cd4 t cells  (Qiagen)


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    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
    Price:
    541
    Category:
    AllPrep DNA RNA Mini Kit
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    Structured Review

    Qiagen cd4 t cells
    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/cd4 t cells/product/Qiagen
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    cd4 t cells - by Bioz Stars, 2020-04
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    Images

    1) Product Images from "Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells"

    Article Title: Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-38809-y

    Kaiso binding to mCGCG motif located in  Ctse  intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme  Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to  Acc II. The genomic DNAs were digested with  Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p 
    Figure Legend Snippet: Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p 

    Techniques Used: Binding Assay, Histone Deacetylase Assay, Mouse Assay, Methylation, Polymerase Chain Reaction, Derivative Assay, Amplification

    Expression of  Il10  in EL4 cells transfected with siRNA for  Ctse  and CD4+ T cells isolated from B6 and MRL mice. ( A ) The knockdown and mRNA expression of  Ctse  in EL4 cells transfected with 5 μM control siRNA (si-Control) or  Ctse  siRNA (si-CTSE). *p 
    Figure Legend Snippet: Expression of Il10 in EL4 cells transfected with siRNA for Ctse and CD4+ T cells isolated from B6 and MRL mice. ( A ) The knockdown and mRNA expression of Ctse in EL4 cells transfected with 5 μM control siRNA (si-Control) or Ctse siRNA (si-CTSE). *p 

    Techniques Used: Expressing, Transfection, Isolation, Mouse Assay

    The expression and methylation status of  Ctse  gene in CD4+ T cells isolated from MRL/lpr lupus-prone (MRL) and C57BL/6 (B6) mice. ( A ) mRNA expression of  Ctse  in CD4+, CD8+, B cells and macrophages in B6 and MRL mice. *** p
    Figure Legend Snippet: The expression and methylation status of Ctse gene in CD4+ T cells isolated from MRL/lpr lupus-prone (MRL) and C57BL/6 (B6) mice. ( A ) mRNA expression of Ctse in CD4+, CD8+, B cells and macrophages in B6 and MRL mice. *** p

    Techniques Used: Expressing, Methylation, Isolation, Mouse Assay

    The increased levels of  CTSE  and  IL10  transcripts in CD4+ T cells from SLE patients. ( A ) and ( B ) mRNA expression of  CTSE  and  IL10  in CD4+ T cells isolated from healthy (n = 8) and the patients with SLE (n = 15). ( C ) mRNA expression of  PDCD4 . There is no significant difference in healthy subjects and patients with SLE. ( D ) The simple correlation between the  CTSE  and  IL10  transcript levels. *p 
    Figure Legend Snippet: The increased levels of CTSE and IL10 transcripts in CD4+ T cells from SLE patients. ( A ) and ( B ) mRNA expression of CTSE and IL10 in CD4+ T cells isolated from healthy (n = 8) and the patients with SLE (n = 15). ( C ) mRNA expression of PDCD4 . There is no significant difference in healthy subjects and patients with SLE. ( D ) The simple correlation between the CTSE and IL10 transcript levels. *p 

    Techniques Used: Expressing, Isolation

    2) Product Images from "Frequency of NFKBIA deletions is low in glioblastomas and skewed in glioblastoma neurospheres"

    Article Title: Frequency of NFKBIA deletions is low in glioblastomas and skewed in glioblastoma neurospheres

    Journal: Molecular Cancer

    doi: 10.1186/1476-4598-12-160

    Copy number variation values (CNVs) in primary GBM (brain tumors, BT) and corresponding neurospheres (NS). A) EGFR amplification in BT and corresponding NS is expressed as EGFR/HGF ratio in comparison to control DNA and shows significant loss of amplification in vitro (**p
    Figure Legend Snippet: Copy number variation values (CNVs) in primary GBM (brain tumors, BT) and corresponding neurospheres (NS). A) EGFR amplification in BT and corresponding NS is expressed as EGFR/HGF ratio in comparison to control DNA and shows significant loss of amplification in vitro (**p

    Techniques Used: Amplification, In Vitro

    3) Product Images from "Frequency of NFKBIA deletions is low in glioblastomas and skewed in glioblastoma neurospheres"

    Article Title: Frequency of NFKBIA deletions is low in glioblastomas and skewed in glioblastoma neurospheres

