allprep dna rna mini kit  (Qiagen)


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    Name:
    AllPrep DNA/RNA Mini Kit
    Description:
    For simultaneous purification of DNA and RNA from cells and tissues. Kit contents: Qiagen AllPrep DNA/RNA Mini Kit, 50 preps, 30mg Sample, 100L Elution Volume, Silica Technology, Spin Column Format, Manual Processing, Genomic DNA, Total RNA Purification, 35 min. Time/Run, Ideal for PCR, Real-time PCR, Microarray, Blotting, For Simultaneous Purification of DNA and RNA from Cells and Tissues, Includes AllPrep DNA Spin Columns, RNeasy Mini Spin Columns, Collection Tubes, RNase-free Water and Buffers. Benefits: High-quality DNA and RNA from the same sample. Maximal yields of DNA and RNA from precious samples. Rapid purification with short, streamlined protocol. Ready-to-use DNA and RNA for any downstream analysis
    Catalog Number:
    80204
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    Category:
    AllPrep DNA/RNA Mini Kit
    Score:
    85
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    Structured Review

    Qiagen allprep dna rna mini kit
    AllPrep DNA/RNA Mini Kit
    For simultaneous purification of DNA and RNA from cells and tissues. Kit contents: Qiagen AllPrep DNA/RNA Mini Kit, 50 preps, 30mg Sample, 100L Elution Volume, Silica Technology, Spin Column Format, Manual Processing, Genomic DNA, Total RNA Purification, 35 min. Time/Run, Ideal for PCR, Real-time PCR, Microarray, Blotting, For Simultaneous Purification of DNA and RNA from Cells and Tissues, Includes AllPrep DNA Spin Columns, RNeasy Mini Spin Columns, Collection Tubes, RNase-free Water and Buffers. Benefits: High-quality DNA and RNA from the same sample. Maximal yields of DNA and RNA from precious samples. Rapid purification with short, streamlined protocol. Ready-to-use DNA and RNA for any downstream analysis
    https://www.bioz.com/result/allprep dna rna mini kit/product/Qiagen
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    Images

    1) Product Images from "Broad activation of latent HIV-1 in vivo"

    Article Title: Broad activation of latent HIV-1 in vivo

    Journal: Nature Communications

    doi: 10.1038/ncomms12731

    Panobinostat and vorinostat non-selectively activate transcription from latent HIV-1 proviruses. ( a ) Representative phylogenetic trees of HIV-1 sequences from HIV-infected participants on suppressive ART who received panobinostat (Pan18) or vorinostat (Vor16) showing the genetic relationship of sequences from each time point. For participant Pan18, the plasma samples were collected ∼1 year and 6 months before initiation of antiretroviral therapy and 14 days following the analytical treatment interruption. Peripheral blood samples were collected at baseline, 2 h after the first dose of panobinostat (TP1), 32 days after the first dose of panobinostat (TP2) and 38 days after the final panobinostat dose. Intestinal lamina propria mononuclear cells were collected at baseline (1 week before the first panobinostat dose) and during week 4 of the panobinostat trial. For participant Vor16, peripheral blood samples were collected at baseline, 7 days after the first dose of vorinostat (TP1), 14 days after the first dose of vorinostat (TP2) and 7 days after the final vorinostat dose. ( b ) Average pairwise distance of cell-associated DNA (Pan n =12, Vor n =12) before and DNA (Pan n =12, Vor n =14) and cell-associated RNA (Pan n = 8, Vor n =3) during vorinostat and panobinostat administration, as well as the plasma HIV-1 RNA following an ATI for the panobinostat trial ( n =7). Each data point represents the group mean±s.e.m. The Wilcoxon signed rank test was used to generate the P values. * P ≤0.05.
    Figure Legend Snippet: Panobinostat and vorinostat non-selectively activate transcription from latent HIV-1 proviruses. ( a ) Representative phylogenetic trees of HIV-1 sequences from HIV-infected participants on suppressive ART who received panobinostat (Pan18) or vorinostat (Vor16) showing the genetic relationship of sequences from each time point. For participant Pan18, the plasma samples were collected ∼1 year and 6 months before initiation of antiretroviral therapy and 14 days following the analytical treatment interruption. Peripheral blood samples were collected at baseline, 2 h after the first dose of panobinostat (TP1), 32 days after the first dose of panobinostat (TP2) and 38 days after the final panobinostat dose. Intestinal lamina propria mononuclear cells were collected at baseline (1 week before the first panobinostat dose) and during week 4 of the panobinostat trial. For participant Vor16, peripheral blood samples were collected at baseline, 7 days after the first dose of vorinostat (TP1), 14 days after the first dose of vorinostat (TP2) and 7 days after the final vorinostat dose. ( b ) Average pairwise distance of cell-associated DNA (Pan n =12, Vor n =12) before and DNA (Pan n =12, Vor n =14) and cell-associated RNA (Pan n = 8, Vor n =3) during vorinostat and panobinostat administration, as well as the plasma HIV-1 RNA following an ATI for the panobinostat trial ( n =7). Each data point represents the group mean±s.e.m. The Wilcoxon signed rank test was used to generate the P values. * P ≤0.05.

    Techniques Used: Infection

    A significant proportion of cell-associated HIV-1 RNA is defective. The percentage of defective virus detected in CD4 + T cells collected from HIV-infected participants on ART before, during and following administration of panobinostat (baseline DNA n =14, RNA n =7; on HDACi DNA n =15, RNA n =9; post HDACi DNA n =14, RNA n =6) or vorinostat (baseline DNA n =14, RNA n =5; on HDACi DNA n =15, RNA n =6; post HDACi DNA n =14, RNA n =3). Each data point represents the group mean, and the error bars represent the s.e.m. * P ≤0.05, ** P ≤0.01. The Wilcoxon signed rank test was used to generate the P values.
    Figure Legend Snippet: A significant proportion of cell-associated HIV-1 RNA is defective. The percentage of defective virus detected in CD4 + T cells collected from HIV-infected participants on ART before, during and following administration of panobinostat (baseline DNA n =14, RNA n =7; on HDACi DNA n =15, RNA n =9; post HDACi DNA n =14, RNA n =6) or vorinostat (baseline DNA n =14, RNA n =5; on HDACi DNA n =15, RNA n =6; post HDACi DNA n =14, RNA n =3). Each data point represents the group mean, and the error bars represent the s.e.m. * P ≤0.05, ** P ≤0.01. The Wilcoxon signed rank test was used to generate the P values.

    Techniques Used: Infection

    2) Product Images from "Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications"

    Article Title: Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications

    Journal:

    doi: 10.1038/nprot.2013.141

    Examples for DNA and RNA quality, and integrity from isolated samples. ( a ) Agarose gel electrophoresis of genomic DNA to verify that there is no DNA degradation resulting in a DNA ladder. ( b ) Representative electropherograms run with Bio-Rad Experion of RNA samples isolated as total RNA, high-molecular-weight RNA (enriched for mRNA) and low-molecular-weight RNA (enriched for ncRNA like miRNA). ( c ) Representative electropherogram for a good-quality RNA. ( d ) Representative electropherogram for a highly-degraded RNA. Abundant human ribosomal RNAs of 5S, 18S, and 28S are indicated.
    Figure Legend Snippet: Examples for DNA and RNA quality, and integrity from isolated samples. ( a ) Agarose gel electrophoresis of genomic DNA to verify that there is no DNA degradation resulting in a DNA ladder. ( b ) Representative electropherograms run with Bio-Rad Experion of RNA samples isolated as total RNA, high-molecular-weight RNA (enriched for mRNA) and low-molecular-weight RNA (enriched for ncRNA like miRNA). ( c ) Representative electropherogram for a good-quality RNA. ( d ) Representative electropherogram for a highly-degraded RNA. Abundant human ribosomal RNAs of 5S, 18S, and 28S are indicated.

    Techniques Used: Isolation, Agarose Gel Electrophoresis, Molecular Weight

    3) Product Images from "Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing"

    Article Title: Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2018.03259

    Cluster diagram of the Bray-Curtis dissimilarities based on the log-transformed relative OTU abundance for each sample. The separated DNA (A) and RNA (B) community groups (with asterisks at the node) exist with significant compositional differences (DNA: r 2 = 0.31718, P = 0.001; RNA: r 2 = 0.27023, P = 0.001) as determined by PERMANOVA. The percent dissimilarity among samples is shown along the horizontal axes.
    Figure Legend Snippet: Cluster diagram of the Bray-Curtis dissimilarities based on the log-transformed relative OTU abundance for each sample. The separated DNA (A) and RNA (B) community groups (with asterisks at the node) exist with significant compositional differences (DNA: r 2 = 0.31718, P = 0.001; RNA: r 2 = 0.27023, P = 0.001) as determined by PERMANOVA. The percent dissimilarity among samples is shown along the horizontal axes.

    Techniques Used: Transformation Assay

    Number of OTUs unveiled by DNA and RNA surveys. The pie chart indicated the OTU numbers mainly at class level; the inner ring represented these classes belong to the phylum; the outer ring indicated the number of OTUs at super-group level.
    Figure Legend Snippet: Number of OTUs unveiled by DNA and RNA surveys. The pie chart indicated the OTU numbers mainly at class level; the inner ring represented these classes belong to the phylum; the outer ring indicated the number of OTUs at super-group level.

    Techniques Used:

    Number of OTUs of higher taxonomic groups (sequences proportion over 1% of the total DNA or RNA abundance) based on the DNA-derived (A) and RNA-derived (B) approaches for each sample. Others refer to groups with relatively lower abundance (sequences proportion
    Figure Legend Snippet: Number of OTUs of higher taxonomic groups (sequences proportion over 1% of the total DNA or RNA abundance) based on the DNA-derived (A) and RNA-derived (B) approaches for each sample. Others refer to groups with relatively lower abundance (sequences proportion

    Techniques Used: Derivative Assay

    Relative abundance of higher taxonomic groups (sequences proportion over 1% of the total DNA or RNA abundance) based on the DNA-derived (A) and RNA-derived (B) approaches for each sample. Others refer to groups with relatively lower abundance (sequences proportion
    Figure Legend Snippet: Relative abundance of higher taxonomic groups (sequences proportion over 1% of the total DNA or RNA abundance) based on the DNA-derived (A) and RNA-derived (B) approaches for each sample. Others refer to groups with relatively lower abundance (sequences proportion

    Techniques Used: Derivative Assay

    (A) Scatter diagram of PC 1 and PC 2 derived from the relative abundance of higher taxonomic groups in the DNA and RNA databases detected in each sample, blue color indicated the sequences was derived from the DNA survey and red color indicated the sequences was derived from the RNA survey. Ma, Mamiellophyceae; Sp, Spirotrichea; Pe, Pelagophyceae; Ba, Bacillariophyta; Dict, Dictyochophyceae; Prym, Prymnesiophyceae. Boxplot representing the RNA: DNA ratios for Mamiellophyceae (B) , Pelagophyceae (C) , and Spirotrichea (D) in all and individual samples.
    Figure Legend Snippet: (A) Scatter diagram of PC 1 and PC 2 derived from the relative abundance of higher taxonomic groups in the DNA and RNA databases detected in each sample, blue color indicated the sequences was derived from the DNA survey and red color indicated the sequences was derived from the RNA survey. Ma, Mamiellophyceae; Sp, Spirotrichea; Pe, Pelagophyceae; Ba, Bacillariophyta; Dict, Dictyochophyceae; Prym, Prymnesiophyceae. Boxplot representing the RNA: DNA ratios for Mamiellophyceae (B) , Pelagophyceae (C) , and Spirotrichea (D) in all and individual samples.

