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Qiaquick minelute pcr purification kit

Manufactured by Qiagen
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The QIAquick MinElute PCR Purification kit is a laboratory instrument designed for the purification of DNA fragments from PCR reactions. It utilizes a silica-membrane technology to efficiently capture and purify DNA, removing unwanted components such as primers, nucleotides, and salts. The purified DNA can then be used for downstream applications.

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Lab products found in correlation

Kapa hifi hotstart pcr kit, by Roche (6 mentions) Nextseq 500 system, by Illumina (5 mentions) Bioruptor ucd 300, by Diagenode (3 mentions) Formaldehyde, by Merck Group (3 mentions) Sybr green chemistry, by Roche (2 mentions) Anti nrsf, by Santa Cruz Biotechnology (2 mentions) Anti histone3 lysine9 dimethyl antibody, by Abcam (2 mentions) Protein a g bead, by Santa Cruz Biotechnology (2 mentions) Protein a g, by Santa Cruz Biotechnology (2 mentions) H3k27me3, by Diagenode (2 mentions) H3k4me3, by Diagenode (2 mentions) H3k4me1, by Diagenode (2 mentions) H3k9me3, by Diagenode (2 mentions) H3k27ac, by Diagenode (2 mentions) H3k36me3 antibodies, by Diagenode (2 mentions) Hiseq 2000, by Illumina (2 mentions) Nextseq 500 machine, by Illumina (1 mentions) Hifi hotstart ready mix, by Illumina (1 mentions) Nextflex adapters, by Illumina (1 mentions) Ampure xp reagent, by Beckman Coulter (1 mentions)

15 protocols using qiaquick minelute pcr purification kit

1

Chromatin Immunoprecipitation of Epigenetic Marks

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Hypothalamic explants treated with either vehicle or CNQX/MK-801 were cross-linked, homogenized, and the nuclei were harvested by centrifugation. Nuclei were sonicated and precleared with Protein-A/G (Santa Cruz, Dallas, TX). They were then immunoprecipitated with 10 μg of either control non-immune serum (IgG) (Cell Signaling; 2729S, Danvers, MA), anti-NRSF (Santa Cruz; sc-25398x, Dallas, TX), anti-Histone3 Lysine9 dimethyl antibody (Abcam; Ab1220, Cambridge, MA), anti-Histone3 Lysine27 tri-methyl antibody (Abcam; Ab6002, Cambridge, MA), or anti-Histone3 Lysine9 tri-methyl antibody (Abcam; Ab8898, Cambridge, MA) overnight at 4°C. Precleared protein A/G beads (Santa Cruz; sc-2003, Dallas, TX) were added to the lysate for 2 h. The beads were washed to remove non-specifically bound protein, then subjected to SDS elution. Eluates were reverse cross-linked, and the bound DNA was purified using the QiaQuick MinElute PCR purification kit (Qiagen, Valencia, CA). Quantitative PCR (qPCR) amplification was done using SYBR Green chemistry (Roche, Indianapolis, IN). Primer sequences used for ChIP analyses are provided in Supplementary Table 2.
Singh-Taylor A., Molet J., Jiang S., Korosi A., Bolton J.L., Noam Y., Simeone K., Cope J., Chen Y., Mortazavi A, & Baram T.Z. (2017). NRSF-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilience. Molecular Psychiatry, 23(3), 648-657.
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2

Multiplex PCR Optimization for Immunoglobulin

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For both protocols, PCR products were purified according to the manufacturer's protocol (QIAQuick MinElute PCR Purification Kit; Qiagen®). Then, six PCR reactions were performed with each of six sense family-specific primers (for the IGHV-Leader protocol) or FR1 primers (for the BIOMED2-FR1 protocol) in combination with an antisense JH primer. PCR conditions were identical to those of multiplex PCR. For each PCR, control was performed on a 2.5% agarose gel.
René C., Prat N., Thuizat A., Broctawik M., Avinens O, & Eliaou J.F. (2014). Comprehensive characterization of immunoglobulin gene rearrangements in patients with chronic lymphocytic leukaemia. Journal of Cellular and Molecular Medicine, 18(6), 979-990.
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3

ATAC-seq Library Preparation Protocol

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5 × 104 cells were washed twice in PBS and resuspended in 500 μl lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl, 0.1% NP-40, pH 7.4). Nuclei were harvested by centrifuge at 500 × g for 10 min at 4°C. Nuclei were suspended in 50 μl of tagmentation mix (10 mM TAPS (Sigma), 5 mM MgCl, pH 8.0 and 2.5 μl Tn5) and incubated at 37°C for 30 min. Tagmentation reaction was terminated by incubating nuclei at room temperature for 2 min followed by incubation at 55°C for 7 min after adding 10 μl of 0.2% SDS. Tn5 tranposase-tagged DNA was purified using QIAquick MinElute PCR Purification kit (Qiagen), amplified using KAPA HiFi Hotstart PCR Kit (KAPA), and sequenced on an Illumina Nextseq500 system using the 75 bp high output sequencing kit. ATAC-seq raw reads were trimmed to remove adaptor sequence and aligned to hg19 or mm9 genome assembly using Bowtie2 (Langmead et al., 2009 (link)) with k=1 and m=1. Only tags that uniquely mapped to the genome were used for further analysis.
Liu X., Zhang Y., Chen Y., Li M., Zhou F., Li K., Cao H., Ni M., Liu Y., Gu Z., Dickerson K.E., Xie S., Hon G.C., Xuan Z., Zhang M.Q., Shao Z, & Xu J. (2017). In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell, 170(5), 1028-1043.e19.
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4

