allprep dna rna mirna universal kit protocol (Qiagen)

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AllPrep DNA RNA miRNA Universal Kit

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For simultaneous purification of genomic DNA and total RNA including miRNA from cells and difficult to lyse tissue Kit contents Qiagen AllPrep DNA RNA miRNA Universal Kit 50 preps Developed for Difficult to lyse Samples High Yields of DNA RNA and miRNA from the Same Sample Delivers High quality Nucleic Acids Ready for Downstream use For Simultaneous Purification of Genomic DNA and Total RNA Including miRNA from Cells and Difficult to lyse Tissue Includes 50 AllPrep DNA Mini Spin Columns 50 RNeasy Mini Spin Columns Collection Tubes and Buffers Benefits High yields of DNA RNA and miRNA from the same sample Developed for difficult to lyse samples e g fiber or lipid rich tissue Delivers high quality nucleic acids ready for downstream use Preoptimized protocols for various sample types Convenient procedure that does not require use of pheno

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80224

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641

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AllPrep DNA RNA miRNA Universal Kit

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Qiagen allprep dna rna mirna universal kit protocol

allprep dna rna mirna universal kit protocol - by Bioz Stars, 2020-07

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Images

1) Product Images from "RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition"

Article Title: RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition

Journal: PLoS ONE

doi: 10.1371/journal.pone.0121659

Comparison of DNA/RNA yields and RNA quality (inset). (A) Comparison between the AllPrep standard protocol (APS; described below figure), enzymatic lysis (Enz), enzymatic/bead beating (Bead), and Mirvana extraction protocols (Mirvana). (B) Comparison between different iterations of the AP protocol, examining the effect of preservation method {P}, lysis conditions {L}, and other extraction modification steps {E}. The data presents changes in yield relative to a control, where each column shows the effect of one factor relative to a control that differed in that factor only. The control was extracted using either the AP standard protocol or a modification as indicated by the X-axis labels below the horizontal lines. The factor that was changed is indicated just below the data column. The dotted line indicates no change relative to control. All data represent averages of three extractions, with error bars indicating the 95% confidence interval, except for the effect of lysozyme, which averaged the relative yield effects from multiple samples (from DL, LH, and HR samples, three replicate extractions each). Inset: RIN = RNA integrity number quality (0 (poor)- 10 (high) range) assessment by Bioanalyzer; NT = no preservation treatment.

Figure Legend Snippet: Comparison of DNA/RNA yields and RNA quality (inset). (A) Comparison between the AllPrep standard protocol (APS; described below figure), enzymatic lysis (Enz), enzymatic/bead beating (Bead), and Mirvana extraction protocols (Mirvana). (B) Comparison between different iterations of the AP protocol, examining the effect of preservation method {P}, lysis conditions {L}, and other extraction modification steps {E}. The data presents changes in yield relative to a control, where each column shows the effect of one factor relative to a control that differed in that factor only. The control was extracted using either the AP standard protocol or a modification as indicated by the X-axis labels below the horizontal lines. The factor that was changed is indicated just below the data column. The dotted line indicates no change relative to control. All data represent averages of three extractions, with error bars indicating the 95% confidence interval, except for the effect of lysozyme, which averaged the relative yield effects from multiple samples (from DL, LH, and HR samples, three replicate extractions each). Inset: RIN = RNA integrity number quality (0 (poor)- 10 (high) range) assessment by Bioanalyzer; NT = no preservation treatment.

Techniques Used: Lysis, Preserving, Modification

2) Product Images from "Comparison of Automated and Manual DNA Isolation Methods of Liquid-Based Cytology Samples"

Article Title: Comparison of Automated and Manual DNA Isolation Methods of Liquid-Based Cytology Samples

Journal: Biopreservation and Biobanking

doi: 10.1089/bio.2018.0148

Schematic representation of DNA procedure from LBC samples. Left side : manual procedure; middle : outline procedure; right side : automated procedure. RT = room temperature; EB = elution buffer; AW1 and AW2 = buffer concentrate provided from AllPrep DNA/RNA/miRNA Universal Kit. LBC, liquid-based cytology.

Figure Legend Snippet: Schematic representation of DNA procedure from LBC samples. Left side : manual procedure; middle : outline procedure; right side : automated procedure. RT = room temperature; EB = elution buffer; AW1 and AW2 = buffer concentrate provided from AllPrep DNA/RNA/miRNA Universal Kit. LBC, liquid-based cytology.

Techniques Used:

3) Product Images from "Establishment of urinary exosome-like vesicles isolation protocol for FHHNC patients and evaluation of different exosomal RNA extraction methods"

Article Title: Establishment of urinary exosome-like vesicles isolation protocol for FHHNC patients and evaluation of different exosomal RNA extraction methods

Journal: Journal of Translational Medicine

doi: 10.1186/s12967-018-1651-z

RNA quantification. a Bar graph of total RNA quantified from FHHNC uEVs by Bioanalyzer—Picochip using the five different extraction methods. MirCURY kit followed by TRIzol LS were the most efficient methods. b A representative electropherogram shows that uEVs contain small RNA, including microRNAs (10–40 nt). As expected, small amounts of rRNA were detected. c miRNA profiling by RT-qPCR of RNA extracted from FHHNC uEVs. miRNA expression pattern is consistent independently of the RNA extraction method

Figure Legend Snippet: RNA quantification. a Bar graph of total RNA quantified from FHHNC uEVs by Bioanalyzer—Picochip using the five different extraction methods. MirCURY kit followed by TRIzol LS were the most efficient methods. b A representative electropherogram shows that uEVs contain small RNA, including microRNAs (10–40 nt). As expected, small amounts of rRNA were detected. c miRNA profiling by RT-qPCR of RNA extracted from FHHNC uEVs. miRNA expression pattern is consistent independently of the RNA extraction method

Techniques Used: Quantitative RT-PCR, Expressing, RNA Extraction

4) Product Images from "Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood"

Article Title: Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood

Journal: Epigenetics

doi: 10.1080/15592294.2018.1507198

Sequencing data collection and analysis workflow. Genomic DNA was isolated from matched offspring blood samples at 2 months (n = 6), 4 months (n = 6), and 10 months of age (n = 6). DNA samples were then split for separate processing steps specific to the ERRBS and HMeDIP-seq methods. All processed samples were amplified and sequenced on an Illumina HiSeq 4000 sequencer using single-end, 50 nt read length. Separate bioinformatics pipelines were used to analyze ERRBS and HMeDIP-seq data. Differentially methylated CpGs (DMCs) were compared to differentially hydroxymethylated regions (DHMRs) for regions of chromosomal overlap. Regions of overlap were then annotated and visualized in the genome browser. The Nfic gene was validated using RT-qPCR on available RNA from the blood samples.