    Techniques Used: Derivative Assay

    4) Product Images from "Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates"

    Article Title: Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates

    Journal: Nature Communications

    doi: 10.1038/s41467-018-05069-9

    Quantifying the progression of MuLV replication and clonal outgrowth of resulting lymphoma. Virus copy number and expression level was quantified by QPCR of genomic DNA ( a ) and RTQPCR of cDNA ( b ) extracted from spleen samples of time course animals. Error bars represent s.d. of 3 technical replicates per DNA/RNA sample. ( c ) Profiles of the relative abundance of the top 50 most clonal integrations from a cross section of mature lymphoma (upper 2 rows) and time course samples (lower 4 rows) are represented as bar graphs. Non-adjusted clonality is indicated in blue, normalized clonality (such that the most abundant integration has a value of 1) are the graphs in red. Asymptomatic animals from early time points display a relatively flat profile whereas later time points and mice with symptomatic lymphoma show clear signs of clonal outgrowth. Shannon entropy values ( E ) are displayed on each graph
    Figure Legend Snippet: Quantifying the progression of MuLV replication and clonal outgrowth of resulting lymphoma. Virus copy number and expression level was quantified by QPCR of genomic DNA ( a ) and RTQPCR of cDNA ( b ) extracted from spleen samples of time course animals. Error bars represent s.d. of 3 technical replicates per DNA/RNA sample. ( c ) Profiles of the relative abundance of the top 50 most clonal integrations from a cross section of mature lymphoma (upper 2 rows) and time course samples (lower 4 rows) are represented as bar graphs. Non-adjusted clonality is indicated in blue, normalized clonality (such that the most abundant integration has a value of 1) are the graphs in red. Asymptomatic animals from early time points display a relatively flat profile whereas later time points and mice with symptomatic lymphoma show clear signs of clonal outgrowth. Shannon entropy values ( E ) are displayed on each graph

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

    5) 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

    6) Product Images from "Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing"

    Article Title: Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing

    Journal: BMC Genomics

    doi: 10.1186/s12864-017-3900-6

    Post-UNG bead-based purifications: library yield data. a Effect of bead to DNA ratio on library sizes. Various combinations of 1:1 and 2:1 bead to DNA ratio were applied for post-ligation and post-UNG purifications. The final purified PCR product was run on Agilent DNA 1000 for size profiling. b Size profiles of libraries made using variations of the UNG step. The first three conditions where bead amount was varied for post-ligation and post-UNG purifications involve a distinct UNG step. The fourth condition also has a separate UNG step but the reaction is used as a template for PCR without purification in between. The next condition combines UNG and PCR reactions where as the last condition omits the UNG treatment all together. The sizes of these libraries were calculated from fragment smear analysis using Agilent’s software. Input was 1μg UHR total RNA. c Yield comparison of libraries made using various formats of the UNG step. As in ( b ) but endpoint data is concentration of the final libraries. n = 3; error bars = Standard Deviation
    Figure Legend Snippet: Post-UNG bead-based purifications: library yield data. a Effect of bead to DNA ratio on library sizes. Various combinations of 1:1 and 2:1 bead to DNA ratio were applied for post-ligation and post-UNG purifications. The final purified PCR product was run on Agilent DNA 1000 for size profiling. b Size profiles of libraries made using variations of the UNG step. The first three conditions where bead amount was varied for post-ligation and post-UNG purifications involve a distinct UNG step. The fourth condition also has a separate UNG step but the reaction is used as a template for PCR without purification in between. The next condition combines UNG and PCR reactions where as the last condition omits the UNG treatment all together. The sizes of these libraries were calculated from fragment smear analysis using Agilent’s software. Input was 1μg UHR total RNA. c Yield comparison of libraries made using various formats of the UNG step. As in ( b ) but endpoint data is concentration of the final libraries. n = 3; error bars = Standard Deviation

    Techniques Used: Ligation, Purification, Polymerase Chain Reaction, Software, Concentration Assay, Standard Deviation

    The Maxima H Minus reverse transcriptase provides higher yield of cDNA and quality of libraries. a cDNA yield assessment. X-axis indicates various UHR RNA input amounts used for mRNA isolation and cDNA synthesis. Double strand cDNA was measured using the Qubit HS DNA assay. Values from this assay were normalized relative to the value obtained when using Superscript II (RT-II) for the 250 ng input. b Diversity of libraries. Libraries were generated from cDNA samples that were prepared using the best performing RT (Maxima) and Superscript II (SS-II). The resulting sequencing data were analyzed for duplicate rates. c ERCC spike-in sequence differences. Mismatch rates were calculated by comparing observed sequences and expected sequences from the known spike-in synthetic RNAs. X-axis represents various UHR RNA input amounts used for mRNA isolation and cDNA synthesis. Y-axis is error rate per 1000 nucleotides. n = 3; error bars = Standard Deviation. * P
    Figure Legend Snippet: The Maxima H Minus reverse transcriptase provides higher yield of cDNA and quality of libraries. a cDNA yield assessment. X-axis indicates various UHR RNA input amounts used for mRNA isolation and cDNA synthesis. Double strand cDNA was measured using the Qubit HS DNA assay. Values from this assay were normalized relative to the value obtained when using Superscript II (RT-II) for the 250 ng input. b Diversity of libraries. Libraries were generated from cDNA samples that were prepared using the best performing RT (Maxima) and Superscript II (SS-II). The resulting sequencing data were analyzed for duplicate rates. c ERCC spike-in sequence differences. Mismatch rates were calculated by comparing observed sequences and expected sequences from the known spike-in synthetic RNAs. X-axis represents various UHR RNA input amounts used for mRNA isolation and cDNA synthesis. Y-axis is error rate per 1000 nucleotides. n = 3; error bars = Standard Deviation. * P

    Techniques Used: Isolation, Generated, Sequencing, Standard Deviation

    7) Product Images from "Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens"

    Article Title: Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0196913

    Comparison of sera exosomal RNA using four different RNA extraction methods. (A) Total RNA yield from ultracentrifugation (UC) and ExoQuick (EQ) treated samples using the RNeasy Mini Kit combined with TRIzol LS, the RNeasy Mini Kit alone, conventional RNA precipitation, and AllPrep DNA/RNA Mini Kit. (B) Demonstration of RNA quality measured by OD 260 /OD 280 in EQ and UC treated samples. Data are shown as the mean ± SD from six independent patient samples. *** P
    Figure Legend Snippet: Comparison of sera exosomal RNA using four different RNA extraction methods. (A) Total RNA yield from ultracentrifugation (UC) and ExoQuick (EQ) treated samples using the RNeasy Mini Kit combined with TRIzol LS, the RNeasy Mini Kit alone, conventional RNA precipitation, and AllPrep DNA/RNA Mini Kit. (B) Demonstration of RNA quality measured by OD 260 /OD 280 in EQ and UC treated samples. Data are shown as the mean ± SD from six independent patient samples. *** P

    Techniques Used: RNA Extraction

    8) Product Images from "Tissue-Specific Stem Cells Obtained by Reprogramming of Non-Obese Diabetic (NOD) Mouse-Derived Pancreatic Cells Confer Insulin Production in Response to Glucose"

    Article Title: Tissue-Specific Stem Cells Obtained by Reprogramming of Non-Obese Diabetic (NOD) Mouse-Derived Pancreatic Cells Confer Insulin Production in Response to Glucose

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0163580

    Expression analysis in iTS-P. (A) RT-PCR analysis for mRNA expression of pluripotency-related markers (Oct3/4, Sox2, Klf4, c-Myc, Esg1, and Rex1) and the pancreas-related marker (Pdx1) in the pancreatic tissue of NOD mice (Panc), the ES cells (ES), and the iTS-P lines (4–2, 4–3, 4–4, 4–7, 4–9 and 4–11). Abbreviations: Oct3/4, octamer-binding transcription factor 3/4; Sox2, SRY (sex determining region Y)-box 2; Klf4, Kruppel-like factor 4; c-Myc, proto-oncogene for avian myelocytomatosis viral oncogene homolog; Esg1, embryonic stem cell-specific gene 1; Rex1, RNA exonuclease 1 homolog; Pdx1, pancreatic and duodenal homeobox 1; GAPDH, glyceraldehyde-3-phosphate dehydrogenase. (B) PCR analysis of genomic DNA isolated from the pancreatic tissue of NOD mice (Panc), ES cells (ES), iTS-P lines (4–2, 4–3, 4–4, 4–7, 4–9, and 4–11) to detect the presence of FUW-OSKM integrated into the chromosomes of iTS-P lines. Primers 2 (O-1), 3 (O-2), and 4 (K) correspond to the cDNA for each protein in FUW-OSKM ( Fig 1A and S1 Table ). When genomic PCR is performed using these primers, the size of the amplified endogenous gene (Endo; shown by open arrowheads) is always larger than that of the cDNA (Tg; shown by solid arrowheads) in FUW-OSKM, since the former products contain intronic sequences. Since primers 1 and 5 are specific to FUW-OSKM, the samples showing amplification with these primers are thought to be the ones carrying FUW-OSKM in their genome. Lane OSKM shows FUW-OSKM plasmid (~10 ng) amplified as a positive control.
    Figure Legend Snippet: Expression analysis in iTS-P. (A) RT-PCR analysis for mRNA expression of pluripotency-related markers (Oct3/4, Sox2, Klf4, c-Myc, Esg1, and Rex1) and the pancreas-related marker (Pdx1) in the pancreatic tissue of NOD mice (Panc), the ES cells (ES), and the iTS-P lines (4–2, 4–3, 4–4, 4–7, 4–9 and 4–11). Abbreviations: Oct3/4, octamer-binding transcription factor 3/4; Sox2, SRY (sex determining region Y)-box 2; Klf4, Kruppel-like factor 4; c-Myc, proto-oncogene for avian myelocytomatosis viral oncogene homolog; Esg1, embryonic stem cell-specific gene 1; Rex1, RNA exonuclease 1 homolog; Pdx1, pancreatic and duodenal homeobox 1; GAPDH, glyceraldehyde-3-phosphate dehydrogenase. (B) PCR analysis of genomic DNA isolated from the pancreatic tissue of NOD mice (Panc), ES cells (ES), iTS-P lines (4–2, 4–3, 4–4, 4–7, 4–9, and 4–11) to detect the presence of FUW-OSKM integrated into the chromosomes of iTS-P lines. Primers 2 (O-1), 3 (O-2), and 4 (K) correspond to the cDNA for each protein in FUW-OSKM ( Fig 1A and S1 Table ). When genomic PCR is performed using these primers, the size of the amplified endogenous gene (Endo; shown by open arrowheads) is always larger than that of the cDNA (Tg; shown by solid arrowheads) in FUW-OSKM, since the former products contain intronic sequences. Since primers 1 and 5 are specific to FUW-OSKM, the samples showing amplification with these primers are thought to be the ones carrying FUW-OSKM in their genome. Lane OSKM shows FUW-OSKM plasmid (~10 ng) amplified as a positive control.