    Journal: Molecular Cancer

    doi: 10.1186/1476-4598-12-160

    Copy number variation values (CNVs) in primary GBM (brain tumors, BT) and corresponding neurospheres (NS). A) EGFR amplification in BT and corresponding NS is expressed as EGFR/HGF ratio in comparison to control DNA and shows significant loss of amplification in vitro (**p
    Figure Legend Snippet: Copy number variation values (CNVs) in primary GBM (brain tumors, BT) and corresponding neurospheres (NS). A) EGFR amplification in BT and corresponding NS is expressed as EGFR/HGF ratio in comparison to control DNA and shows significant loss of amplification in vitro (**p

    Techniques Used: Amplification, In Vitro

    4) Product Images from "Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells"

    Article Title: Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-38809-y

    Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p
    Figure Legend Snippet: Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p

    Techniques Used: Binding Assay, Histone Deacetylase Assay, Mouse Assay, Methylation, Polymerase Chain Reaction, Derivative Assay, Amplification

    5) Product Images from "Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells"

    Article Title: Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-38809-y

    Luciferase assay of Kaiso regulatory region of the Ctse gene. ( A ) Nucleotide sequences of CGCG motif in Kaiso regulatory region expanding chromosome 1: 131641487–131642069, and AGGAG motif in PU.1 promoter region expanding chromosome 1: 131661764–131662059 in prepared pGL4.10 [ luc2 ] Vector constructs. ( B ) pGL4.10 [ luc2 ] Vector constructs (1 μg) were transfected into EL4 cells with pRL-TK plasmid and Firefly/Renilla ratio of pGL4.10 (empty vector) was set as 1.0. MRL/MRL construct showed significantly higher luciferase activity compared with pGL4.10-B6/B6 construct (***p
    Figure Legend Snippet: Luciferase assay of Kaiso regulatory region of the Ctse gene. ( A ) Nucleotide sequences of CGCG motif in Kaiso regulatory region expanding chromosome 1: 131641487–131642069, and AGGAG motif in PU.1 promoter region expanding chromosome 1: 131661764–131662059 in prepared pGL4.10 [ luc2 ] Vector constructs. ( B ) pGL4.10 [ luc2 ] Vector constructs (1 μg) were transfected into EL4 cells with pRL-TK plasmid and Firefly/Renilla ratio of pGL4.10 (empty vector) was set as 1.0. MRL/MRL construct showed significantly higher luciferase activity compared with pGL4.10-B6/B6 construct (***p

    Techniques Used: Luciferase, Plasmid Preparation, Construct, Transfection, Activity Assay

    Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p
    Figure Legend Snippet: Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p

    Techniques Used: Binding Assay, Histone Deacetylase Assay, Mouse Assay, Methylation, Polymerase Chain Reaction, Derivative Assay, Amplification

    The binding of Kaiso on the mCGCG motif of Kaiso regulatory region of Ctse gene. ( A ) Biotin-labeled and methylated probe (B6-Me) was incubated with 28 μg of nuclear protein from EL4 cells, and putative Kaiso and DNA complexes is indicated by asterisk in lane 2. The formation of Kaiso and DNA complexes was inhibited by excess amounts of unlabeled competitor (lane 3). The Kaiso and DNA complexes demonstrated supershift by the addition of 4 μg of anti-Kaiso Ab (arrow head in lane 4). ( B ) Biotin-labeled, unmethylated (MRL), and methylated (MRL-Me) probes were incubated with 28 μg of nuclear protein from EL4 cells. The putative Kaiso and DNA complexes are indicated by asterisks in lanes 2 and 7 and they reveal no supershift with anti-Kaiso Ab and anti-HDAC3 Ab.
    Figure Legend Snippet: The binding of Kaiso on the mCGCG motif of Kaiso regulatory region of Ctse gene. ( A ) Biotin-labeled and methylated probe (B6-Me) was incubated with 28 μg of nuclear protein from EL4 cells, and putative Kaiso and DNA complexes is indicated by asterisk in lane 2. The formation of Kaiso and DNA complexes was inhibited by excess amounts of unlabeled competitor (lane 3). The Kaiso and DNA complexes demonstrated supershift by the addition of 4 μg of anti-Kaiso Ab (arrow head in lane 4). ( B ) Biotin-labeled, unmethylated (MRL), and methylated (MRL-Me) probes were incubated with 28 μg of nuclear protein from EL4 cells. The putative Kaiso and DNA complexes are indicated by asterisks in lanes 2 and 7 and they reveal no supershift with anti-Kaiso Ab and anti-HDAC3 Ab.