Figure Legend Snippet: Sequencing data collection and analysis workflow. Genomic DNA was isolated from matched offspring blood samples at 2 months (n = 6), 4 months (n = 6), and 10 months of age (n = 6). DNA samples were then split for separate processing steps specific to the ERRBS and HMeDIP-seq methods. All processed samples were amplified and sequenced on an Illumina HiSeq 4000 sequencer using single-end, 50 nt read length. Separate bioinformatics pipelines were used to analyze ERRBS and HMeDIP-seq data. Differentially methylated CpGs (DMCs) were compared to differentially hydroxymethylated regions (DHMRs) for regions of chromosomal overlap. Regions of overlap were then annotated and visualized in the genome browser. The Nfic gene was validated using RT-qPCR on available RNA from the blood samples.

Techniques Used: Sequencing, Isolation, Amplification, Methylation, Quantitative RT-PCR

5) Product Images from "Establishment of urinary exosome-like vesicles isolation protocol for FHHNC patients and evaluation of different exosomal RNA extraction methods"

Article Title: Establishment of urinary exosome-like vesicles isolation protocol for FHHNC patients and evaluation of different exosomal RNA extraction methods

Journal: Journal of Translational Medicine

doi: 10.1186/s12967-018-1651-z

Techniques Used: Quantitative RT-PCR, Expressing, RNA Extraction

6) Product Images from "Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma"

Article Title: Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma

Journal: BMC Cancer

doi: 10.1186/s12885-017-3711-9

Aberrant transcriptome expression pivotal to eBL lymphomagenesis. a Schematic illustration of the aberrant gene expression and miRNA mediated regulatory changes that would initiate lymphomagenesis as a result of DNA damage. Combined loss of p53 function due to small interfering RNA-mediated regulation of ATM and NLK together with upregulation of TFAP4, would facilitate survival of cells with the c-myc-Igh chromosomal translocation and MYC induced cell cycle progression initiating eBL tumor development. ATM checkpoint kinase, transduces genomic stress signals to halt cell cycle progression in response to DNA damage. It is critical in the regulation of apoptosis and lymphomagenesis in c-myc induced lymphomas. ATM is downregulated in eBL and it is targeted by 4 miRs that are Upregulated in eBL. NLK is required for the upregulation of P53 expression in response to DNA damage. It interacts with P53 to enhance its stability and activity by abrogating MDM2 mediated degradation. NLK is downregulated in eBL tumor cells and also targeted by 2 miRs that are upregulated in eBL tumor cells. TFAP4/AP4 is a central mediator of cell cycle progression in response to c-MYC activation. b RNA seq. Expression counts of MYC , TFAP4 , ATM and NLK in eBL tumor cells and GC B cells. c Hierarchical clustering of eBL and GC B cells based on the expression profiles of MYC , TFAP4 , ATM and NLK also revealed a clear separation of the two groups. d . miRNA seq. Expression counts of hsa-miR-26a-5p, hsa-miR-27b-3p, hsa-miR-30b-5p, miR-17~92-cluster members (hsa-miR-19b-3p, and hsa-miR-92a-3p), and let-7-family miRs (hsa-let-7a-5p, hsa-let-7b-5p, hsa-let-7d-5p, hsa-let-7e-5p, and hsa-let-7 g-5p) in eBL tumor cells and GC B cells

Figure Legend Snippet: Aberrant transcriptome expression pivotal to eBL lymphomagenesis. a Schematic illustration of the aberrant gene expression and miRNA mediated regulatory changes that would initiate lymphomagenesis as a result of DNA damage. Combined loss of p53 function due to small interfering RNA-mediated regulation of ATM and NLK together with upregulation of TFAP4, would facilitate survival of cells with the c-myc-Igh chromosomal translocation and MYC induced cell cycle progression initiating eBL tumor development. ATM checkpoint kinase, transduces genomic stress signals to halt cell cycle progression in response to DNA damage. It is critical in the regulation of apoptosis and lymphomagenesis in c-myc induced lymphomas. ATM is downregulated in eBL and it is targeted by 4 miRs that are Upregulated in eBL. NLK is required for the upregulation of P53 expression in response to DNA damage. It interacts with P53 to enhance its stability and activity by abrogating MDM2 mediated degradation. NLK is downregulated in eBL tumor cells and also targeted by 2 miRs that are upregulated in eBL tumor cells. TFAP4/AP4 is a central mediator of cell cycle progression in response to c-MYC activation. b RNA seq. Expression counts of MYC , TFAP4 , ATM and NLK in eBL tumor cells and GC B cells. c Hierarchical clustering of eBL and GC B cells based on the expression profiles of MYC , TFAP4 , ATM and NLK also revealed a clear separation of the two groups. d . miRNA seq. Expression counts of hsa-miR-26a-5p, hsa-miR-27b-3p, hsa-miR-30b-5p, miR-17~92-cluster members (hsa-miR-19b-3p, and hsa-miR-92a-3p), and let-7-family miRs (hsa-let-7a-5p, hsa-let-7b-5p, hsa-let-7d-5p, hsa-let-7e-5p, and hsa-let-7 g-5p) in eBL tumor cells and GC B cells

Techniques Used: Expressing, Small Interfering RNA, Translocation Assay, Activity Assay, Activation Assay, RNA Sequencing Assay

7) Product Images from "MicroRNA-30 modulates metabolic inflammation by regulating notch signaling in adipose tissue macrophages"

Article Title: MicroRNA-30 modulates metabolic inflammation by regulating notch signaling in adipose tissue macrophages