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Marker, Mouse Assay, Binding Assay, Polymerase Chain Reaction, Isolation, Amplification, Plasmid Preparation, Positive Control

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    Amplification:

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    Synthesized:

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    Quantitative RT-PCR:

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    Article Snippet: To ensure a consistent hypoxic exposure, the O2 concentration in the cages was checked at hourly intervals during the day and every 3 hours at night. .. Western immunoblot assays and real-time PCR were conducted, as described and validated previously by our laboratory., , We isolated and quantified RNA and protein by Allprep DNA/RNA Mini Kit according to the manufacturer’s instructions (Qiagen Inc, Valencia, CA Cat # 80204). .. Isolated messenger RNA (mRNA) was analyzed using a Beckman Spectrophotometer at 260/280 wavelength UV rays to check for quality and quantity.

    Article Title: Determinants of Orofacial Clefting I: Effects of 5-Aza-2′-deoxycytidine on Cellular Processes and Gene Expression during Development of the First Branchial Arch
    Article Snippet: For individual TaqMan quantitative real-time PCR (qRT-PCR) and for TaqMan array card-based gene expression profiling, 1-BAs of AzaD- or vehicle exposed embryos were microdissected 6, 9 and 12 hours post-exposure and pooled for analyses ( ). .. 1-BA tissue from three independent pools of 12 to 15 staged embryos was collected, total RNA and genomic DNA extracted (AllPrep DNA/RNA Mini Kit; Qiagen Inc., Valencia, CA), and stored at −80°C.

    Article Title: Differentiation of Human Neural Stem Cells into Motor Neurons Stimulates Mitochondrial Biogenesis and Decreases Glycolytic Flux
    Article Snippet: For TOM20 analysis, pixel values were normalized to the number of cells in each image identified by DAPI nuclear staining. .. For quantitative PCR (qPCR) analysis of hESC-derived cells, DNA and RNA were extracted at 7-day time points through day 28 using the AllPrep DNA/RNA Mini Kit (Qiagen). .. For iPSC-derived cells, RNA was extracted at day 0 (D0) and D21 with the RNeasy or RNeasy Plus Micro Kit (Qiagen), and DNA was extracted with the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer's instructions.

    Article Title: Fluid Flow Regulation of Revascularization and Cellular Organization in a Bioengineered Liver Platform
    Article Snippet: Paragraph title: RNA extraction and real-time polymerase chain reaction ... Total RNA was extracted from a small sample of reseeded liver scaffolds using the Allprep DNA/RNA Mini Kit (Qiagen, Germantown, MD) with DNAse treatment. cDNA was synthesized from 500 ng of total RNA using Superscript III First Strand Synthesis (Life Technologies, Carlsbad, CA).

    Article Title: Generalized disruption of inherited genomic imprints leads to wide-ranging placental defects and dysregulated fetal growth
    Article Snippet: RNA was extracted using either the AllPrep DNA/RNA Micro or Mini Kit (Qiagen). .. RNA was extracted using either the AllPrep DNA/RNA Micro or Mini Kit (Qiagen).

    Article Title: Ribosomal protein gene deletions in Diamond-Blackfan anemia
    Article Snippet: Paragraph title: Reverse transcription and quantitative PCR ... RNA and DNA were isolated from peripheral blood mononuclear cells after separation of whole blood by Ficoll-Paque PLUS (GE Health Sciences) and expansion for 1-5 days in RPMI medium supplemented with 10% FBS, 2mM l -glutamine, and 5 ng/mL of concanavalin A (Sigma-Aldrich) with the AllPrep Mini Kit (QIAGEN), and quantified by fluorescence using the Qubit RNA Assay or the dsDNA HS Assay (Invitrogen).

    Microarray:

    Article Title: Candidate serum biomarkers for early intestinal cancer using 15N metabolic labeling and quantitative proteomics in the Apcmin/+ mouse
    Article Snippet: DNA and RNA were isolated concurrently using the Qiagen All-prep Mini-kit. .. Once isolated, optical density readings and concentrations of both the DNA and RNA were determined using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific) and RNA quality was determined using a Agilent 2100 Bioanalyzer.

    Immunocytochemistry:

    Article Title: Determinants of Orofacial Clefting I: Effects of 5-Aza-2′-deoxycytidine on Cellular Processes and Gene Expression during Development of the First Branchial Arch
    Article Snippet: These three treatment periods were selected on the basis of preliminary data (TaqMan qRT-PCR and immunocytochemistry) that demonstrated: (1) significant, temporal, and differential expression of several genes, and (2) a striking temporal decrease in cell proliferation and marked increase in apoptosis within tissue of the 1-BA. .. 1-BA tissue from three independent pools of 12 to 15 staged embryos was collected, total RNA and genomic DNA extracted (AllPrep DNA/RNA Mini Kit; Qiagen Inc., Valencia, CA), and stored at −80°C.

    Expressing:

    Article Title: Determinants of Orofacial Clefting I: Effects of 5-Aza-2′-deoxycytidine on Cellular Processes and Gene Expression during Development of the First Branchial Arch
    Article Snippet: These three treatment periods were selected on the basis of preliminary data (TaqMan qRT-PCR and immunocytochemistry) that demonstrated: (1) significant, temporal, and differential expression of several genes, and (2) a striking temporal decrease in cell proliferation and marked increase in apoptosis within tissue of the 1-BA. .. 1-BA tissue from three independent pools of 12 to 15 staged embryos was collected, total RNA and genomic DNA extracted (AllPrep DNA/RNA Mini Kit; Qiagen Inc., Valencia, CA), and stored at −80°C.

    Article Title: Fluid Flow Regulation of Revascularization and Cellular Organization in a Bioengineered Liver Platform
    Article Snippet: Total RNA was extracted from a small sample of reseeded liver scaffolds using the Allprep DNA/RNA Mini Kit (Qiagen, Germantown, MD) with DNAse treatment. cDNA was synthesized from 500 ng of total RNA using Superscript III First Strand Synthesis (Life Technologies, Carlsbad, CA). .. Reverse transcription polymerase chain reaction (RT-PCR) was performed using Taqman Master Mix (Life Technologies) with mouse KLF2 , integrin β1 , integrin β3 , and eNOS taqman probes with GAPDH housekeeping gene (Life Technologies).

    Article Title: Universal Artificial Antigen Presenting Cells to Selectively Propagate T Cells Expressing Chimeric Antigen Receptor Independent of Specificity
    Article Snippet: The direct TCR expression assay (DTEA), as previously reported, was used to measure the abundance of mRNA transcripts coding for 45 TCR α alleles, 46 TCR β alleles, 13 TCR γ alleles, and 5 TCR δ alleles from RNA obtained on Day 0 (T cells in PBMC before electroporation) and Day 21 (from T cells after electroporation/ propagation). .. RNA was extracted from thawed samples using the ALLprep DNA/RNA mini kit (Qiagen; Cat. No. 80204).

    Article Title: Ribosomal protein gene deletions in Diamond-Blackfan anemia
    Article Snippet: RNA and DNA were isolated from peripheral blood mononuclear cells after separation of whole blood by Ficoll-Paque PLUS (GE Health Sciences) and expansion for 1-5 days in RPMI medium supplemented with 10% FBS, 2mM l -glutamine, and 5 ng/mL of concanavalin A (Sigma-Aldrich) with the AllPrep Mini Kit (QIAGEN), and quantified by fluorescence using the Qubit RNA Assay or the dsDNA HS Assay (Invitrogen). .. All PCR reactions were linear over 3 orders of magnitude bracketing the experimental results and were > 95% efficient.

    Article Title: Effects of intratracheally instilled laser printer-emitted engineered nanoparticles in a mouse model: A case study of toxicological implications from nanomaterials released during consumer use
    Article Snippet: Paragraph title: 2.8. Methylation and expression analysis of transposable element LINE-1 ... RNA and DNA were extracted simultaneously from flash-frozen cells and lung tissue of mice instilled with PEPs (2.5 mg/kg) or vehicle control (DI H2 O) using the AllPrep Mini Kit (Qiagen, Valencia, CA) for simultaneous RNA and DNA isolation according to the manufacturer's protocol.

    Article Title: Candidate serum biomarkers for early intestinal cancer using 15N metabolic labeling and quantitative proteomics in the Apcmin/+ mouse
    Article Snippet: DNA and RNA were isolated concurrently using the Qiagen All-prep Mini-kit. .. Once isolated, optical density readings and concentrations of both the DNA and RNA were determined using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific) and RNA quality was determined using a Agilent 2100 Bioanalyzer.

    Genome Wide:

    Article Title: Expression quantitative trait loci (eQTLs) in human placentas suggest developmental origins of complex diseases
    Article Snippet: Nucleic acids (e.g. genomic DNA and total RNA) were extracted from the samples stored in RNALater using the QIAmp DNA mini kit (Qiagen, #51306) and RNeasy mini kit (Qiagen, #74106), respectively, according to the manufacturer’s instruction (Qiagen, 80204). .. On each sample, we generated about 20 million single-end RNAseq reads.

    Western Blot:

    Article Title: Antenatal Maternal Hypoxic Stress
    Article Snippet: To ensure a consistent hypoxic exposure, the O2 concentration in the cages was checked at hourly intervals during the day and every 3 hours at night. .. Western immunoblot assays and real-time PCR were conducted, as described and validated previously by our laboratory., , We isolated and quantified RNA and protein by Allprep DNA/RNA Mini Kit according to the manufacturer’s instructions (Qiagen Inc, Valencia, CA Cat # 80204). .. Isolated messenger RNA (mRNA) was analyzed using a Beckman Spectrophotometer at 260/280 wavelength UV rays to check for quality and quantity.

    Derivative Assay:

    Article Title: Pan-cancer analysis of somatic copy number alterations implicates IRS4 and IGF2 in enhancer hijacking
    Article Snippet: In addition, patient derived TIC enriched spheroid cells were pelleted by centrifugation (800 rpm, 4°C, 5 min) and washed two times with PBS to get rid of the residual media. .. DNA and RNA of primary patient tissue and spheroids were isolated using DNeasy® Blood & Tissue Kit (Qiagen) and AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instruction.

    Electroporation:

    Article Title: Universal Artificial Antigen Presenting Cells to Selectively Propagate T Cells Expressing Chimeric Antigen Receptor Independent of Specificity
    Article Snippet: The direct TCR expression assay (DTEA), as previously reported, was used to measure the abundance of mRNA transcripts coding for 45 TCR α alleles, 46 TCR β alleles, 13 TCR γ alleles, and 5 TCR δ alleles from RNA obtained on Day 0 (T cells in PBMC before electroporation) and Day 21 (from T cells after electroporation/ propagation). .. RNA was extracted from thawed samples using the ALLprep DNA/RNA mini kit (Qiagen; Cat. No. 80204).