    Techniques Used: Binding Assay, Labeling, Methylation, Incubation

    Expression of Il10 in EL4 cells transfected with siRNA for Ctse and CD4+ T cells isolated from B6 and MRL mice. ( A ) The knockdown and mRNA expression of Ctse in EL4 cells transfected with 5 μM control siRNA (si-Control) or Ctse siRNA (si-CTSE). *p
    Figure Legend Snippet: Expression of Il10 in EL4 cells transfected with siRNA for Ctse and CD4+ T cells isolated from B6 and MRL mice. ( A ) The knockdown and mRNA expression of Ctse in EL4 cells transfected with 5 μM control siRNA (si-Control) or Ctse siRNA (si-CTSE). *p

    Techniques Used: Expressing, Transfection, Isolation, Mouse Assay

    The expression and methylation status of Ctse gene in CD4+ T cells isolated from MRL/lpr lupus-prone (MRL) and C57BL/6 (B6) mice. ( A ) mRNA expression of Ctse in CD4+, CD8+, B cells and macrophages in B6 and MRL mice. *** p
    Figure Legend Snippet: The expression and methylation status of Ctse gene in CD4+ T cells isolated from MRL/lpr lupus-prone (MRL) and C57BL/6 (B6) mice. ( A ) mRNA expression of Ctse in CD4+, CD8+, B cells and macrophages in B6 and MRL mice. *** p

    Techniques Used: Expressing, Methylation, Isolation, Mouse Assay

    Related Articles

    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.

    Synthesized:

    Article Title: Decreased expression of the immediate early protein, ICP4, by deletion of the tegument protein VP22 of equine herpesvirus type 1
    Article Snippet: .. Total RNA and DNA of infected cells were extracted using AllPrep DNA/RNA Mini Kit (QIAGEN K.K., Hilden, Germany) at 0 and 1 hrpi. cDNA was synthesized from 0.5 µ g of total RNA using ReverTra Ace (TOYOBO, Osaka, Japan). .. The real-time PCR assay was carried out using SYBR Premix Ex Taq II (Takara Bio Inc., Otsu, Japan) according to the manufacturer’s instructions.

    Cytometry:

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: Males and females with the proper genotype were crossed to obtain GFP+ males with the three possible Dnmt3L genotypes; paired testes were collected at 6 dpp and were processed as mentioned above to allow for the isolation of Dnmt3L (+/+), (+/-) and (-/-) GFP+ primitive type A spermatogonia by flow cytometry. .. RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA.

    Immunostaining:

    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: 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. .. Whole embryos were also collected 6, 9 and 12 hours post-treatment, fixed in 4% paraformaldehyde (PFA), embedded in OCT (optimal cutting temperature compound, Tissue-Tek 4583, Sakura Finetek USA, Inc., Torrance, CA), frozen at −80°C, cryosectioned and processed as described by Oh et al. [ ], either for staining with hematoxylin and eosin, or immunostaining with phospho-histone-H3 or activated caspase-3 antibody, to assess cell proliferation or apoptosis, respectively.

    Adsorption:

    Article Title: Decreased expression of the immediate early protein, ICP4, by deletion of the tegument protein VP22 of equine herpesvirus type 1
    Article Snippet: After 1 hr adsorption, cells were washed three times with MEM and incubated at 37°C in a 5% CO2 atmosphere in 1 ml/well of MEM, and this time point was defined as 0 hrpi. .. Total RNA and DNA of infected cells were extracted using AllPrep DNA/RNA Mini Kit (QIAGEN K.K., Hilden, Germany) at 0 and 1 hrpi. cDNA was synthesized from 0.5 µ g of total RNA using ReverTra Ace (TOYOBO, Osaka, Japan).

    SYBR Green Assay:

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA. .. For a given sequence, primers were designed to flank the restriction sites of interest and real-time PCR was performed on the different digested templates using the QuantiTect ™ SYBR® Green PCR kit (Qiagen) according to the manufacturer's suggested conditions for use of the Mx3000P PCR machine (Stratagene).