Journal: International journal of obesity (2005)

doi: 10.1038/s41366-018-0114-1

DLL4 Expression is Elevated in Obese ATMs HFD-induced obesity was studied as described in Fig 1 legend. At 22-weeks-old, visceral adipose tissue and adipose SVF were analyzed for DLL4 expression. ( A C ) Immunofluorescent staining of whole-mount epididymal fat. Scale bar = 20 μm. Presented are representative confocal micrographs of Notch1 ( A ) or DLL4 ( C ). ( B D ) Image quantification of Notch1 ( B ) or DLL4 ( D ) in adipose tissue. The values are shown as mean ± SEM and are from a single experiment representative of 2 independent experiments with 5 mice per experimental group. ( E ) Flow cytometry dot plots of DLL4 + ATMs in epididymal fat. CD11b int are denoted as infiltrating (“Inf”) and CD11b hi are denoted as resident (“Res”). ( F ) Quantification of DLL4 + ATM cell counts represented per mouse and per gram fat. Values are presented as mean ± SEM and are from a single experiment representative of 2 independent experiments with 4 biological replicates (pools of 1–6 mice) per experimental group. Statistical significance was determined by Student’s t-test. *p

Figure Legend Snippet: DLL4 Expression is Elevated in Obese ATMs HFD-induced obesity was studied as described in Fig 1 legend. At 22-weeks-old, visceral adipose tissue and adipose SVF were analyzed for DLL4 expression. ( A C ) Immunofluorescent staining of whole-mount epididymal fat. Scale bar = 20 μm. Presented are representative confocal micrographs of Notch1 ( A ) or DLL4 ( C ). ( B D ) Image quantification of Notch1 ( B ) or DLL4 ( D ) in adipose tissue. The values are shown as mean ± SEM and are from a single experiment representative of 2 independent experiments with 5 mice per experimental group. ( E ) Flow cytometry dot plots of DLL4 + ATMs in epididymal fat. CD11b int are denoted as infiltrating (“Inf”) and CD11b hi are denoted as resident (“Res”). ( F ) Quantification of DLL4 + ATM cell counts represented per mouse and per gram fat. Values are presented as mean ± SEM and are from a single experiment representative of 2 independent experiments with 4 biological replicates (pools of 1–6 mice) per experimental group. Statistical significance was determined by Student’s t-test. *p

Techniques Used: Expressing, Staining, Mouse Assay, Flow Cytometry, Cytometry

$HFD-Induced Obesity Stimulates ATM Inflammation and miRNA Dysregulation To study HFD-induced obesity, male C57BL/6J mice were fed NCD or HFD for 16 weeks until 22-weeks-old. ( A ) Representative photo of mice after 16 weeks of NCD or HFD feeding. ( B ) Weekly measurements of body weight growth. ( C ) DEXA body composition after 16 weeks of diet. ( D ) Oral glucose tolerance test (GTT) after 16 weeks of diet. ( E ) Area under the curve (A.U.C.) for GTT. Represented are A.U.C. above baseline (ABV BL) or total A.U.C. ( F ) Flow cytometry dot plots of F4/80 + /CD11b + /CD11c + ATMs in the epididymal fat stromal vascular fraction (SVF) of NCD- or HFD-fed mice. ( G ) Fold percentage increase quantification of F4/80 + /CD11b + cells in the SVF (denoted as “ATMs”) and CD11c + ATMs. Lean mice were fed either NCD or 10% low-fat diet (LFD). Obese mice were fed 60% HFD. ( H–J ) Pooled F4/80+ ATMs from epididymal fat were used for transcriptome and miRNA microarrays. ( H ) Transcriptome microarray heatmap of differentially expressed mRNAs in ATMs related to macrophage polarization. ( I ) MicroRNA heatmap of differentially expressed miRNAs in ATMs. ( J ) MicroRNA array volcano plot depicting linear fold change (FC) vs. ANOVA p-value significance. ( K–M ) qRT-PCR expression validation of miRs 30a-5p, 30c-5p, and 30e-5p. For (A–F), the values are shown as mean ± SEM and are from a single experiment representative of at least 3 independent experiments with 5 mice per experimental group. For (G) data shown as mean ± SEM of 4 independent experiments with 5 mice per experimental group. For (H–M), the data shown are mean ± SEM and are from 3–4 independent experiments with 20 pooled NCD mice and 10 pooled HFD mice per experiment. Statistical differences were determined by using Student’s t-test. *p$
Figure Legend Snippet: HFD-Induced Obesity Stimulates ATM Inflammation and miRNA Dysregulation To study HFD-induced obesity, male C57BL/6J mice were fed NCD or HFD for 16 weeks until 22-weeks-old. ( A ) Representative photo of mice after 16 weeks of NCD or HFD feeding. ( B ) Weekly measurements of body weight growth. ( C ) DEXA body composition after 16 weeks of diet. ( D ) Oral glucose tolerance test (GTT) after 16 weeks of diet. ( E ) Area under the curve (A.U.C.) for GTT. Represented are A.U.C. above baseline (ABV BL) or total A.U.C. ( F ) Flow cytometry dot plots of F4/80 + /CD11b + /CD11c + ATMs in the epididymal fat stromal vascular fraction (SVF) of NCD- or HFD-fed mice. ( G ) Fold percentage increase quantification of F4/80 + /CD11b + cells in the SVF (denoted as “ATMs”) and CD11c + ATMs. Lean mice were fed either NCD or 10% low-fat diet (LFD). Obese mice were fed 60% HFD. ( H–J ) Pooled F4/80+ ATMs from epididymal fat were used for transcriptome and miRNA microarrays. ( H ) Transcriptome microarray heatmap of differentially expressed mRNAs in ATMs related to macrophage polarization. ( I ) MicroRNA heatmap of differentially expressed miRNAs in ATMs. ( J ) MicroRNA array volcano plot depicting linear fold change (FC) vs. ANOVA p-value significance. ( K–M ) qRT-PCR expression validation of miRs 30a-5p, 30c-5p, and 30e-5p. For (A–F), the values are shown as mean ± SEM and are from a single experiment representative of at least 3 independent experiments with 5 mice per experimental group. For (G) data shown as mean ± SEM of 4 independent experiments with 5 mice per experimental group. For (H–M), the data shown are mean ± SEM and are from 3–4 independent experiments with 20 pooled NCD mice and 10 pooled HFD mice per experiment. Statistical differences were determined by using Student’s t-test. *p