    Infection:

    Article Title: Interleukin 1 receptor antagonist mediates the antiinflammatory and antifibrotic effect of mesenchymal stem cells during lung injury
    Article Snippet: Some mice were infected with 1 × 109 particles of a retrovirus encoding human IL1RN (provided by P. Robbins, University of Pittsburgh, Pittsburgh, PA) or had an osmotic pump (ALZET, Cupertino, CA) that secreted 0.5 mg/kg/hr of recombinant human IL1RN (ProSpec-Tany TehcnoGene, Rehovot, Israel) surgically implanted into their peritoneal cavity 1 day before BLM exposure. .. The left lung was then removed, flash-frozen in liquid nitrogen, and used to harvest genomic DNA and total RNA, using the AllPrep DNA/RNA Mini Kit (Qiagen).

    Article Title: CYTOMEGALOVIRUS VECTORS VIOLATE CD8+ T CELL EPITOPE RECOGNITION PARADIGMS
    Article Snippet: Infected cell preparations were > 95% CD4+ T cells and > 50% SIV-infected following enrichment and were used at an effector:target ratio of 80:1. .. Prior to MHC-II restriction assays, mRNA from these transfectants was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen), amplified by RT-PCR using a universal primer pair (5′-GACACTGATGGTGCTGAGC-3′ and 5′-GCTGCACTGTGAAGCTCTC-3′) spanning the highly polymorphic β1 region of Mamu-DRB , and sequence confirmed.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: CYTOMEGALOVIRUS VECTORS VIOLATE CD8+ T CELL EPITOPE RECOGNITION PARADIGMS
    Article Snippet: Mamu-DRA*01:05 was paired with DRB1*10:07 , DRB1 * 04:06, DRB1 * 03:09, DRB5*03:01, DRB*w2:01, and DRB*w26:03, while Mamu-DRA*01:021 was paired with DRB*w4:01 . .. Prior to MHC-II restriction assays, mRNA from these transfectants was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen), amplified by RT-PCR using a universal primer pair (5′-GACACTGATGGTGCTGAGC-3′ and 5′-GCTGCACTGTGAAGCTCTC-3′) spanning the highly polymorphic β1 region of Mamu-DRB , and sequence confirmed. .. MHC-II transfectants and BLCL were pulsed with the Gag peptide of interest at a final concentration of 5 μg/ml for 90 minutes (37°C) then washed twice with warm PBS and once with warm R10 to remove unbound peptide before being used to stimulate freshly isolated PBMC at an effector:target ratio of 10:1.

    Article Title: A Kunitz Protease Inhibitor from Dermacentor variabilis, a Vector for Spotted Fever Group Rickettsiae, Limits Rickettsia montanensis Invasion
    Article Snippet: Total RNA was isolated from tissues or cells by use of an ALLPrep DNA/RNA Mini kit according to the manufacturer's procedures (Qiagen, Valencia, CA). .. For expression analysis, transcripts were amplified using a Brilliant II Sybr green QRT-PCR master mix kit according to the manufacturer's instructions (Agilent Technologies, Santa Clara, CA).

    Generated:

    Article Title: CYTOMEGALOVIRUS VECTORS VIOLATE CD8+ T CELL EPITOPE RECOGNITION PARADIGMS
    Article Snippet: Autologous B-lymphoblastoid cell lines (BLCL) were generated by infecting rhesus PBMC with Herpesvirus papio ( ). .. Prior to MHC-II restriction assays, mRNA from these transfectants was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen), amplified by RT-PCR using a universal primer pair (5′-GACACTGATGGTGCTGAGC-3′ and 5′-GCTGCACTGTGAAGCTCTC-3′) spanning the highly polymorphic β1 region of Mamu-DRB , and sequence confirmed.

    Article Title: Expression quantitative trait loci (eQTLs) in human placentas suggest developmental origins of complex diseases
    Article Snippet: Nucleic acids (e.g. genomic DNA and total RNA) were extracted from the samples stored in RNALater using the QIAmp DNA mini kit (Qiagen, #51306) and RNeasy mini kit (Qiagen, #74106), respectively, according to the manufacturer’s instruction (Qiagen, 80204). .. RNA sequencing library prepared using RiboZero kit (Illumina, San Diego, CA, USA), followed with sequencing on Illumina High-Seq 2500 platform.

    DNA HS Assay:

    Article Title: QseC inhibition as an antivirulence approach for colitis-associated bacteria
    Article Snippet: Nucleic acids were extracted using phenol-chloroform bead-beating, followed by DNA/RNA separation and purification using the AllPrep DNA/RNA Mini Kit (Qiagen). .. Nucleic acids were extracted using phenol-chloroform bead-beating, followed by DNA/RNA separation and purification using the AllPrep DNA/RNA Mini Kit (Qiagen).

    DNA Sequencing:

    Article Title: Pan-cancer analysis of somatic copy number alterations implicates IRS4 and IGF2 in enhancer hijacking
    Article Snippet: Paragraph title: Isolation of nucleic acids for DNA sequencing and RNA expression analysis ... DNA and RNA of primary patient tissue and spheroids were isolated using DNeasy® Blood & Tissue Kit (Qiagen) and AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instruction.

    Sequencing:

    Article Title: CYTOMEGALOVIRUS VECTORS VIOLATE CD8+ T CELL EPITOPE RECOGNITION PARADIGMS
    Article Snippet: Mamu-DRA*01:05 was paired with DRB1*10:07 , DRB1 * 04:06, DRB1 * 03:09, DRB5*03:01, DRB*w2:01, and DRB*w26:03, while Mamu-DRA*01:021 was paired with DRB*w4:01 . .. Prior to MHC-II restriction assays, mRNA from these transfectants was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen), amplified by RT-PCR using a universal primer pair (5′-GACACTGATGGTGCTGAGC-3′ and 5′-GCTGCACTGTGAAGCTCTC-3′) spanning the highly polymorphic β1 region of Mamu-DRB , and sequence confirmed. .. MHC-II transfectants and BLCL were pulsed with the Gag peptide of interest at a final concentration of 5 μg/ml for 90 minutes (37°C) then washed twice with warm PBS and once with warm R10 to remove unbound peptide before being used to stimulate freshly isolated PBMC at an effector:target ratio of 10:1.

    Article Title: QseC inhibition as an antivirulence approach for colitis-associated bacteria
    Article Snippet: Paragraph title: 16S rRNA Gene Surveys of Stool and Sequence Analysis. ... Nucleic acids were extracted using phenol-chloroform bead-beating, followed by DNA/RNA separation and purification using the AllPrep DNA/RNA Mini Kit (Qiagen).

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: RNA was isolated from the NKTCL cases using the AllPrep DNA/RNA Mini Kit (Qiagen Inc., Valencia, CA). .. RNA was isolated from the NKTCL cases using the AllPrep DNA/RNA Mini Kit (Qiagen Inc., Valencia, CA).

    Article Title: Expression quantitative trait loci (eQTLs) in human placentas suggest developmental origins of complex diseases
    Article Snippet: Nucleic acids (e.g. genomic DNA and total RNA) were extracted from the samples stored in RNALater using the QIAmp DNA mini kit (Qiagen, #51306) and RNeasy mini kit (Qiagen, #74106), respectively, according to the manufacturer’s instruction (Qiagen, 80204). .. Nucleic acids (e.g. genomic DNA and total RNA) were extracted from the samples stored in RNALater using the QIAmp DNA mini kit (Qiagen, #51306) and RNeasy mini kit (Qiagen, #74106), respectively, according to the manufacturer’s instruction (Qiagen, 80204).

    Injection:

    Article Title: Interleukin 1 receptor antagonist mediates the antiinflammatory and antifibrotic effect of mesenchymal stem cells during lung injury
    Article Snippet: Murine MSCs (5 × 105 in 200 μl of PBS) were injected into the jugular vein immediately after BLM administration. .. The left lung was then removed, flash-frozen in liquid nitrogen, and used to harvest genomic DNA and total RNA, using the AllPrep DNA/RNA Mini Kit (Qiagen).

    Article Title: Determinants of Orofacial Clefting I: Effects of 5-Aza-2′-deoxycytidine on Cellular Processes and Gene Expression during Development of the First Branchial Arch
    Article Snippet: AzaD or vehicle was delivered via single intraperitoneal injection to pregnant females on GD 9.5 and embryos were collected on GD-15.5 and -17.5. .. 1-BA tissue from three independent pools of 12 to 15 staged embryos was collected, total RNA and genomic DNA extracted (AllPrep DNA/RNA Mini Kit; Qiagen Inc., Valencia, CA), and stored at −80°C.

    Recombinant:

    Article Title: Interleukin 1 receptor antagonist mediates the antiinflammatory and antifibrotic effect of mesenchymal stem cells during lung injury
    Article Snippet: Some mice were infected with 1 × 109 particles of a retrovirus encoding human IL1RN (provided by P. Robbins, University of Pittsburgh, Pittsburgh, PA) or had an osmotic pump (ALZET, Cupertino, CA) that secreted 0.5 mg/kg/hr of recombinant human IL1RN (ProSpec-Tany TehcnoGene, Rehovot, Israel) surgically implanted into their peritoneal cavity 1 day before BLM exposure. .. The left lung was then removed, flash-frozen in liquid nitrogen, and used to harvest genomic DNA and total RNA, using the AllPrep DNA/RNA Mini Kit (Qiagen).

    DNA Extraction:

    Article Title: Effects of intratracheally instilled laser printer-emitted engineered nanoparticles in a mouse model: A case study of toxicological implications from nanomaterials released during consumer use
    Article Snippet: Relative gene expression was analyzed using the 2−ΔΔCT method with polymerase (RNA) II (DNA directed) polypeptide A ( POLR2a ) as the internal control. .. RNA and DNA were extracted simultaneously from flash-frozen cells and lung tissue of mice instilled with PEPs (2.5 mg/kg) or vehicle control (DI H2 O) using the AllPrep Mini Kit (Qiagen, Valencia, CA) for simultaneous RNA and DNA isolation according to the manufacturer's protocol. .. Analyses of methylation and expression of LINE-1 were performed by methylation-sensitive qRT-PCR as reported earlier in detail by the authors ( ).

    RNA Sequencing Assay:

    Article Title: Expression quantitative trait loci (eQTLs) in human placentas suggest developmental origins of complex diseases
    Article Snippet: Nucleic acids (e.g. genomic DNA and total RNA) were extracted from the samples stored in RNALater using the QIAmp DNA mini kit (Qiagen, #51306) and RNeasy mini kit (Qiagen, #74106), respectively, according to the manufacturer’s instruction (Qiagen, 80204). .. Nucleic acids (e.g. genomic DNA and total RNA) were extracted from the samples stored in RNALater using the QIAmp DNA mini kit (Qiagen, #51306) and RNeasy mini kit (Qiagen, #74106), respectively, according to the manufacturer’s instruction (Qiagen, 80204).