    Incubation:

    Article Title: Decreased expression of the immediate early protein, ICP4, by deletion of the tegument protein VP22 of equine herpesvirus type 1
    Article Snippet: After 1 hr adsorption, cells were washed three times with MEM and incubated at 37°C in a 5% CO2 atmosphere in 1 ml/well of MEM, and this time point was defined as 0 hrpi. .. Total RNA and DNA of infected cells were extracted using AllPrep DNA/RNA Mini Kit (QIAGEN K.K., Hilden, Germany) at 0 and 1 hrpi. cDNA was synthesized from 0.5 µ g of total RNA using ReverTra Ace (TOYOBO, Osaka, Japan).

    Expressing:

    Article Title: Decreased expression of the immediate early protein, ICP4, by deletion of the tegument protein VP22 of equine herpesvirus type 1
    Article Snippet: These data indicated that the band, which was not detected in EHV-1∆VP22 at 2 hrpi in the , is ICP4 and that expression level of ICP4 was decreased to be marginally detectable. .. Total RNA and DNA of infected cells were extracted using AllPrep DNA/RNA Mini Kit (QIAGEN K.K., Hilden, Germany) at 0 and 1 hrpi. cDNA was synthesized from 0.5 µ g of total RNA using ReverTra Ace (TOYOBO, Osaka, Japan).

    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.

    Flow Cytometry:

    Article Title: Increased HIV-1 transcriptional activity and infectious burden in peripheral blood and gut-associated CD4+ T cells expressing CD30
    Article Snippet: Quantification of cell-associated HIV-1 RNA and DNA Purification of HIV-1 DNA and RNA from sorted cell populations was achieved using a Qiagen AllPrep DNA/RNA mini Kit, and following the manufacturer’s standard protocol, with an additional DNAse treatment (QIAgen). .. Given the small number of CD30+ cells that could be obtained from flow sorting, these cell fractions were spiked into uninfected carrier PBMC to maximize HIV-1 DNA and RNA recovery and normalize extraction efficiency between CD30+ and CD30- CD4+ T cell populations.

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: Males and females with the proper genotype were crossed to obtain GFP+ males with the three possible Dnmt3L genotypes; paired testes were collected at 6 dpp and were processed as mentioned above to allow for the isolation of Dnmt3L (+/+), (+/-) and (-/-) GFP+ primitive type A spermatogonia by flow cytometry. .. RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA.

    Infection:

    Article Title: Decreased expression of the immediate early protein, ICP4, by deletion of the tegument protein VP22 of equine herpesvirus type 1
    Article Snippet: .. Total RNA and DNA of infected cells were extracted using AllPrep DNA/RNA Mini Kit (QIAGEN K.K., Hilden, Germany) at 0 and 1 hrpi. cDNA was synthesized from 0.5 µ g of total RNA using ReverTra Ace (TOYOBO, Osaka, Japan). .. The real-time PCR assay was carried out using SYBR Premix Ex Taq II (Takara Bio Inc., Otsu, Japan) according to the manufacturer’s instructions.

    Polymerase Chain Reaction:

    Article Title: Increased HIV-1 transcriptional activity and infectious burden in peripheral blood and gut-associated CD4+ T cells expressing CD30
    Article Snippet: Quantification of cell-associated HIV-1 RNA and DNA Purification of HIV-1 DNA and RNA from sorted cell populations was achieved using a Qiagen AllPrep DNA/RNA mini Kit, and following the manufacturer’s standard protocol, with an additional DNAse treatment (QIAgen). .. Spiking rare cells also allowed for the input of similar amounts of RNA into each PCR reaction.

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA. .. For a given sequence, primers were designed to flank the restriction sites of interest and real-time PCR was performed on the different digested templates using the QuantiTect ™ SYBR® Green PCR kit (Qiagen) according to the manufacturer's suggested conditions for use of the Mx3000P PCR machine (Stratagene).

    Article Title: Decreased expression of the immediate early protein, ICP4, by deletion of the tegument protein VP22 of equine herpesvirus type 1
    Article Snippet: Total RNA and DNA of infected cells were extracted using AllPrep DNA/RNA Mini Kit (QIAGEN K.K., Hilden, Germany) at 0 and 1 hrpi. cDNA was synthesized from 0.5 µ g of total RNA using ReverTra Ace (TOYOBO, Osaka, Japan). .. Primer pairs used for quantitative realtime PCR were listed in .