Techniques Used: Mouse Assay, Flow Cytometry, Cytometry, Microarray, Quantitative RT-PCR, Expressing

DNA Methylation-Dependent Regulation of miR-30 As shown in Figure 1 , F4/80+ ATMs were isolated from epididymal fat of 22-week-old HFD-induced obese and lean mice. Gene expression and DNA methylation were evaluated in ATMs. ( A ) Volcano plot displaying linear FC of genes encoding epigenetic modification enzymes and factors. Fold change and p value observations were extracted from transcriptome microarrays (See Figure 1 and Figure S1 ). ( B ) IGB visualization of meDIP-seq peak intensity of DNA methylation in the Nfyc promoter CpG island. ( C ) Methylation-specific PCR quantification of DNA methylation (DNAme) in the Nfyc promoter CpG island. For (A and C), values presented are representative of 3 independent experiments with 20 pooled NCD mice and 10 pooled HFD mice per experiment. For (B), data are representative of one experiment of 60 pooled LFD and 30 pooled HFD mice. Statistical differences were determined by using Student’s t-test. *p

Figure Legend Snippet: DNA Methylation-Dependent Regulation of miR-30 As shown in Figure 1 , F4/80+ ATMs were isolated from epididymal fat of 22-week-old HFD-induced obese and lean mice. Gene expression and DNA methylation were evaluated in ATMs. ( A ) Volcano plot displaying linear FC of genes encoding epigenetic modification enzymes and factors. Fold change and p value observations were extracted from transcriptome microarrays (See Figure 1 and Figure S1 ). ( B ) IGB visualization of meDIP-seq peak intensity of DNA methylation in the Nfyc promoter CpG island. ( C ) Methylation-specific PCR quantification of DNA methylation (DNAme) in the Nfyc promoter CpG island. For (A and C), values presented are representative of 3 independent experiments with 20 pooled NCD mice and 10 pooled HFD mice per experiment. For (B), data are representative of one experiment of 60 pooled LFD and 30 pooled HFD mice. Statistical differences were determined by using Student’s t-test. *p

Techniques Used: DNA Methylation Assay, Isolation, Mouse Assay, Expressing, Modification, Methylated DNA Immunoprecipitation, Methylation, Polymerase Chain Reaction

8) Product Images from "Epigenetic regulation of lateralized fetal spinal gene expression underlies hemispheric asymmetries"

Article Title: Epigenetic regulation of lateralized fetal spinal gene expression underlies hemispheric asymmetries

Journal: eLife

doi: 10.7554/eLife.22784

Epigenetic regulation of gene expression asymmetries in human fetal spinal cord. ( A ) Asymmetrically expressed miRNA transcripts at 8, 10 and 12 weeks PC. The extent of expression asymmetries is measured in log 2 (fold change). Red bars show rightward asymmetrically expressed microRNA transcripts, blue bars show leftward asymmetrically expressed miRNA transcripts. ( B ) Number of CpG sites showing differential DNA methylation per chromosome, compared between the left and right spinal cord for 8 and 10 weeks PC. Depicted are only CpG sites with methylation asymmetries in both samples. Red bars represent the number of CpG sites that showed significantly higher DNA methylation on the right side, blue bars show the number of CpG sites that showed significantly more DNA methylation on the left side. ( C ) Percentage of differential DNA methylation in leftward (blue) and rightward (red) asymmetrically methylated CpG sites as a function of p-value. ( D ) Percentage of gene expression asymmetries on each chromosome at 8 weeks PC that can be explained by regulation via asymmetrically expressed miRNAs or asymmetric DNA methylation of CpG sites within and 1500 nucleotides upstream of the expressed genes. The source files of asymmetrically expressed miRNAs, asymmetrically expressed targets of miRNAs, enriched KEGG pathways and differentially methylated CpG sites are available in Figure 3—source data 1 , Figure 3—source data 2 , Figure 3—source data 3 , and Figure 3—source data 4 respectively. DOI: http://dx.doi.org/10.7554/eLife.22784.006 10.7554/eLife.22784.007 Asymmetrically expressed miRNAs per week. DOI: http://dx.doi.org/10.7554/eLife.22784.007 10.7554/eLife.22784.008 Asymmetrically expressed RNA targets of asymmetrically expressed miRNAs per week. DOI: http://dx.doi.org/10.7554/eLife.22784.008 10.7554/eLife.22784.009 Enriched KEGG pathways per week and side of the spinal cord. DOI: http://dx.doi.org/10.7554/eLife.22784.009 10.7554/eLife.22784.010 Asymmetrically methylated CpG sites per week and side of the spinal cord. DOI: http://dx.doi.org/10.7554/eLife.22784.010