    Fluorescence:

    Article Title: Ribosomal protein gene deletions in Diamond-Blackfan anemia
    Article Snippet: Array data were deposited in the NCBI/Gene Expression Omnibus database under accession number . .. RNA and DNA were isolated from peripheral blood mononuclear cells after separation of whole blood by Ficoll-Paque PLUS (GE Health Sciences) and expansion for 1-5 days in RPMI medium supplemented with 10% FBS, 2mM l -glutamine, and 5 ng/mL of concanavalin A (Sigma-Aldrich) with the AllPrep Mini Kit (QIAGEN), and quantified by fluorescence using the Qubit RNA Assay or the dsDNA HS Assay (Invitrogen). .. RNA was reverse-transcribed using the iScript cDNA Synthesis Kit (Bio-Rad) after normalization of input RNA in a 20-μL reaction volume following the manufacturer's instructions, and diluted 1:4 after heat inactivation.

    Methylation:

    Article Title: Epigenetic impact of simulated maternal grooming on estrogen receptor alpha within the developing amygdala
    Article Snippet: Genomic DNA was isolated using Qiagen’s AllPrep Mini Kit (Cat. #80204, Valencia, CA). .. Genomic DNA was isolated using Qiagen’s AllPrep Mini Kit (Cat. #80204, Valencia, CA).

    Article Title: Effects of intratracheally instilled laser printer-emitted engineered nanoparticles in a mouse model: A case study of toxicological implications from nanomaterials released during consumer use
    Article Snippet: Paragraph title: 2.8. Methylation and expression analysis of transposable element LINE-1 ... RNA and DNA were extracted simultaneously from flash-frozen cells and lung tissue of mice instilled with PEPs (2.5 mg/kg) or vehicle control (DI H2 O) using the AllPrep Mini Kit (Qiagen, Valencia, CA) for simultaneous RNA and DNA isolation according to the manufacturer's protocol.

    Isolation:

    Article Title: Antenatal Maternal Hypoxic Stress
    Article Snippet: To ensure a consistent hypoxic exposure, the O2 concentration in the cages was checked at hourly intervals during the day and every 3 hours at night. .. Western immunoblot assays and real-time PCR were conducted, as described and validated previously by our laboratory., , We isolated and quantified RNA and protein by Allprep DNA/RNA Mini Kit according to the manufacturer’s instructions (Qiagen Inc, Valencia, CA Cat # 80204). .. Isolated messenger RNA (mRNA) was analyzed using a Beckman Spectrophotometer at 260/280 wavelength UV rays to check for quality and quantity.

    Article Title: Pan-cancer analysis of somatic copy number alterations implicates IRS4 and IGF2 in enhancer hijacking
    Article Snippet: In addition, patient derived TIC enriched spheroid cells were pelleted by centrifugation (800 rpm, 4°C, 5 min) and washed two times with PBS to get rid of the residual media. .. DNA and RNA of primary patient tissue and spheroids were isolated using DNeasy® Blood & Tissue Kit (Qiagen) and AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instruction. .. RNA extracted in Oslo was isolated using Standard TRIZOL methods (Invitrogen, Carlsbad, CA), as specified by the manufacturer's instructions.

    Article Title: Differentiation of Human Neural Stem Cells into Motor Neurons Stimulates Mitochondrial Biogenesis and Decreases Glycolytic Flux
    Article Snippet: For quantitative PCR (qPCR) analysis of hESC-derived cells, DNA and RNA were extracted at 7-day time points through day 28 using the AllPrep DNA/RNA Mini Kit (Qiagen). .. For iPSC-derived cells, RNA was extracted at day 0 (D0) and D21 with the RNeasy or RNeasy Plus Micro Kit (Qiagen), and DNA was extracted with the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer's instructions.

    Article Title: A Kunitz Protease Inhibitor from Dermacentor variabilis, a Vector for Spotted Fever Group Rickettsiae, Limits Rickettsia montanensis Invasion
    Article Snippet: To demonstrate that DvKPI was of tick origin, both rabbit and sheep sera were processed for Western blotting and probed using anti-DvKPI. .. Total RNA was isolated from tissues or cells by use of an ALLPrep DNA/RNA Mini kit according to the manufacturer's procedures (Qiagen, Valencia, CA). .. For expression analysis, transcripts were amplified using a Brilliant II Sybr green QRT-PCR master mix kit according to the manufacturer's instructions (Agilent Technologies, Santa Clara, CA).

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: The purity of activated NK cells was evaluated with CD56-allophycocyanin and CD3-phycoerythrin staining, and > 95% CD56+ /CD3− cells were used for subsequent analysis. .. RNA was isolated from the NKTCL cases using the AllPrep DNA/RNA Mini Kit (Qiagen Inc., Valencia, CA). .. Quality and integrity of the RNA was determined with the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

    Article Title: Epigenetic impact of simulated maternal grooming on estrogen receptor alpha within the developing amygdala
    Article Snippet: Then, this section of tissue was placed rostral side up and a cut was made along the optic tract followed by another cut at approximately 60 deg to form an approximate triangle. .. Genomic DNA was isolated using Qiagen’s AllPrep Mini Kit (Cat. #80204, Valencia, CA). .. DNA concentrations were determined using the Qubit Quantification Platform (Cat. # , Invitrogen, Carlsbad, CA).

    Article Title: Ribosomal protein gene deletions in Diamond-Blackfan anemia
    Article Snippet: Array data were deposited in the NCBI/Gene Expression Omnibus database under accession number . .. RNA and DNA were isolated from peripheral blood mononuclear cells after separation of whole blood by Ficoll-Paque PLUS (GE Health Sciences) and expansion for 1-5 days in RPMI medium supplemented with 10% FBS, 2mM l -glutamine, and 5 ng/mL of concanavalin A (Sigma-Aldrich) with the AllPrep Mini Kit (QIAGEN), and quantified by fluorescence using the Qubit RNA Assay or the dsDNA HS Assay (Invitrogen). .. RNA was reverse-transcribed using the iScript cDNA Synthesis Kit (Bio-Rad) after normalization of input RNA in a 20-μL reaction volume following the manufacturer's instructions, and diluted 1:4 after heat inactivation.

    Article Title: Candidate serum biomarkers for early intestinal cancer using 15N metabolic labeling and quantitative proteomics in the Apcmin/+ mouse
    Article Snippet: The area within 4 mm of any tumor was avoided to prevent contamination with hyperplastic tissue. .. DNA and RNA were isolated concurrently using the Qiagen All-prep Mini-kit. .. Once isolated, optical density readings and concentrations of both the DNA and RNA were determined using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific) and RNA quality was determined using a Agilent 2100 Bioanalyzer.

    Mouse Assay:

    Article Title: Interleukin 1 receptor antagonist mediates the antiinflammatory and antifibrotic effect of mesenchymal stem cells during lung injury
    Article Snippet: Some mice were infected with 1 × 109 particles of a retrovirus encoding human IL1RN (provided by P. Robbins, University of Pittsburgh, Pittsburgh, PA) or had an osmotic pump (ALZET, Cupertino, CA) that secreted 0.5 mg/kg/hr of recombinant human IL1RN (ProSpec-Tany TehcnoGene, Rehovot, Israel) surgically implanted into their peritoneal cavity 1 day before BLM exposure. .. The left lung was then removed, flash-frozen in liquid nitrogen, and used to harvest genomic DNA and total RNA, using the AllPrep DNA/RNA Mini Kit (Qiagen).

    Article Title: Effects of intratracheally instilled laser printer-emitted engineered nanoparticles in a mouse model: A case study of toxicological implications from nanomaterials released during consumer use
    Article Snippet: Relative gene expression was analyzed using the 2−ΔΔCT method with polymerase (RNA) II (DNA directed) polypeptide A ( POLR2a ) as the internal control. .. RNA and DNA were extracted simultaneously from flash-frozen cells and lung tissue of mice instilled with PEPs (2.5 mg/kg) or vehicle control (DI H2 O) using the AllPrep Mini Kit (Qiagen, Valencia, CA) for simultaneous RNA and DNA isolation according to the manufacturer's protocol. .. Analyses of methylation and expression of LINE-1 were performed by methylation-sensitive qRT-PCR as reported earlier in detail by the authors ( ).

    Article Title: Candidate serum biomarkers for early intestinal cancer using 15N metabolic labeling and quantitative proteomics in the Apcmin/+ mouse
    Article Snippet: Four male (C57BL/6J- ApcMin /+ x BTBR) F1 Min mice were aged to 110 days and then sacrificed. .. DNA and RNA were isolated concurrently using the Qiagen All-prep Mini-kit.

    Polymerase Chain Reaction:

    Article Title: Stem Cells, Neural Progenitors, and Engineered Stem Cells
    Article Snippet: AllPrep DNA / RNA Mini Kit (Qiagen, Valencia, CA). .. AllPrep DNA / RNA Mini Kit (Qiagen, Valencia, CA).

    Article Title: A Kunitz Protease Inhibitor from Dermacentor variabilis, a Vector for Spotted Fever Group Rickettsiae, Limits Rickettsia montanensis Invasion
    Article Snippet: Total RNA was isolated from tissues or cells by use of an ALLPrep DNA/RNA Mini kit according to the manufacturer's procedures (Qiagen, Valencia, CA). .. Total RNA was isolated from tissues or cells by use of an ALLPrep DNA/RNA Mini kit according to the manufacturer's procedures (Qiagen, Valencia, CA).

    Article Title: QseC inhibition as an antivirulence approach for colitis-associated bacteria
    Article Snippet: Nucleic acids were extracted using phenol-chloroform bead-beating, followed by DNA/RNA separation and purification using the AllPrep DNA/RNA Mini Kit (Qiagen). .. Nucleic acids were extracted using phenol-chloroform bead-beating, followed by DNA/RNA separation and purification using the AllPrep DNA/RNA Mini Kit (Qiagen).

    Article Title: Detection of a Novel Ehrlichia Species in Haemaphysalis longicornis Tick from China
    Article Snippet: Paragraph title: DNA preparation and polymerase chain reaction amplification of Ehrlichia DNA ... Total tick nucleic acids were extracted simultaneously by using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer's instructions.

    Article Title: Generalized disruption of inherited genomic imprints leads to wide-ranging placental defects and dysregulated fetal growth
    Article Snippet: RNA was extracted using either the AllPrep DNA/RNA Micro or Mini Kit (Qiagen). .. RNA was extracted using either the AllPrep DNA/RNA Micro or Mini Kit (Qiagen).

    Article Title: Ribosomal protein gene deletions in Diamond-Blackfan anemia
    Article Snippet: RNA and DNA were isolated from peripheral blood mononuclear cells after separation of whole blood by Ficoll-Paque PLUS (GE Health Sciences) and expansion for 1-5 days in RPMI medium supplemented with 10% FBS, 2mM l -glutamine, and 5 ng/mL of concanavalin A (Sigma-Aldrich) with the AllPrep Mini Kit (QIAGEN), and quantified by fluorescence using the Qubit RNA Assay or the dsDNA HS Assay (Invitrogen). .. Quantitative PCR (qPCR) was performed in triplicate for each reaction in a 20-μL reaction volume of 1× SsoFast EvaGreen Supermix (Bio-Rad) and 500nM primers with 40 ng of gDNA or 1 μL of diluted cDNA reaction mixture on a Bio-Rad CFX96 instrument with initial denature of 98°C for 5 minutes, 40 cycles of 98°C for 5 seconds, and 60°C for 5 seconds, followed by melt-curve analysis for reaction specificity.