    Injection:

    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: Clinical and Mucosal Immune Correlates of HIV-1 Semen Levels in Antiretroviral-Naive Men
    Article Snippet: Bacterial Load Quantification For bacterial load quantification, 500 μL of thawed SP was lysed using a combination of chemical and mechanical methods and purified using AllPrep DNA/RNA Mini Kit (QIAGEN). .. Using the DNA fraction, bacterial load was quantfied, measured as bacterial 16S recombinant RNA (rRNA) gene copy/mL of SP using a broad-coverage qPCR assay, described previously [ ].

    Nucleic Acid Purification:

    Article Title: Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy
    Article Snippet: Paragraph title: Nucleic acid purification ... Total RNA and DNA were purified from colonic mucosal tissue using the AllPrep DNA/RNA Mini Kit (Qiagen).

    DNA Extraction:

    Article Title: Identification of Molecular Tumor Markers in Renal Cell Carcinomas with TFE3 Protein Expression by RNA Sequencing 1Identification of Molecular Tumor Markers in Renal Cell Carcinomas with TFE3 Protein Expression by RNA Sequencing 1 2
    Article Snippet: .. DNA extraction was done with AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) from 3 x 10 µm section of the same frozen tumor blocks used for RNA-Seq. ..

    RNA Sequencing Assay:

    Article Title: Identification of Molecular Tumor Markers in Renal Cell Carcinomas with TFE3 Protein Expression by RNA Sequencing 1Identification of Molecular Tumor Markers in Renal Cell Carcinomas with TFE3 Protein Expression by RNA Sequencing 1 2
    Article Snippet: .. DNA extraction was done with AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) from 3 x 10 µm section of the same frozen tumor blocks used for RNA-Seq. ..

    Methylation:

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA. .. Briefly, the DNA was either mock digested (sham group), or digested with methylation-sensitive restriction enzymes (NotI, HpaII or HhaI), which cleave DNA if the restriction site(s) are unmethylated, or with a methylation-dependent restriction enzyme (McrBC), which cleaves DNA only if it is methylated.

    Mutagenesis:

    Article Title: Identification of Molecular Tumor Markers in Renal Cell Carcinomas with TFE3 Protein Expression by RNA Sequencing 1Identification of Molecular Tumor Markers in Renal Cell Carcinomas with TFE3 Protein Expression by RNA Sequencing 1 2
    Article Snippet: Paragraph title: Mutation Analysis Using RNA-Seq Data ... DNA extraction was done with AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) from 3 x 10 µm section of the same frozen tumor blocks used for RNA-Seq.

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: Paragraph title: Isolation of Dnmt3L mutant germ cells and DNA Methylation Analysis ... RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA.

    Isolation:

    Article Title: Association between TLR-9 polymorphisms and colon cancer susceptibility in Saudi Arabian female patients
    Article Snippet: .. Total RNA isolation Total RNA was extracted from 40 colon cancer tissues and 40 matched normal colon tissues using an AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s protocol. .. The isolated RNA concentration, purity, and quality were determined using an Agilent 2100 Bioanalyzer system and Agilent Small RNA analysis kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer’s instructions.

    Article Title: FIV establishes a latent infection in feline peripheral blood CD4+ T lymphocytes in vivo during the asymptomatic phase of infection
    Article Snippet: .. Real-time PCR assays Cell-associated RNA and DNA were co-isolated utilizing a commercial kit (AllPrep DNA/RNA Mini Kit, Qiagen, Valencia, CA) while plasma or culture media-associated vRNA was isolated using a different commercial kit (QIAamp Viral RNA Mini Kit, Qiagen) according to manufacturers' instructions. .. DNase treatment of isolated RNA was accomplished with TURBO DNase (Ambion, Austin, TX).

    Article Title: Redefining transcriptional regulation of the APOE gene and its association with Alzheimer’s disease
    Article Snippet: .. DNA/RNA extraction and APOE genotyping Genomic DNA was isolated from frozen PMB using the AllPrep DNA/RNA Mini Kit (Qiagen). .. Nucleic acid concentrations were measured by NanoPhotometer (Implen), and samples were stored at –20°C prior to use.