Figure Legend Snippet: Epigenetic regulation of gene expression asymmetries in human fetal spinal cord. ( A ) Asymmetrically expressed miRNA transcripts at 8, 10 and 12 weeks PC. The extent of expression asymmetries is measured in log 2 (fold change). Red bars show rightward asymmetrically expressed microRNA transcripts, blue bars show leftward asymmetrically expressed miRNA transcripts. ( B ) Number of CpG sites showing differential DNA methylation per chromosome, compared between the left and right spinal cord for 8 and 10 weeks PC. Depicted are only CpG sites with methylation asymmetries in both samples. Red bars represent the number of CpG sites that showed significantly higher DNA methylation on the right side, blue bars show the number of CpG sites that showed significantly more DNA methylation on the left side. ( C ) Percentage of differential DNA methylation in leftward (blue) and rightward (red) asymmetrically methylated CpG sites as a function of p-value. ( D ) Percentage of gene expression asymmetries on each chromosome at 8 weeks PC that can be explained by regulation via asymmetrically expressed miRNAs or asymmetric DNA methylation of CpG sites within and 1500 nucleotides upstream of the expressed genes. The source files of asymmetrically expressed miRNAs, asymmetrically expressed targets of miRNAs, enriched KEGG pathways and differentially methylated CpG sites are available in Figure 3—source data 1 , Figure 3—source data 2 , Figure 3—source data 3 , and Figure 3—source data 4 respectively. DOI: http://dx.doi.org/10.7554/eLife.22784.006 10.7554/eLife.22784.007 Asymmetrically expressed miRNAs per week. DOI: http://dx.doi.org/10.7554/eLife.22784.007 10.7554/eLife.22784.008 Asymmetrically expressed RNA targets of asymmetrically expressed miRNAs per week. DOI: http://dx.doi.org/10.7554/eLife.22784.008 10.7554/eLife.22784.009 Enriched KEGG pathways per week and side of the spinal cord. DOI: http://dx.doi.org/10.7554/eLife.22784.009 10.7554/eLife.22784.010 Asymmetrically methylated CpG sites per week and side of the spinal cord. DOI: http://dx.doi.org/10.7554/eLife.22784.010

Techniques Used: Expressing, DNA Methylation Assay, Methylation

9) Product Images from "Hepatic Tumor Formation in Adult Mice Developmentally Exposed to Organotin"

Article Title: Hepatic Tumor Formation in Adult Mice Developmentally Exposed to Organotin

Journal: Environmental Health Perspectives

doi: 10.1289/EHP5414

Body weight, white adipose tissue weight, adipose magnetic resonance imaging (MRI), and liver lipid of male and female mice developmentally exposed to tributyltin or vehicle. (A) Female mice were fed a phytoestrogen-free diet and treated with tributyltin (TBT) in their drinking water beginning 2 weeks prior to breeding lasting through gestation and lactation. Offspring were then weaned at 3 weeks of age and fed the same phytoestrogen-free diet until euthanasia at 14, 20, or 45 weeks of age. (B) Body weights, white adipose tissue depot [either inguinal (iWAT) or scapular (scWAT)], and brown adipose tissue (BAT) wet weights in 14-week-old animals developmentally exposed to TBT or VEH are displayed; VEH-treated females, n = 4 (from two litters with two pups per litter); VEH-treated males, n = 3 (from two litters); TBT-treated females, n = 3 (from two litters); TBT-treated males, n = 4 (from two litters, two pups per litter). (C) Representative full-body MRI scans are presented on the left and quantitation of surface area is presented on the right for 20-week-old animals: for VEH-treated females, n = 2 (from one litter); for TBT-treated females, n = 4 (from two litters with two pups per litter); for VEH-treated males, n = 2 ; and for TBT-treated males, n = 4 . (D) Macroscopic images of liver tissue at 20 weeks, and Oil Red O stained, left liver lobes are presented on the left with quantitation of Oil Red O staining on the right, n = 6 for VEH-treated males, n = 10 for TBT-treated males, n = 7 for VEH-treated females, and n = 9 for TBT-treated females. Scale bars: 100 μ m . In all graphs, VEH bars are hatched and T BT bars are solid, all bars represent the mean ± standard error of the mean (SEM) and t -tests were performed to ascertain significance (* p

Figure Legend Snippet: Body weight, white adipose tissue weight, adipose magnetic resonance imaging (MRI), and liver lipid of male and female mice developmentally exposed to tributyltin or vehicle. (A) Female mice were fed a phytoestrogen-free diet and treated with tributyltin (TBT) in their drinking water beginning 2 weeks prior to breeding lasting through gestation and lactation. Offspring were then weaned at 3 weeks of age and fed the same phytoestrogen-free diet until euthanasia at 14, 20, or 45 weeks of age. (B) Body weights, white adipose tissue depot [either inguinal (iWAT) or scapular (scWAT)], and brown adipose tissue (BAT) wet weights in 14-week-old animals developmentally exposed to TBT or VEH are displayed; VEH-treated females, n = 4 (from two litters with two pups per litter); VEH-treated males, n = 3 (from two litters); TBT-treated females, n = 3 (from two litters); TBT-treated males, n = 4 (from two litters, two pups per litter). (C) Representative full-body MRI scans are presented on the left and quantitation of surface area is presented on the right for 20-week-old animals: for VEH-treated females, n = 2 (from one litter); for TBT-treated females, n = 4 (from two litters with two pups per litter); for VEH-treated males, n = 2 ; and for TBT-treated males, n = 4 . (D) Macroscopic images of liver tissue at 20 weeks, and Oil Red O stained, left liver lobes are presented on the left with quantitation of Oil Red O staining on the right, n = 6 for VEH-treated males, n = 10 for TBT-treated males, n = 7 for VEH-treated females, and n = 9 for TBT-treated females. Scale bars: 100 μ m . In all graphs, VEH bars are hatched and T BT bars are solid, all bars represent the mean ± standard error of the mean (SEM) and t -tests were performed to ascertain significance (* p

Techniques Used: Magnetic Resonance Imaging, Mouse Assay, Quantitation Assay, Staining

Overrepresentation analysis (ORA) using publicly available mouse and human liver disease data sets. An ORA was conducted using the genes differentially expressed in the tumors from TBT-exposed males with publicly available mouse and human RNA-seq data sets in distinct liver disease states (GSE14520, LIHC TCGA, GSE48452, GSE83596, GSE59930). ORA for (A) 45 week adenoma over TBT liver, (B) 45 week adenoma over VEH liver, and (C) 20 week TBT liver over VEH liver. Significant enrichment was detected in all data sets. Closed bars represent all overlapping genes in log 2 scale, whereas open bars and gray bars represent the subset of all genes that are also present in the growth hormone receptor (GHR) signature. Note: HCC, hepatocellular carcinoma; LIHC, liver hepatocellular carcinoma; NASH, nonalcoholic steatohepatitis.