    Co-Culture Assay:

    Article Title: Universal Artificial Antigen Presenting Cells to Selectively Propagate T Cells Expressing Chimeric Antigen Receptor Independent of Specificity
    Article Snippet: The resulting CD3+ CD56neg T cells (2 to 3 x 106 from each sample) were snap frozen as were 2 x 106 cells directly harvested at Day 21 of co-culture. .. RNA was extracted from thawed samples using the ALLprep DNA/RNA mini kit (Qiagen; Cat. No. 80204).

    Purification:

    Article Title: CYTOMEGALOVIRUS VECTORS VIOLATE CD8+ T CELL EPITOPE RECOGNITION PARADIGMS
    Article Snippet: Autologous SIV-infected target cells were produced by spinoculation of activated CD4+ T cells with sucrose-purified SIVmac239, followed by 4 days of culture and then purification with CD4 microbeads and LS columns (Miltenyi Biotec), as previously described ( ). .. Prior to MHC-II restriction assays, mRNA from these transfectants was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen), amplified by RT-PCR using a universal primer pair (5′-GACACTGATGGTGCTGAGC-3′ and 5′-GCTGCACTGTGAAGCTCTC-3′) spanning the highly polymorphic β1 region of Mamu-DRB , and sequence confirmed.

    Article Title: FAM111B MUTATION IS ASSOCIATED WITH INHERITED EXOCRINE PANCREATIC DYSFUNCTION
    Article Snippet: Bone marrow stromal cells and lymphoblasts were prepared and cultured as previously described. .. Genomic DNA was purified from patient blood samples using the AllPrep DNA/RNA Mini Kit (Qiagen, Venlo, The Netherlands). .. Saliva samples were collected with the Oragene Dx collection kit (DNA Genotek, Kanata, Canada).

    Article Title: QseC inhibition as an antivirulence approach for colitis-associated bacteria
    Article Snippet: Stool was collected and pooled on pid 115, homogenized in RNA later (Ambion), held at 4 °C overnight, and stored at −80 °C before processing. .. Nucleic acids were extracted using phenol-chloroform bead-beating, followed by DNA/RNA separation and purification using the AllPrep DNA/RNA Mini Kit (Qiagen). .. DNA was quantified using a NanoPhotometer Pearl spectrophotometer (Denville) and stored at −20 °C before undergoing 16S rRNA gene amplification by PCR.

    Chromatin Immunoprecipitation:

    Article Title: Expression quantitative trait loci (eQTLs) in human placentas suggest developmental origins of complex diseases
    Article Snippet: Nucleic acids (e.g. genomic DNA and total RNA) were extracted from the samples stored in RNALater using the QIAmp DNA mini kit (Qiagen, #51306) and RNeasy mini kit (Qiagen, #74106), respectively, according to the manufacturer’s instruction (Qiagen, 80204). .. On each sample, we generated about 20 million single-end RNAseq reads.

    Plasmid Preparation:

    Article Title: CYTOMEGALOVIRUS VECTORS VIOLATE CD8+ T CELL EPITOPE RECOGNITION PARADIGMS
    Article Snippet: Construction of single Mamu-DR allomorph transfectants was performed as previously described , except that Mamu-DR alleles were inserted into plasmid pCEP4 (Invitrogen) rather than pcDNC3.1. .. Prior to MHC-II restriction assays, mRNA from these transfectants was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen), amplified by RT-PCR using a universal primer pair (5′-GACACTGATGGTGCTGAGC-3′ and 5′-GCTGCACTGTGAAGCTCTC-3′) spanning the highly polymorphic β1 region of Mamu-DRB , and sequence confirmed.

    Software:

    Article Title: Antenatal Maternal Hypoxic Stress
    Article Snippet: Western immunoblot assays and real-time PCR were conducted, as described and validated previously by our laboratory., , We isolated and quantified RNA and protein by Allprep DNA/RNA Mini Kit according to the manufacturer’s instructions (Qiagen Inc, Valencia, CA Cat # 80204). .. Western immunoblot assays and real-time PCR were conducted, as described and validated previously by our laboratory., , We isolated and quantified RNA and protein by Allprep DNA/RNA Mini Kit according to the manufacturer’s instructions (Qiagen Inc, Valencia, CA Cat # 80204).

    Article Title: A Kunitz Protease Inhibitor from Dermacentor variabilis, a Vector for Spotted Fever Group Rickettsiae, Limits Rickettsia montanensis Invasion
    Article Snippet: Total RNA was isolated from tissues or cells by use of an ALLPrep DNA/RNA Mini kit according to the manufacturer's procedures (Qiagen, Valencia, CA). .. Total RNA was isolated from tissues or cells by use of an ALLPrep DNA/RNA Mini kit according to the manufacturer's procedures (Qiagen, Valencia, CA).

    Article Title: Candidate serum biomarkers for early intestinal cancer using 15N metabolic labeling and quantitative proteomics in the Apcmin/+ mouse
    Article Snippet: DNA and RNA were isolated concurrently using the Qiagen All-prep Mini-kit. .. The McArdle Laboratory for Cancer Research Microarray facility collected data for each sample on Agilent Mus musculus 8×60k (G4852A) gene expression microarrays.

    SYBR Green Assay:

    Article Title: Generalized disruption of inherited genomic imprints leads to wide-ranging placental defects and dysregulated fetal growth
    Article Snippet: RNA was extracted using either the AllPrep DNA/RNA Micro or Mini Kit (Qiagen). .. RNA was extracted using either the AllPrep DNA/RNA Micro or Mini Kit (Qiagen).

    RNA Extraction:

    Article Title: Fluid Flow Regulation of Revascularization and Cellular Organization in a Bioengineered Liver Platform
    Article Snippet: Paragraph title: RNA extraction and real-time polymerase chain reaction ... Total RNA was extracted from a small sample of reseeded liver scaffolds using the Allprep DNA/RNA Mini Kit (Qiagen, Germantown, MD) with DNAse treatment. cDNA was synthesized from 500 ng of total RNA using Superscript III First Strand Synthesis (Life Technologies, Carlsbad, CA).

    RNA Expression:

    Article Title: Pan-cancer analysis of somatic copy number alterations implicates IRS4 and IGF2 in enhancer hijacking
    Article Snippet: Paragraph title: Isolation of nucleic acids for DNA sequencing and RNA expression analysis ... DNA and RNA of primary patient tissue and spheroids were isolated using DNeasy® Blood & Tissue Kit (Qiagen) and AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instruction.

    Spectrophotometry:

    Article Title: Differentiation of Human Neural Stem Cells into Motor Neurons Stimulates Mitochondrial Biogenesis and Decreases Glycolytic Flux
    Article Snippet: For quantitative PCR (qPCR) analysis of hESC-derived cells, DNA and RNA were extracted at 7-day time points through day 28 using the AllPrep DNA/RNA Mini Kit (Qiagen). .. For iPSC-derived cells, RNA was extracted at day 0 (D0) and D21 with the RNeasy or RNeasy Plus Micro Kit (Qiagen), and DNA was extracted with the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer's instructions.

    DNA Methylation Assay:

    Article Title: Epigenetic impact of simulated maternal grooming on estrogen receptor alpha within the developing amygdala
    Article Snippet: Paragraph title: 2.3. Quantification of DNA methylation ... Genomic DNA was isolated using Qiagen’s AllPrep Mini Kit (Cat. #80204, Valencia, CA).

    Produced:

    Article Title: CYTOMEGALOVIRUS VECTORS VIOLATE CD8+ T CELL EPITOPE RECOGNITION PARADIGMS
    Article Snippet: Autologous SIV-infected target cells were produced by spinoculation of activated CD4+ T cells with sucrose-purified SIVmac239, followed by 4 days of culture and then purification with CD4 microbeads and LS columns (Miltenyi Biotec), as previously described ( ). .. Prior to MHC-II restriction assays, mRNA from these transfectants was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen), amplified by RT-PCR using a universal primer pair (5′-GACACTGATGGTGCTGAGC-3′ and 5′-GCTGCACTGTGAAGCTCTC-3′) spanning the highly polymorphic β1 region of Mamu-DRB , and sequence confirmed.

    Lysis:

    Article Title: Candidate serum biomarkers for early intestinal cancer using 15N metabolic labeling and quantitative proteomics in the Apcmin/+ mouse
    Article Snippet: Samples from all tumors as well as normal epithelial scrapings were taken from each animal and stored in Qiagen RLT Plus lysis buffer. .. DNA and RNA were isolated concurrently using the Qiagen All-prep Mini-kit.

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    Qiagen allprep dna rna mini kit
    TFAM binding of linear <t>DNA</t> and <t>RNA</t> substrates by EMSA. Increasing amounts of TFAM were bound to 20 fM of each biotinylated substrate as follows; (A) dsDNA control sequence LSP, 0–1.44 μM TFAM with five-fold serial dilutions, apparent K d of 6 nM, (B) dsDNA control sequence scrambled LSP, with serial dilutions of TFAM as in (A), apparent K d of 100 nM, (C) dsRNA:DNA hybrid with 0–3.5 μM TFAM with two-fold serial dilutions, (D) ss poly [rArC] 12 , with TFAM dilutions as in panel (C), (E) poly [rU] 20 , with TFAM dilutions as in (C), (F) dsRNA 5681 , with TFAM dilutions as in panel (C).
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    TFAM binding of linear DNA and RNA substrates by EMSA. Increasing amounts of TFAM were bound to 20 fM of each biotinylated substrate as follows; (A) dsDNA control sequence LSP, 0–1.44 μM TFAM with five-fold serial dilutions, apparent K d of 6 nM, (B) dsDNA control sequence scrambled LSP, with serial dilutions of TFAM as in (A), apparent K d of 100 nM, (C) dsRNA:DNA hybrid with 0–3.5 μM TFAM with two-fold serial dilutions, (D) ss poly [rArC] 12 , with TFAM dilutions as in panel (C), (E) poly [rU] 20 , with TFAM dilutions as in (C), (F) dsRNA 5681 , with TFAM dilutions as in panel (C).

    Journal: PLoS ONE

    Article Title: Mitochondrial Transcription Factor A (TFAM) Binds to RNA Containing 4-Way Junctions and Mitochondrial tRNA

    doi: 10.1371/journal.pone.0142436

    Figure Lengend Snippet: TFAM binding of linear DNA and RNA substrates by EMSA. Increasing amounts of TFAM were bound to 20 fM of each biotinylated substrate as follows; (A) dsDNA control sequence LSP, 0–1.44 μM TFAM with five-fold serial dilutions, apparent K d of 6 nM, (B) dsDNA control sequence scrambled LSP, with serial dilutions of TFAM as in (A), apparent K d of 100 nM, (C) dsRNA:DNA hybrid with 0–3.5 μM TFAM with two-fold serial dilutions, (D) ss poly [rArC] 12 , with TFAM dilutions as in panel (C), (E) poly [rU] 20 , with TFAM dilutions as in (C), (F) dsRNA 5681 , with TFAM dilutions as in panel (C).

    Article Snippet: Total cellular RNA was isolated from cultured 3T3sw cells using the AllPrep DNA/RNA mini kit (Qiagen).