    Article Title: Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors
    Article Snippet: .. Isolation of DNA and RNA from mucosal samples and cDNA synthesis Using the AllPrep DNA/RNA Mini Kit (Qiagen), RNA and DNA were isolated from ~ 8 mg of mucosal tissue that had been preserved in Allprotect Tissue Reagent (Qiagen). .. The manufacturer’s instructions were followed except for extended homogenization and additional enzymatic lysis steps as reported in [ ].

    Article Title: Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors
    Article Snippet: .. Using the AllPrep DNA/RNA Mini Kit (Qiagen), RNA and DNA were isolated from ~ 8 mg of mucosal tissue that had been preserved in Allprotect Tissue Reagent (Qiagen). .. The manufacturer’s instructions were followed except for extended homogenization and additional enzymatic lysis steps as reported in [ ].

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: Paragraph title: Isolation of Dnmt3L mutant germ cells and DNA Methylation Analysis ... RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA.

    Mouse Assay:

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: Isolation of Dnmt3L mutant germ cells and DNA Methylation Analysis Dnmt3L +/- females were crossed with GOF18/deltaPE-Oct-4/GFP males to obtain [Dnmt3L +/- , GFP+ ] mice. .. RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA.

    Sequencing:

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA. .. For a given sequence, primers were designed to flank the restriction sites of interest and real-time PCR was performed on the different digested templates using the QuantiTect ™ SYBR® Green PCR kit (Qiagen) according to the manufacturer's suggested conditions for use of the Mx3000P PCR machine (Stratagene).

    Quantitative RT-PCR:

    Article Title: FIV establishes a latent infection in feline peripheral blood CD4+ T lymphocytes in vivo during the asymptomatic phase of infection
    Article Snippet: Real-time PCR assays Cell-associated RNA and DNA were co-isolated utilizing a commercial kit (AllPrep DNA/RNA Mini Kit, Qiagen, Valencia, CA) while plasma or culture media-associated vRNA was isolated using a different commercial kit (QIAamp Viral RNA Mini Kit, Qiagen) according to manufacturers' instructions. .. RNA was reverse transcribed into cDNA with the OriGene 1st Strand cDNA Synthesis System for Quantitative RT-PCR (Origene, Rockville, MD).

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: .. RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA. .. Quantitative analysis of DNA methylation using real-time PCR, or qAMP, was conducted to analyze the DNA methylation status of a number of sequences as described [ ].

    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.

    Lysis:

    Article Title: Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors
    Article Snippet: Isolation of DNA and RNA from mucosal samples and cDNA synthesis Using the AllPrep DNA/RNA Mini Kit (Qiagen), RNA and DNA were isolated from ~ 8 mg of mucosal tissue that had been preserved in Allprotect Tissue Reagent (Qiagen). .. The manufacturer’s instructions were followed except for extended homogenization and additional enzymatic lysis steps as reported in [ ].

    Article Title: Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors
    Article Snippet: Using the AllPrep DNA/RNA Mini Kit (Qiagen), RNA and DNA were isolated from ~ 8 mg of mucosal tissue that had been preserved in Allprotect Tissue Reagent (Qiagen). .. The manufacturer’s instructions were followed except for extended homogenization and additional enzymatic lysis steps as reported in [ ].

    Article Title: Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy
    Article Snippet: .. A further optimised tissue homogenisation and lysis protocol comprising mechanical bead beating, lysis buffer replacement and enzymatic treatment, in combination with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) resulted in efficient and simultaneous purification of microbial and human RNA and DNA from a single mucosal colonic tissue sample. .. The present work provides a unique possibility to study RNA and DNA from the same mucosal biopsy sample, making a direct comparison between metabolically active microbes and total microbial DNA.

    Article Title: Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy
    Article Snippet: Total RNA and DNA were purified from colonic mucosal tissue using the AllPrep DNA/RNA Mini Kit (Qiagen). .. Manufacturer’s instructions were followed with the exception of the lysis steps, where three tissue lysis protocols (Protocol 1, 2 and 3) were performed and evaluated (Fig. ; Additional file ).