Figure Legend Snippet: Overrepresentation analysis (ORA) using publicly available mouse and human liver disease data sets. An ORA was conducted using the genes differentially expressed in the tumors from TBT-exposed males with publicly available mouse and human RNA-seq data sets in distinct liver disease states (GSE14520, LIHC TCGA, GSE48452, GSE83596, GSE59930). ORA for (A) 45 week adenoma over TBT liver, (B) 45 week adenoma over VEH liver, and (C) 20 week TBT liver over VEH liver. Significant enrichment was detected in all data sets. Closed bars represent all overlapping genes in log 2 scale, whereas open bars and gray bars represent the subset of all genes that are also present in the growth hormone receptor (GHR) signature. Note: HCC, hepatocellular carcinoma; LIHC, liver hepatocellular carcinoma; NASH, nonalcoholic steatohepatitis.

Techniques Used: RNA Sequencing Assay

Histology of tributyltin (TBT)-treated liver adenomas in male mice. (A) At 45 weeks of age, liver adenomas were observed in many lobes of the liver in male mice. One vehicle (VEH)-exposed liver and two representative tumors are displayed with hematoxylin and eosin and Ki67 immunohistochemistry staining (left panels). The right panel shows a quantitation of Ki67 immunostaining [VEH-exposed liver (V), hatched bar, n = 6 ; TBT-exposed liver (T), n = 6 ; Adenoma (A), n = 7 ]. Bars represent mean ± standard error of the mean (SEM). *** p

Figure Legend Snippet: Histology of tributyltin (TBT)-treated liver adenomas in male mice. (A) At 45 weeks of age, liver adenomas were observed in many lobes of the liver in male mice. One vehicle (VEH)-exposed liver and two representative tumors are displayed with hematoxylin and eosin and Ki67 immunohistochemistry staining (left panels). The right panel shows a quantitation of Ki67 immunostaining [VEH-exposed liver (V), hatched bar, n = 6 ; TBT-exposed liver (T), n = 6 ; Adenoma (A), n = 7 ]. Bars represent mean ± standard error of the mean (SEM). *** p

Techniques Used: Mouse Assay, Immunohistochemistry, Staining, Quantitation Assay, Immunostaining

Expression of members of the growth hormone receptor (GHR)/STAT5 signaling pathway in male mice developmentally exposed to tributyltin. (A) Representative images of immunohistochemical staining of major urinary protein 1 (MUP1) protein in vehicle (VEH)-treated liver and adenomas from tributyltin (TBT)-treated 45-week-old male mice ( n = 5 ; scale bars: 100 μ m ). (B) Immunoblot analysis of growth hormone receptor (GHR) protein levels in liver tissue from VEH- ( n = 6 ) and TBT-exposed ( n = 5 ) males and adenoma tissue from TBT-exposed males ( n = 7 ) at 45 weeks of age (left panels) with quantitation of the immunoblots (right panels). GHR level was normalized to GAPDH protein level in each lysate. Ponceau stain is displayed beneath each blot. Bars represent the mean ± standard error of the mean ( SEM ) . * p

Figure Legend Snippet: Expression of members of the growth hormone receptor (GHR)/STAT5 signaling pathway in male mice developmentally exposed to tributyltin. (A) Representative images of immunohistochemical staining of major urinary protein 1 (MUP1) protein in vehicle (VEH)-treated liver and adenomas from tributyltin (TBT)-treated 45-week-old male mice ( n = 5 ; scale bars: 100 μ m ). (B) Immunoblot analysis of growth hormone receptor (GHR) protein levels in liver tissue from VEH- ( n = 6 ) and TBT-exposed ( n = 5 ) males and adenoma tissue from TBT-exposed males ( n = 7 ) at 45 weeks of age (left panels) with quantitation of the immunoblots (right panels). GHR level was normalized to GAPDH protein level in each lysate. Ponceau stain is displayed beneath each blot. Bars represent the mean ± standard error of the mean ( SEM ) . * p

Techniques Used: Expressing, Mouse Assay, Immunohistochemistry, Staining, Quantitation Assay, Western Blot

10) Product Images from "Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer"

Article Title: Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer

Journal: Scientific Reports

doi: 10.1038/s41598-017-17811-2

Study workflow. RNA and DNA were simultaneously extracted from 23 breast cancer ER+/HER2− tumors and their paired adjacent non-malignant tissues. Strand-specific paired-end RNA sequencing and comparative genomic hybridization (CGH) were performed. Quality control steps and RNA-Seq validation were performed and led to the elimination of one patient due to poor strand specificity in this sample. This strategy allowed the study of the differential expression of ncNATs and PCTs between tumors and non-malignant tissues and performance of differential correlation analysis of ncNAT/PCT pairs. Three lists of genes with deregulated ncNAT expression in tumors that could potentially affect the corresponding PC expression were extracted, and their coding genes were subjected to survival analysis with an external cohort (TCGA).

Figure Legend Snippet: Study workflow. RNA and DNA were simultaneously extracted from 23 breast cancer ER+/HER2− tumors and their paired adjacent non-malignant tissues. Strand-specific paired-end RNA sequencing and comparative genomic hybridization (CGH) were performed. Quality control steps and RNA-Seq validation were performed and led to the elimination of one patient due to poor strand specificity in this sample. This strategy allowed the study of the differential expression of ncNATs and PCTs between tumors and non-malignant tissues and performance of differential correlation analysis of ncNAT/PCT pairs. Three lists of genes with deregulated ncNAT expression in tumors that could potentially affect the corresponding PC expression were extracted, and their coding genes were subjected to survival analysis with an external cohort (TCGA).