    Techniques: Binding Assay, Sequencing

    Binding kinetics of TFAM to RNA and DNA substrates using surface plasmon resonance. (A-D) Sensograms displaying the TFAM binding and dissociation rates of (A) a DNA 4-way junction, (B) an RNA 4-way junction, (C) linear double-stranded DNA, and (D) purified mitochondrial tRNAs. Individual tracings represent a single value in a range of TFAM concentrations in each of the experiments. (E) Kinetic data derived from these tracings include associate rate constant ( k a ), dissociate rate constant ( k d ) and the apparent dissociation constant ( K d ) for each of these substrates.

    Journal: PLoS ONE

    Article Title: Mitochondrial Transcription Factor A (TFAM) Binds to RNA Containing 4-Way Junctions and Mitochondrial tRNA

    doi: 10.1371/journal.pone.0142436

    Figure Lengend Snippet: Binding kinetics of TFAM to RNA and DNA substrates using surface plasmon resonance. (A-D) Sensograms displaying the TFAM binding and dissociation rates of (A) a DNA 4-way junction, (B) an RNA 4-way junction, (C) linear double-stranded DNA, and (D) purified mitochondrial tRNAs. Individual tracings represent a single value in a range of TFAM concentrations in each of the experiments. (E) Kinetic data derived from these tracings include associate rate constant ( k a ), dissociate rate constant ( k d ) and the apparent dissociation constant ( K d ) for each of these substrates.

    Article Snippet: Total cellular RNA was isolated from cultured 3T3sw cells using the AllPrep DNA/RNA mini kit (Qiagen).

    Techniques: Binding Assay, SPR Assay, Purification, Derivative Assay

    TFAM-bound mitochondrial tRNAs are processed and have mature ends. (A) Schematic for PCR detection of unprocessed tRNAs showing a tRNA flanked by putative RNA sequences from adjacent genes. PCR primer positions used on cDNAs are shown as arrows. Expected PCR fragments from unprocessed 5’ ends (i), unprocessed 3’ ends (ii) and internal tRNA (iii) are displayed. (B and C) PCR templates in lane 1 from total cellular cDNA, lane 2 templates made excluding reverse transcriptase, lane 3 templates are from TFAM-RNA IP, and lane 4 from TFAM-DNA IP. Samples for lanes 2, 3, and 4 are identical to those used for data obtained in Fig 4 , which further controls for the sample preparation and PCR procedures. (B) PCR amplicons detecting 5’ flanking regions from each tRNA as in (Ai). V (internal) serves as a control for the TFAM-RIP reaction using tRNA internal primers as in (Aiii). (C) PCR amplicons detecting 3’ flanking regions from each tRNA as in (Aii). P(internal) serves as a control for RT-PCR using tRNA internal primers as in (Aiii). (D and E) 3’-end sequence frequency of multiple clones isolated from tRNA Val RNA circularization is pie-graph displayed. (D) tRNA Val sequences isolated from total cellular RNA, n = 104. (E) TFAM-RIP isolated tRNA Val sequences, n = 67.

    Journal: PLoS ONE

    Article Title: Mitochondrial Transcription Factor A (TFAM) Binds to RNA Containing 4-Way Junctions and Mitochondrial tRNA

    doi: 10.1371/journal.pone.0142436

    Figure Lengend Snippet: TFAM-bound mitochondrial tRNAs are processed and have mature ends. (A) Schematic for PCR detection of unprocessed tRNAs showing a tRNA flanked by putative RNA sequences from adjacent genes. PCR primer positions used on cDNAs are shown as arrows. Expected PCR fragments from unprocessed 5’ ends (i), unprocessed 3’ ends (ii) and internal tRNA (iii) are displayed. (B and C) PCR templates in lane 1 from total cellular cDNA, lane 2 templates made excluding reverse transcriptase, lane 3 templates are from TFAM-RNA IP, and lane 4 from TFAM-DNA IP. Samples for lanes 2, 3, and 4 are identical to those used for data obtained in Fig 4 , which further controls for the sample preparation and PCR procedures. (B) PCR amplicons detecting 5’ flanking regions from each tRNA as in (Ai). V (internal) serves as a control for the TFAM-RIP reaction using tRNA internal primers as in (Aiii). (C) PCR amplicons detecting 3’ flanking regions from each tRNA as in (Aii). P(internal) serves as a control for RT-PCR using tRNA internal primers as in (Aiii). (D and E) 3’-end sequence frequency of multiple clones isolated from tRNA Val RNA circularization is pie-graph displayed. (D) tRNA Val sequences isolated from total cellular RNA, n = 104. (E) TFAM-RIP isolated tRNA Val sequences, n = 67.

    Article Snippet: Total cellular RNA was isolated from cultured 3T3sw cells using the AllPrep DNA/RNA mini kit (Qiagen).

    Techniques: Polymerase Chain Reaction, Sample Prep, Reverse Transcription Polymerase Chain Reaction, Sequencing, Clone Assay, Isolation

    TFAM bound RNA represents a lesser fraction of TFAM bound DNA. (A) Immunofluorescence images of TFAM in untreated cells (i), cells treated with RNase (ii), DNase (iii) or both DNase and RNase (iv). (B) Relative mean fluorescence of TFAM retained during nuclease treatments shown in (A). (C) Levels of TFAM-bound tRNA relative to TFAM-bound to the corresponding mtDNA. Parallel RNA and DNA immunoprecipitations from the same samples were quantified by RT-PCR and PCR, respectively. Relative bound tRNA level is expressed as a percentage of bound mtDNA.

    Journal: PLoS ONE

    Article Title: Mitochondrial Transcription Factor A (TFAM) Binds to RNA Containing 4-Way Junctions and Mitochondrial tRNA

    doi: 10.1371/journal.pone.0142436

    Figure Lengend Snippet: TFAM bound RNA represents a lesser fraction of TFAM bound DNA. (A) Immunofluorescence images of TFAM in untreated cells (i), cells treated with RNase (ii), DNase (iii) or both DNase and RNase (iv). (B) Relative mean fluorescence of TFAM retained during nuclease treatments shown in (A). (C) Levels of TFAM-bound tRNA relative to TFAM-bound to the corresponding mtDNA. Parallel RNA and DNA immunoprecipitations from the same samples were quantified by RT-PCR and PCR, respectively. Relative bound tRNA level is expressed as a percentage of bound mtDNA.

    Article Snippet: Total cellular RNA was isolated from cultured 3T3sw cells using the AllPrep DNA/RNA mini kit (Qiagen).

    Techniques: Immunofluorescence, Fluorescence, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction

    TFAM binding of complex DNA and RNA substrates by EMSA. Varying amounts of TFAM were bound to 20 fM of each biotinylated substrate with as follows; (A) Stem-loop RNA, 2.4–0.0375 μM TFAM with two-fold serial dilutions, (B) dsRNA with internal 8 nucleotide mismatch loop, TFAM dilutions as in (A), apparent K d of 2.04 μM, (C) Alternating, four arm RNA:DNA 4-way junction, TFAM dilutions as in (A), apparent K d of 299 nM, (D) RNA 4-way junction, 600–9.375 nM TFAM with two-fold serial dilutions, apparent K d of 270 nM, (E) Mixed pairing RNA and DNA 4-way junction, TFAM dilutions as in (A), apparent K d of 63 nM, (F) DNA 4-way junction, TFAM dilutions as in (D), apparent K d of 63 nM. Left lane in each panel is free template without TFAM. Substrate diagrams appear to the right of each panel with RNA depicted in red and DNA in blue.

    Journal: PLoS ONE

    Article Title: Mitochondrial Transcription Factor A (TFAM) Binds to RNA Containing 4-Way Junctions and Mitochondrial tRNA

    doi: 10.1371/journal.pone.0142436

    Figure Lengend Snippet: TFAM binding of complex DNA and RNA substrates by EMSA. Varying amounts of TFAM were bound to 20 fM of each biotinylated substrate with as follows; (A) Stem-loop RNA, 2.4–0.0375 μM TFAM with two-fold serial dilutions, (B) dsRNA with internal 8 nucleotide mismatch loop, TFAM dilutions as in (A), apparent K d of 2.04 μM, (C) Alternating, four arm RNA:DNA 4-way junction, TFAM dilutions as in (A), apparent K d of 299 nM, (D) RNA 4-way junction, 600–9.375 nM TFAM with two-fold serial dilutions, apparent K d of 270 nM, (E) Mixed pairing RNA and DNA 4-way junction, TFAM dilutions as in (A), apparent K d of 63 nM, (F) DNA 4-way junction, TFAM dilutions as in (D), apparent K d of 63 nM. Left lane in each panel is free template without TFAM. Substrate diagrams appear to the right of each panel with RNA depicted in red and DNA in blue.

    Article Snippet: Total cellular RNA was isolated from cultured 3T3sw cells using the AllPrep DNA/RNA mini kit (Qiagen).

    Techniques: Binding Assay

    Cluster diagram of Bray-Curtis similarities calculated from square-root transformed relative OTU abundances for each sample. The asterisk at the node in the dendrogram separating DNA and RNA surveys indicates significant compositional differences between these two groups (R = 0.5506, p = 0.0001) determined by the ANOSIM.

    Journal: Frontiers in Microbiology

    Article Title: Microbial Eukaryote Diversity and Activity in the Water Column of the South China Sea Based on DNA and RNA High Throughput Sequencing

    doi: 10.3389/fmicb.2017.01121

    Figure Lengend Snippet: Cluster diagram of Bray-Curtis similarities calculated from square-root transformed relative OTU abundances for each sample. The asterisk at the node in the dendrogram separating DNA and RNA surveys indicates significant compositional differences between these two groups (R = 0.5506, p = 0.0001) determined by the ANOSIM.

    Article Snippet: Total DNA and RNA were extracted simultaneously from each cryopreserved filter membrane using AllPrep DNA/RNA kit (Qiagen, USA) based on an initial mechanical cell disruption employing bead beating (Stoeck et al., ) followed by chemical disruption using lysis buffer provided in the kit.

    Techniques: Transformation Assay

    Relative abundance of RNA (y-axis) and DNA (x-axis) reads for each OTU in representative microbial eukaryotes assemblages, Acantharea, Dinophyceae, Ciliophora, and MAST, in the water column of the South China Sea.

    Journal: Frontiers in Microbiology

    Article Title: Microbial Eukaryote Diversity and Activity in the Water Column of the South China Sea Based on DNA and RNA High Throughput Sequencing

    doi: 10.3389/fmicb.2017.01121

    Figure Lengend Snippet: Relative abundance of RNA (y-axis) and DNA (x-axis) reads for each OTU in representative microbial eukaryotes assemblages, Acantharea, Dinophyceae, Ciliophora, and MAST, in the water column of the South China Sea.

    Article Snippet: Total DNA and RNA were extracted simultaneously from each cryopreserved filter membrane using AllPrep DNA/RNA kit (Qiagen, USA) based on an initial mechanical cell disruption employing bead beating (Stoeck et al., ) followed by chemical disruption using lysis buffer provided in the kit.

    Techniques:

    Alpha-diversity measures (Chao1 and Observed species) for the pooled samples from the two sampling sites grouped by water depths, shallow (5, 25, and 75 m), middle (200, 300, and 500 m), and deep (1,000, 1,500, 2,000, and 3,900 m), revealed by DNA and RNA, respectively. The line in each box plot indicates the median, the box delimits the 25th and 75th percentile, and the whisker is the range.