    Article Title: Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy
    Article Snippet: .. The finding of bead beating and enzymatic lysis in combination with the AllPrep DNA/RNA Mini Kit being superior in breaking the ‘hard-to-lyse’ cell walls of the Firmicutes phylum (Fig. ) resulted in development of protocol 3 in an attempt to use enzymatic lysis and bead beating and still preserve microbial and human RNA. .. Protocol 3 is a combination of protocol 2 and a modified version of the enzymatic lysis procedure for stool samples published by Franzosa and colleagues [ ].

    Purification:

    Article Title: Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors
    Article Snippet: Isolation of DNA and RNA from mucosal samples and cDNA synthesis Using the AllPrep DNA/RNA Mini Kit (Qiagen), RNA and DNA were isolated from ~ 8 mg of mucosal tissue that had been preserved in Allprotect Tissue Reagent (Qiagen). .. For optimal RNA purification, on column DNAse treatment was included as described in the DNA/RNA Mini Kit protocol.

    Article Title: Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors
    Article Snippet: Using the AllPrep DNA/RNA Mini Kit (Qiagen), RNA and DNA were isolated from ~ 8 mg of mucosal tissue that had been preserved in Allprotect Tissue Reagent (Qiagen). .. For optimal RNA purification, on column DNAse treatment was included as described in the DNA/RNA Mini Kit protocol.

    Article Title: Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy
    Article Snippet: .. A further optimised tissue homogenisation and lysis protocol comprising mechanical bead beating, lysis buffer replacement and enzymatic treatment, in combination with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) resulted in efficient and simultaneous purification of microbial and human RNA and DNA from a single mucosal colonic tissue sample. .. The present work provides a unique possibility to study RNA and DNA from the same mucosal biopsy sample, making a direct comparison between metabolically active microbes and total microbial DNA.

    Article Title: Clinical and Mucosal Immune Correlates of HIV-1 Semen Levels in Antiretroviral-Naive Men
    Article Snippet: .. Bacterial Load Quantification For bacterial load quantification, 500 μL of thawed SP was lysed using a combination of chemical and mechanical methods and purified using AllPrep DNA/RNA Mini Kit (QIAGEN). ..

    Article Title: Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy
    Article Snippet: .. Total RNA and DNA were purified from colonic mucosal tissue using the AllPrep DNA/RNA Mini Kit (Qiagen). .. Manufacturer’s instructions were followed with the exception of the lysis steps, where three tissue lysis protocols (Protocol 1, 2 and 3) were performed and evaluated (Fig. ; Additional file ).

    Real-time Polymerase Chain Reaction:

    Article Title: FIV establishes a latent infection in feline peripheral blood CD4+ T lymphocytes in vivo during the asymptomatic phase of infection
    Article Snippet: .. Real-time PCR assays Cell-associated RNA and DNA were co-isolated utilizing a commercial kit (AllPrep DNA/RNA Mini Kit, Qiagen, Valencia, CA) while plasma or culture media-associated vRNA was isolated using a different commercial kit (QIAamp Viral RNA Mini Kit, Qiagen) according to manufacturers' instructions. .. DNase treatment of isolated RNA was accomplished with TURBO DNase (Ambion, Austin, TX).

    Article Title: Increased HIV-1 transcriptional activity and infectious burden in peripheral blood and gut-associated CD4+ T cells expressing CD30
    Article Snippet: Quantification of cell-associated HIV-1 RNA and DNA Purification of HIV-1 DNA and RNA from sorted cell populations was achieved using a Qiagen AllPrep DNA/RNA mini Kit, and following the manufacturer’s standard protocol, with an additional DNAse treatment (QIAgen). .. Quantitative PCR was performed to determine the levels of HIV-1 cell-associated RNA (caRNA), proviral DNA (pvDNA), and CCR5 in each subgroup.

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA. .. Quantitative analysis of DNA methylation using real-time PCR, or qAMP, was conducted to analyze the DNA methylation status of a number of sequences as described [ ].

    Article Title: Clinical and Mucosal Immune Correlates of HIV-1 Semen Levels in Antiretroviral-Naive Men
    Article Snippet: Bacterial Load Quantification For bacterial load quantification, 500 μL of thawed SP was lysed using a combination of chemical and mechanical methods and purified using AllPrep DNA/RNA Mini Kit (QIAGEN). .. Using the DNA fraction, bacterial load was quantfied, measured as bacterial 16S recombinant RNA (rRNA) gene copy/mL of SP using a broad-coverage qPCR assay, described previously [ ].

    Article Title: Decreased expression of the immediate early protein, ICP4, by deletion of the tegument protein VP22 of equine herpesvirus type 1
    Article Snippet: Total RNA and DNA of infected cells were extracted using AllPrep DNA/RNA Mini Kit (QIAGEN K.K., Hilden, Germany) at 0 and 1 hrpi. cDNA was synthesized from 0.5 µ g of total RNA using ReverTra Ace (TOYOBO, Osaka, Japan). .. The real-time PCR assay was carried out using SYBR Premix Ex Taq II (Takara Bio Inc., Otsu, Japan) according to the manufacturer’s instructions.

    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.

    Homogenization:

    Article Title: Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors
    Article Snippet: Isolation of DNA and RNA from mucosal samples and cDNA synthesis Using the AllPrep DNA/RNA Mini Kit (Qiagen), RNA and DNA were isolated from ~ 8 mg of mucosal tissue that had been preserved in Allprotect Tissue Reagent (Qiagen). .. The manufacturer’s instructions were followed except for extended homogenization and additional enzymatic lysis steps as reported in [ ].

    Article Title: Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors
    Article Snippet: Using the AllPrep DNA/RNA Mini Kit (Qiagen), RNA and DNA were isolated from ~ 8 mg of mucosal tissue that had been preserved in Allprotect Tissue Reagent (Qiagen). .. The manufacturer’s instructions were followed except for extended homogenization and additional enzymatic lysis steps as reported in [ ].

    Article Title: Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy
    Article Snippet: .. A further optimised tissue homogenisation and lysis protocol comprising mechanical bead beating, lysis buffer replacement and enzymatic treatment, in combination with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) resulted in efficient and simultaneous purification of microbial and human RNA and DNA from a single mucosal colonic tissue sample. .. The present work provides a unique possibility to study RNA and DNA from the same mucosal biopsy sample, making a direct comparison between metabolically active microbes and total microbial DNA.

    DNA Methylation Assay:

    Article Title: Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L
    Article Snippet: .. RNA and DNA were simultaneously extracted using the AllPrep DNA/RNA Mini kit according to the manufacturer's protocol (Qiagen); the RNA was used in qRT-PCR analyses as described above, while DNA methylation analyses were carried out on the DNA. .. Quantitative analysis of DNA methylation using real-time PCR, or qAMP, was conducted to analyze the DNA methylation status of a number of sequences as described [ ].

    Concentration Assay:

    Article Title: Association between TLR-9 polymorphisms and colon cancer susceptibility in Saudi Arabian female patients
    Article Snippet: Total RNA isolation Total RNA was extracted from 40 colon cancer tissues and 40 matched normal colon tissues using an AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s protocol. .. The isolated RNA concentration, purity, and quality were determined using an Agilent 2100 Bioanalyzer system and Agilent Small RNA analysis kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer’s instructions.

    DNA Purification:

    Article Title: Increased HIV-1 transcriptional activity and infectious burden in peripheral blood and gut-associated CD4+ T cells expressing CD30
    Article Snippet: .. Quantification of cell-associated HIV-1 RNA and DNA Purification of HIV-1 DNA and RNA from sorted cell populations was achieved using a Qiagen AllPrep DNA/RNA mini Kit, and following the manufacturer’s standard protocol, with an additional DNAse treatment (QIAgen). .. Given the small number of CD30+ cells that could be obtained from flow sorting, these cell fractions were spiked into uninfected carrier PBMC to maximize HIV-1 DNA and RNA recovery and normalize extraction efficiency between CD30+ and CD30- CD4+ T cell populations.

    Staining:

    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: 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. .. Whole embryos were also collected 6, 9 and 12 hours post-treatment, fixed in 4% paraformaldehyde (PFA), embedded in OCT (optimal cutting temperature compound, Tissue-Tek 4583, Sakura Finetek USA, Inc., Torrance, CA), frozen at −80°C, cryosectioned and processed as described by Oh et al. [ ], either for staining with hematoxylin and eosin, or immunostaining with phospho-histone-H3 or activated caspase-3 antibody, to assess cell proliferation or apoptosis, respectively.

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