Techniques Used: RNA Sequencing Assay, Hybridization, Expressing

11) Product Images from "MicroRNA-30 modulates metabolic inflammation by regulating notch signaling in adipose tissue macrophages"

Article Title: MicroRNA-30 modulates metabolic inflammation by regulating notch signaling in adipose tissue macrophages

Journal: International journal of obesity (2005)

doi: 10.1038/s41366-018-0114-1

Techniques Used: DNA Methylation Assay, Isolation, Mouse Assay, Expressing, Modification, Methylated DNA Immunoprecipitation, Methylation, Polymerase Chain Reaction

12) Product Images from "CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer"

Article Title: CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer

Journal: BMC Cancer

doi: 10.1186/s12885-017-3453-8

The ALKBH3 gene promoter region. a The ALKBH3 gene promoter is transcriptionally active in variant human mammary epithelial cells (vHMEC) based on available data from the Roadmap Epigenetic Consortium (Roadmap Epigenomics Consortium, Nature 2015). Data for vHMEC are shown here for markers associated with active transcription (H3K4me3 and H3K36me3) together with repressive markers (H3K27me3, H3K9me3, H3K4me1 and 5-methylcytosine (DNA methyl)). Additionally, DNAse and RNA sequencing results from vHMEC cells are shown – reflecting chromatin accessibility and mRNA expression, respectively. b The ALKBH3 gene promoter region is shown with respect to the FANTOM5 transcription start site (TSS) as arrows p1 and p2 along with the 1st exon and the promoter-associated CpG island (UCSC defined). The CpG methylation assay for ALKBH3 was designed to include CpG sites proximal to the TSS and the regions selected is indicated by a black box (labelled R) covering three closely spaced CpG dinucleotides found -50, −53 and -58 bp upstream of the major TSS (p1 region in FANTOM5). Additionally, the region where statistically significant associations were revealed between CpG methylation and loss of expression for the ALKBH3 gene in tumors is marked out and labelled for expression as “Xprs” (see further information in Additional file 1 )

Figure Legend Snippet: The ALKBH3 gene promoter region. a The ALKBH3 gene promoter is transcriptionally active in variant human mammary epithelial cells (vHMEC) based on available data from the Roadmap Epigenetic Consortium (Roadmap Epigenomics Consortium, Nature 2015). Data for vHMEC are shown here for markers associated with active transcription (H3K4me3 and H3K36me3) together with repressive markers (H3K27me3, H3K9me3, H3K4me1 and 5-methylcytosine (DNA methyl)). Additionally, DNAse and RNA sequencing results from vHMEC cells are shown – reflecting chromatin accessibility and mRNA expression, respectively. b The ALKBH3 gene promoter region is shown with respect to the FANTOM5 transcription start site (TSS) as arrows p1 and p2 along with the 1st exon and the promoter-associated CpG island (UCSC defined). The CpG methylation assay for ALKBH3 was designed to include CpG sites proximal to the TSS and the regions selected is indicated by a black box (labelled R) covering three closely spaced CpG dinucleotides found -50, −53 and -58 bp upstream of the major TSS (p1 region in FANTOM5). Additionally, the region where statistically significant associations were revealed between CpG methylation and loss of expression for the ALKBH3 gene in tumors is marked out and labelled for expression as “Xprs” (see further information in Additional file 1 )

Techniques Used: Variant Assay, RNA Sequencing Assay, Expressing, CpG Methylation Assay

13) Product Images from "The HDAC inhibitor valproate induces a bivalent status of the CD20 promoter in CLL patients suggesting distinct epigenetic regulation of CD20 expression in CLL in vivo"

Article Title: The HDAC inhibitor valproate induces a bivalent status of the CD20 promoter in CLL patients suggesting distinct epigenetic regulation of CD20 expression in CLL in vivo

Journal: Oncotarget

doi: 10.18632/oncotarget.16964

Global H3K27me3 is increased by valproate in CLL patients and in the I83-E95 CLL cell line I83-E95 cells and circulating untreated CLL cells from patients were incubated with or without 1000 μM of valproate. After 48 hours total protein extracts were prepared and global H3K27me3 was analysed by Western blot. β-actin was used as equal loading control. One out of two independent experiments is shown. For experiment number 2, please see Supplementary Figure 1 .

Figure Legend Snippet: Global H3K27me3 is increased by valproate in CLL patients and in the I83-E95 CLL cell line I83-E95 cells and circulating untreated CLL cells from patients were incubated with or without 1000 μM of valproate. After 48 hours total protein extracts were prepared and global H3K27me3 was analysed by Western blot. β-actin was used as equal loading control. One out of two independent experiments is shown. For experiment number 2, please see Supplementary Figure 1 .

Techniques Used: Incubation, Western Blot

Valproate transiently recruits the transcriptional repressor EZH2 to the CD20 promoter in vivo but not in vitro I83-E95 cells were incubated with or without valproate (VPA) at 1000 μM for 72 hours and subjected to ChIP with anti-EZH2 antibody ( A ). Patient samples collected after 0 and 72 hours of valproate-treatment from cycle 1 ( C ) and cycle 2 ( E ) of the PREVAIL study were subjected to ChIP with anti-EZH2 antibody. Levels of EZH2 on the CD20 promoter were evaluated by densitometry analysis and expressed in graphs ( B , D , F ). (Mean values, bars ± s.e.m, n = 3; ns: not significant). Due to sample limitation, experiments C–F were performed once.

Figure Legend Snippet: Valproate transiently recruits the transcriptional repressor EZH2 to the CD20 promoter in vivo but not in vitro I83-E95 cells were incubated with or without valproate (VPA) at 1000 μM for 72 hours and subjected to ChIP with anti-EZH2 antibody ( A ). Patient samples collected after 0 and 72 hours of valproate-treatment from cycle 1 ( C ) and cycle 2 ( E ) of the PREVAIL study were subjected to ChIP with anti-EZH2 antibody. Levels of EZH2 on the CD20 promoter were evaluated by densitometry analysis and expressed in graphs ( B , D , F ). (Mean values, bars ± s.e.m, n = 3; ns: not significant). Due to sample limitation, experiments C–F were performed once.