    Journal: Frontiers in Microbiology

    Article Title: Microbial Eukaryote Diversity and Activity in the Water Column of the South China Sea Based on DNA and RNA High Throughput Sequencing

    doi: 10.3389/fmicb.2017.01121

    Figure Lengend Snippet: Alpha-diversity measures (Chao1 and Observed species) for the pooled samples from the two sampling sites grouped by water depths, shallow (5, 25, and 75 m), middle (200, 300, and 500 m), and deep (1,000, 1,500, 2,000, and 3,900 m), revealed by DNA and RNA, respectively. The line in each box plot indicates the median, the box delimits the 25th and 75th percentile, and the whisker is the range.

    Article Snippet: Total DNA and RNA were extracted simultaneously from each cryopreserved filter membrane using AllPrep DNA/RNA kit (Qiagen, USA) based on an initial mechanical cell disruption employing bead beating (Stoeck et al., ) followed by chemical disruption using lysis buffer provided in the kit.

    Techniques: Sampling, Whisker Assay

    Overview of assemblages of microbial eukaryotes in the South China Sea water column at the supergroup taxonomic level. Relative sequence number in DNA survey (A) and RNA survey (B) ; relative OTU number in DNA survey (C) and RNA survey (D) .

    Journal: Frontiers in Microbiology

    Article Title: Microbial Eukaryote Diversity and Activity in the Water Column of the South China Sea Based on DNA and RNA High Throughput Sequencing

    doi: 10.3389/fmicb.2017.01121

    Figure Lengend Snippet: Overview of assemblages of microbial eukaryotes in the South China Sea water column at the supergroup taxonomic level. Relative sequence number in DNA survey (A) and RNA survey (B) ; relative OTU number in DNA survey (C) and RNA survey (D) .

    Article Snippet: Total DNA and RNA were extracted simultaneously from each cryopreserved filter membrane using AllPrep DNA/RNA kit (Qiagen, USA) based on an initial mechanical cell disruption employing bead beating (Stoeck et al., ) followed by chemical disruption using lysis buffer provided in the kit.

    Techniques: Sequencing

    Relative sequence abundance of microbial eukaryotes in the water column at the two sampling sites, as revealed by DNA (A,B) and RNA (C,D) surveys.

    Journal: Frontiers in Microbiology

    Article Title: Microbial Eukaryote Diversity and Activity in the Water Column of the South China Sea Based on DNA and RNA High Throughput Sequencing

    doi: 10.3389/fmicb.2017.01121

    Figure Lengend Snippet: Relative sequence abundance of microbial eukaryotes in the water column at the two sampling sites, as revealed by DNA (A,B) and RNA (C,D) surveys.

    Article Snippet: Total DNA and RNA were extracted simultaneously from each cryopreserved filter membrane using AllPrep DNA/RNA kit (Qiagen, USA) based on an initial mechanical cell disruption employing bead beating (Stoeck et al., ) followed by chemical disruption using lysis buffer provided in the kit.

    Techniques: Sequencing, Sampling

    Cluster diagram of the Bray-Curtis dissimilarities based on the log-transformed relative OTU abundance for each sample. The separated DNA (A) and RNA (B) community groups (with asterisks at the node) exist with significant compositional differences (DNA: r 2 = 0.31718, P = 0.001; RNA: r 2 = 0.27023, P = 0.001) as determined by PERMANOVA. The percent dissimilarity among samples is shown along the horizontal axes.

    Journal: Frontiers in Microbiology

    Article Title: Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

    doi: 10.3389/fmicb.2018.03259

    Figure Lengend Snippet: Cluster diagram of the Bray-Curtis dissimilarities based on the log-transformed relative OTU abundance for each sample. The separated DNA (A) and RNA (B) community groups (with asterisks at the node) exist with significant compositional differences (DNA: r 2 = 0.31718, P = 0.001; RNA: r 2 = 0.27023, P = 0.001) as determined by PERMANOVA. The percent dissimilarity among samples is shown along the horizontal axes.

    Article Snippet: The total DNA and RNA were extracted simultaneously from each sample using the AllPrep DNA/RNA Mini Kit (Qiagen, #80204, Germany).

    Techniques: Transformation Assay

    Number of OTUs unveiled by DNA and RNA surveys. The pie chart indicated the OTU numbers mainly at class level; the inner ring represented these classes belong to the phylum; the outer ring indicated the number of OTUs at super-group level.

    Journal: Frontiers in Microbiology

    Article Title: Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

    doi: 10.3389/fmicb.2018.03259

    Figure Lengend Snippet: Number of OTUs unveiled by DNA and RNA surveys. The pie chart indicated the OTU numbers mainly at class level; the inner ring represented these classes belong to the phylum; the outer ring indicated the number of OTUs at super-group level.

    Article Snippet: The total DNA and RNA were extracted simultaneously from each sample using the AllPrep DNA/RNA Mini Kit (Qiagen, #80204, Germany).

    Techniques:

    Number of OTUs of higher taxonomic groups (sequences proportion over 1% of the total DNA or RNA abundance) based on the DNA-derived (A) and RNA-derived (B) approaches for each sample. Others refer to groups with relatively lower abundance (sequences proportion

    Journal: Frontiers in Microbiology

    Article Title: Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

    doi: 10.3389/fmicb.2018.03259

    Figure Lengend Snippet: Number of OTUs of higher taxonomic groups (sequences proportion over 1% of the total DNA or RNA abundance) based on the DNA-derived (A) and RNA-derived (B) approaches for each sample. Others refer to groups with relatively lower abundance (sequences proportion

    Article Snippet: The total DNA and RNA were extracted simultaneously from each sample using the AllPrep DNA/RNA Mini Kit (Qiagen, #80204, Germany).

    Techniques: Derivative Assay

    Relative abundance of higher taxonomic groups (sequences proportion over 1% of the total DNA or RNA abundance) based on the DNA-derived (A) and RNA-derived (B) approaches for each sample. Others refer to groups with relatively lower abundance (sequences proportion

    Journal: Frontiers in Microbiology

    Article Title: Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

    doi: 10.3389/fmicb.2018.03259

    Figure Lengend Snippet: Relative abundance of higher taxonomic groups (sequences proportion over 1% of the total DNA or RNA abundance) based on the DNA-derived (A) and RNA-derived (B) approaches for each sample. Others refer to groups with relatively lower abundance (sequences proportion

    Article Snippet: The total DNA and RNA were extracted simultaneously from each sample using the AllPrep DNA/RNA Mini Kit (Qiagen, #80204, Germany).

    Techniques: Derivative Assay

    (A) Scatter diagram of PC 1 and PC 2 derived from the relative abundance of higher taxonomic groups in the DNA and RNA databases detected in each sample, blue color indicated the sequences was derived from the DNA survey and red color indicated the sequences was derived from the RNA survey. Ma, Mamiellophyceae; Sp, Spirotrichea; Pe, Pelagophyceae; Ba, Bacillariophyta; Dict, Dictyochophyceae; Prym, Prymnesiophyceae. Boxplot representing the RNA: DNA ratios for Mamiellophyceae (B) , Pelagophyceae (C) , and Spirotrichea (D) in all and individual samples.

    Journal: Frontiers in Microbiology

    Article Title: Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

    doi: 10.3389/fmicb.2018.03259

    Figure Lengend Snippet: (A) Scatter diagram of PC 1 and PC 2 derived from the relative abundance of higher taxonomic groups in the DNA and RNA databases detected in each sample, blue color indicated the sequences was derived from the DNA survey and red color indicated the sequences was derived from the RNA survey. Ma, Mamiellophyceae; Sp, Spirotrichea; Pe, Pelagophyceae; Ba, Bacillariophyta; Dict, Dictyochophyceae; Prym, Prymnesiophyceae. Boxplot representing the RNA: DNA ratios for Mamiellophyceae (B) , Pelagophyceae (C) , and Spirotrichea (D) in all and individual samples.

    Article Snippet: The total DNA and RNA were extracted simultaneously from each sample using the AllPrep DNA/RNA Mini Kit (Qiagen, #80204, Germany).

    Techniques: Derivative Assay

    Abundance distributions of COGs in metagenomes (DNA-level) and metatranscriptomes (RNA-level) of cecal microbiota from two flying squirrels (FS1 and FS2). Only abundant COGs that constituted > 0.5% in either library are shown.

    Journal: Frontiers in Microbiology

    Article Title: Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling

    doi: 10.3389/fmicb.2017.02622

    Figure Lengend Snippet: Abundance distributions of COGs in metagenomes (DNA-level) and metatranscriptomes (RNA-level) of cecal microbiota from two flying squirrels (FS1 and FS2). Only abundant COGs that constituted > 0.5% in either library are shown.

    Article Snippet: Total DNA and RNA were isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN), according to manufacturer's instructions.

    Techniques:

    Glycoside hydrolases (GHs) detected in metagenomes (DNA-level) and metatranscriptomes (RNA-level) of cecal microbiota from two flying squirrels (FS1 and FS2). Only abundant GHs that constituted > 0.05% in either library are shown.

    Journal: Frontiers in Microbiology

    Article Title: Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling

    doi: 10.3389/fmicb.2017.02622

    Figure Lengend Snippet: Glycoside hydrolases (GHs) detected in metagenomes (DNA-level) and metatranscriptomes (RNA-level) of cecal microbiota from two flying squirrels (FS1 and FS2). Only abundant GHs that constituted > 0.05% in either library are shown.

    Article Snippet: Total DNA and RNA were isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN), according to manufacturer's instructions.

    Techniques:

    Genus-level taxonomic compositions of metagenomes (DNA-level) and metatranscriptomes (RNA-level) of cecal microbiota from two flying squirrels (FS1 and FS2). Top 30 abundant genera that constituted > 0.5% in either library are shown, with their phyla in parentheses.

    Journal: Frontiers in Microbiology

    Article Title: Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling

    doi: 10.3389/fmicb.2017.02622

    Figure Lengend Snippet: Genus-level taxonomic compositions of metagenomes (DNA-level) and metatranscriptomes (RNA-level) of cecal microbiota from two flying squirrels (FS1 and FS2). Top 30 abundant genera that constituted > 0.5% in either library are shown, with their phyla in parentheses.

    Article Snippet: Total DNA and RNA were isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN), according to manufacturer's instructions.

    Techniques:

    Abundance distributions of KOs in metagenomes (DNA-level) and metatranscriptomes (RNA-level) of cecal microbiota from two flying squirrels (FS1 and FS2). Only abundant KOs that constituted > 0.5% in either library are shown.

    Journal: Frontiers in Microbiology

    Article Title: Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling

    doi: 10.3389/fmicb.2017.02622

    Figure Lengend Snippet: Abundance distributions of KOs in metagenomes (DNA-level) and metatranscriptomes (RNA-level) of cecal microbiota from two flying squirrels (FS1 and FS2). Only abundant KOs that constituted > 0.5% in either library are shown.

    Article Snippet: Total DNA and RNA were isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN), according to manufacturer's instructions.

    Techniques: