell migration (D) , tube formation (E) , and proliferation (F) assays of the HUVECs were performed as described in Material and Methods. (C–F): n = 4. ## , p
Figure Legend Snippet: Induction of migration and tube formation of HUVECs by MVs from adipose-derived stem cells (ASCs). (A): Conditioned medium was subjected to standard serial centrifugation for MV isolation. The isolated pellet was examined with scanning electron microscopy (scale bar = 1 µm). (B): ASCs were maintained in growth medium or preconditioned with endothelial differentiation medium for 4 days. After washing, the ASCs were then incubated for 2 days in endothelial basal medium/1% FBS with or without the presence of GW4869. Western blot analysis of the MVs was performed with Alix, an MV marker. Each lane represented an MV lysate from 3 × 10 6 cells. (C): The protein content of MVs and MV-P from ASCs were determined. (D–F): HUVECs were treated with 30 µg/ml (protein concentration) MV or MV-P. HUVECs in fresh endothelial basal medium/1% FBS was used as a control. Cell migration (D) , tube formation (E) , and proliferation (F) assays of the HUVECs were performed as described in Material and Methods. (C–F): n = 4. ## , p

Techniques Used: Migration, Derivative Assay, Centrifugation, Isolation, Electron Microscopy, Incubation, Western Blot, Marker, Protein Concentration

Related Articles

Amplification:

Article Title: ?9-Tetrahydrocannabinol Disrupts Estrogen-Signaling through Up-Regulation of Estrogen Receptor β (ERβ)
Article Snippet: .. From both cells, total RNA was extracted, and cDNA synthesizing and cRNA labeling were conducted using a Low RNA Fluorescent Linear Amplification kit (Agilent, Palo Alto, CA, USA). .. Labeled cRNA (Cy3 to controls, Cy5 to Δ9 -THC samples) was hybridized to human oligo DNA microarray slides (Agilent, Palo Alto, CA) that are spotted with human genes.

RNA Sequencing Assay:

Article Title: Tumour-vasculature development via endothelial-to-mesenchymal transition after radiotherapy controls CD44v6+ cancer cell and macrophage polarization
Article Snippet: .. RNA-seq analysis Total RNA was isolated from HUVECs, and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). .. RNA-seq libraries were constructed using the SENSE mRNA-Seq Library Prep Kit (Lexogen), according to the manufacturer’s instructions, and were sequenced as 100 bp paired-end runs on the HiSeq 2000 platform (Illumina).

Isolation:

Article Title: Tumour-vasculature development via endothelial-to-mesenchymal transition after radiotherapy controls CD44v6+ cancer cell and macrophage polarization
Article Snippet: .. RNA-seq analysis Total RNA was isolated from HUVECs, and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). .. RNA-seq libraries were constructed using the SENSE mRNA-Seq Library Prep Kit (Lexogen), according to the manufacturer’s instructions, and were sequenced as 100 bp paired-end runs on the HiSeq 2000 platform (Illumina).

Labeling:

Article Title: ?9-Tetrahydrocannabinol Disrupts Estrogen-Signaling through Up-Regulation of Estrogen Receptor β (ERβ)
Article Snippet: .. From both cells, total RNA was extracted, and cDNA synthesizing and cRNA labeling were conducted using a Low RNA Fluorescent Linear Amplification kit (Agilent, Palo Alto, CA, USA). .. Labeled cRNA (Cy3 to controls, Cy5 to Δ9 -THC samples) was hybridized to human oligo DNA microarray slides (Agilent, Palo Alto, CA) that are spotted with human genes.

Microarray:

Article Title: Selection and Application of Tissue microRNAs for Nonendoscopic Diagnosis of Barrett’s Esophagus
Article Snippet: .. The extracted material was compiled to form 2 NE, 2 BNE, and 2 BE pools of miRNAs for Agilent Technologies Human miRNA Microarray v1.0; 20 NE and 21 BE (BE and BNE) for Nanostring Human miRNA Expression Assay v2. ..

Article Title: PMA and Ionomycin Induce Glioblastoma Cell Death: Activation-Induced Cell-Death-Like Phenomena Occur in Glioma Cells
Article Snippet: .. The mRNA expression of NFAT1and Fas obtained from microarray analysis in 111 clinical samples was analyzed with cluster analysis and Pearson correlation analysis. .. The expression of NFAT1 was significantly correlated with that of Fas (R = 0.627, P < 0.01) in gliomas ( ).

Formalin-fixed Paraffin-Embedded:

Article Title: Biobanking: Objectives, Requirements, and Future Challenges—Experiences from the Munich Vascular Biobank
Article Snippet: .. Analysis of RNA Quality from FFPE Biospecimens by RIN and RNA Fragmentation RNA integrity number (RIN) was determined by Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany) in accordance with the manufacturer’s instructions. ..

Expressing:

Article Title: Selection and Application of Tissue microRNAs for Nonendoscopic Diagnosis of Barrett’s Esophagus
Article Snippet: .. The extracted material was compiled to form 2 NE, 2 BNE, and 2 BE pools of miRNAs for Agilent Technologies Human miRNA Microarray v1.0; 20 NE and 21 BE (BE and BNE) for Nanostring Human miRNA Expression Assay v2. ..

Article Title: PMA and Ionomycin Induce Glioblastoma Cell Death: Activation-Induced Cell-Death-Like Phenomena Occur in Glioma Cells
Article Snippet: .. The mRNA expression of NFAT1and Fas obtained from microarray analysis in 111 clinical samples was analyzed with cluster analysis and Pearson correlation analysis. .. The expression of NFAT1 was significantly correlated with that of Fas (R = 0.627, P < 0.01) in gliomas ( ).

Sequencing:

Article Title: Decreasing miRNA sequencing bias using a single adapter and circularization approach
Article Snippet: .. Using RealSeq®-AC and TruSeq®, we prepared sequencing libraries from a reference sample of total RNA (Agilent) obtained from nine different human tissues and cell lines. .. We sequenced both libraries to a coverage of ten million reads and counted the number of miRNAs identified (with ten or more reads of each) by each kit at different sequencing coverages by random subsampling (Additional file : Figure S6).

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 88
    Agilent technologies 2100 bioanalyzer rna 6000 nano kit
    2100 Bioanalyzer Rna 6000 Nano Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/2100 bioanalyzer rna 6000 nano kit/product/Agilent technologies
    Average 88 stars, based on 15 article reviews
    Price from $9.99 to $1999.99
    2100 bioanalyzer rna 6000 nano kit - by Bioz Stars, 2020-07
    88/100 stars
      Buy from Supplier

    99
    Agilent technologies agilent 2100 bioanalyzer
    Agilent 2100 Bioanalyzer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 6798 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/agilent 2100 bioanalyzer/product/Agilent technologies
    Average 99 stars, based on 6798 article reviews
    Price from $9.99 to $1999.99
    agilent 2100 bioanalyzer - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    Image Search Results