Techniques Used: In Vivo, In Vitro, Incubation, Chromatin Immunoprecipitation

Valproate induces simultaneous H3K9ac and H3K27me3 in the CD20 promoter in CLL patients in vivo but not in the I83-E95 CLL cell line I83-E95 cells were incubated with or without valproate (VPA) at 1000 μM for 72 hours and subjected to ChIP with anti-H3K9ac ( A , top) or anti-H3K27me3 (A, bottom) antibodies. Patient samples collected after 0 and 72 hours of valproate-treatment from cycle 1 ( C ) and cycle 2 ( E ) of the PREVAIL study were subjected to ChIP with anti-H3K9ac and anti-H3K27me3 antibodies. Levels of H3K9ac and H3K27me3 on the CD20 promoter were evaluated by densitometry analysis and expressed in graphs ( B , D , F ). (Mean values, bars ± s.e.m, n = 3). Stars indicate statistical significance (* p

Figure Legend Snippet: Valproate induces simultaneous H3K9ac and H3K27me3 in the CD20 promoter in CLL patients in vivo but not in the I83-E95 CLL cell line I83-E95 cells were incubated with or without valproate (VPA) at 1000 μM for 72 hours and subjected to ChIP with anti-H3K9ac ( A , top) or anti-H3K27me3 (A, bottom) antibodies. Patient samples collected after 0 and 72 hours of valproate-treatment from cycle 1 ( C ) and cycle 2 ( E ) of the PREVAIL study were subjected to ChIP with anti-H3K9ac and anti-H3K27me3 antibodies. Levels of H3K9ac and H3K27me3 on the CD20 promoter were evaluated by densitometry analysis and expressed in graphs ( B , D , F ). (Mean values, bars ± s.e.m, n = 3). Stars indicate statistical significance (* p

Techniques Used: In Vivo, Incubation, Chromatin Immunoprecipitation

Valproate induces expression of the transcriptional repressor EZH2 in CLL patients I83-E95 cells and circulating untreated CLL cells from patients were incubated with or without 1000 μM of valproate. After 48 hours’ levels of EZH2 mRNA in I83-E95 cells ( A , mean values, bars ± s.e.m, n = 4, * p

Figure Legend Snippet: Valproate induces expression of the transcriptional repressor EZH2 in CLL patients I83-E95 cells and circulating untreated CLL cells from patients were incubated with or without 1000 μM of valproate. After 48 hours’ levels of EZH2 mRNA in I83-E95 cells ( A , mean values, bars ± s.e.m, n = 4, * p

Techniques Used: Expressing, Incubation

CD20 expression is induced by valproate in the I83-E95 CLL cell line I83-E95 cells were treated for 0h or 72h with valproate (VPA) at 1000 μM. CD20 expression was analysed by qPCR ( A ), FACS ( B ), and Western blot ( C ). (Mean values, bars ± s.e.m, n = 3). Global acetylation of H3K9 was assessed by Western blot (C) and β-actin was used as equal loading control. Stars indicate statistical significance (* p

Figure Legend Snippet: CD20 expression is induced by valproate in the I83-E95 CLL cell line I83-E95 cells were treated for 0h or 72h with valproate (VPA) at 1000 μM. CD20 expression was analysed by qPCR ( A ), FACS ( B ), and Western blot ( C ). (Mean values, bars ± s.e.m, n = 3). Global acetylation of H3K9 was assessed by Western blot (C) and β-actin was used as equal loading control. Stars indicate statistical significance (* p

Techniques Used: Expressing, Real-time Polymerase Chain Reaction, FACS, Western Blot

14) Product Images from "Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood"

Article Title: Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood

Journal: Epigenetics

doi: 10.1080/15592294.2018.1507198

Techniques Used: Sequencing, Isolation, Amplification, Methylation, Quantitative RT-PCR

15) Product Images from "Establishment of urinary exosome-like vesicles isolation protocol for FHHNC patients and evaluation of different exosomal RNA extraction methods"

Article Title: Establishment of urinary exosome-like vesicles isolation protocol for FHHNC patients and evaluation of different exosomal RNA extraction methods

Journal: Journal of Translational Medicine

doi: 10.1186/s12967-018-1651-z

Techniques Used: Quantitative RT-PCR, Expressing, RNA Extraction

DNA Extraction:

Article Title: DNA methylation changes in endometrium and correlation with gene expression during the transition from pre-receptive to receptive phase
Article Snippet: .. DNA extraction and DNA methylation measurement Genomic DNA was isolated from approximately 20 mg of endometrial tissue using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Venlo, The Netherlands) according to manufacturer’s original protocol. .. DNA hybridization to Infinium HumanMethylation 450 K BeadChip (Illumina, San Diego, CA, USA) was performed at USC Epigenome Center (Los Angeles, CA, USA) according to manufacturer’s specifications.

Isolation:

Article Title: Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma
Article Snippet: .. RNA and small RNA isolation Total RNA and Small RNA molecules were extracted from eBL FNA samples in RNAlater using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen) according to manufacturer’s instructions. .. Small RNA abundance and integrity were determined after isolation using Nanodrop-ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, Massachusetts, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively.

other:

Article Title: Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer
Article Snippet: DNA/RNA/miRNA extraction DNA, RNA and miRNA were simultaneously extracted using an All Prep DNA/RNA/miRNA Universal kit (Qiagen, Belgium) according to the manufacturer’s protocol.

allprep dna rna mirna universal kit protocol (Qiagen)

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1) Product Images from "RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition"

2) Product Images from "Comparison of Automated and Manual DNA Isolation Methods of Liquid-Based Cytology Samples"

3) Product Images from "Establishment of urinary exosome-like vesicles isolation protocol for FHHNC patients and evaluation of different exosomal RNA extraction methods"

4) Product Images from "Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood"

5) Product Images from "Establishment of urinary exosome-like vesicles isolation protocol for FHHNC patients and evaluation of different exosomal RNA extraction methods"

6) Product Images from "Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma"

7) Product Images from "MicroRNA-30 modulates metabolic inflammation by regulating notch signaling in adipose tissue macrophages"

8) Product Images from "Epigenetic regulation of lateralized fetal spinal gene expression underlies hemispheric asymmetries"

9) Product Images from "Hepatic Tumor Formation in Adult Mice Developmentally Exposed to Organotin"

10) Product Images from "Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer"

11) Product Images from "MicroRNA-30 modulates metabolic inflammation by regulating notch signaling in adipose tissue macrophages"

12) Product Images from "CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer"

13) Product Images from "The HDAC inhibitor valproate induces a bivalent status of the CD20 promoter in CLL patients suggesting distinct epigenetic regulation of CD20 expression in CLL in vivo"

14) Product Images from "Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood"

15) Product Images from "Establishment of urinary exosome-like vesicles isolation protocol for FHHNC patients and evaluation of different exosomal RNA extraction methods"

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