ATAC-seq protocol for profiling chromatin accessibility

Cited 2 times
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ATAC-seq was performed as previously described with modifications [63 (link)]. Briefly, 5 × 104 G1ER cells were washed twice in PBS and resuspended in 500 μl lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, pH 7.4). Nuclei were harvested by centrifugation at 500×g for 10 min at 4 °C. Nuclei were suspended in 50 μl of tagmentation mix (10 mM TAPS, 5 mM MgCl2, pH 8.0, and 2.5 μl Τn5) and incubated at 37 °C for 30 min. Tagmentation reaction was terminated by incubating nuclei at room temperature for 2 min followed by incubation at 55 °C for 7 min after adding 10 μl of 0.2% SDS. Tn5 transposase-tagged DNA was purified using QIAquick MinElute PCR Purification kit (Qiagen) and amplified using KAPA HiFi Hotstart PCR Kit (KAPA). ATAC-seq libraries were sequenced on an Illumina NextSeq500 system using the 75-bp high output kit. Raw reads were trimmed to remove adaptor sequence and aligned to mouse genome assembly (mm10) using Bowtie2 [59 (link)] with default parameters. Only tags that uniquely mapped to the genome were used for analysis. ATAC-seq peaks were identified using MACS with the “--nomodel” parameter [60 (link)]. To compare signals at promoters, enhancers, and other genomic regions between samples, we calculated FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for each region.
Liu X., Chen Y., Zhang Y., Liu Y., Liu N., Botten G.A., Cao H., Orkin S.H., Zhang M.Q, & Xu J. (2020). Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biology, 21, 59.
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5

Histone ChIP-seq Protocol for Epigenomics

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Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated using a Diagenode Bioruptor UCD-300 for 3x 10 min (30 s on; 30 s off). 67 μl of chromatin (1 million cells) was incubated with 229 μl dilution buffer, 3 μl protease inhibitor cocktail and 0.5-1 μg of H3K27ac, H3K4me3, H3K4me1, H3K27me3, H3K9me3 or H3K36me3 antibodies (Diagenode) and incubated overnight at 4°C with rotation. Protein A/G magnetic beads were washed in dilution buffer with 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and rotated for 60 min at 4°C. Beads were washed with 400μl buffer for 5 min at 4°C with five rounds of washes. After washing chromatin was eluted using elution buffer for 20 min. Supernatant was collected, 8 μl 5M NaCl, 3μl proteinase K were added and samples were incubated for 4 hr at 65°C.Finally samples were purified using QIAGEN; Qiaquick MinElute PCR purification Kit and eluted in 20 μl EB. Detailed protocols can be found on the Blueprint website (http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/Histone_ChIP_May2013.pdf).
Novakovic B., Habibi E., Wang S.Y., Arts R.J., Davar R., Megchelenbrink W., Kim B., Kuznetsova T., Kox M., Zwaag J., Matarese F., van Heeringen S.J., Janssen-Megens E.M., Sharifi N., Wang C., Keramati F., Schoonenberg V., Flicek P., Clarke L., Pickkers P., Heath S., Gut I., Netea M.G., Martens J.H., Logie C, & Stunnenberg H.G. (2016). β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance. Cell, 167(5), 1354-1368.e14.
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6

Chromatin Immunoprecipitation of Epigenetic Marks

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Hypothalamic explants treated with either vehicle or CNQX/MK-801 were cross-linked, homogenized, and the nuclei were harvested by centrifugation. Nuclei were sonicated and precleared with Protein-A/G (Santa Cruz). They were then immunoprecipitated with 10 μg of either control non-immune serum (IgG) (Cell Signaling; 2729S, Danvers, MA, USA), anti-NRSF (Santa Cruz; sc-25398x), anti-Histone3 Lysine 9 dimethyl antibody (Abcam; Ab1220, Cambridge, MA, USA), anti-Histone3 Lysine 27 tri-methyl antibody (Abcam; Ab6002), or anti-Histone3 Lysine 9 tri-methyl antibody (Abcam; Ab8898) overnight at 4 °C. Precleared protein A/G beads (Santa Cruz; sc-2003) were added to the lysate for 2 h. The beads were washed to remove non-specifically bound protein, then subjected to SDS elution. Eluates were reverse cross-linked, and the bound DNA was purified using the QiaQuick MinElute PCR purification kit (Qiagen, Valencia, CA, USA). Quantitative PCR (qPCR) amplification was done using SYBR Green chemistry (Roche, Indianapolis, IN, USA). Primer sequences used for ChIP analyses are provided in Supplementary Table 2.
Singh-Taylor A., Molet J., Jiang S., Korosi A., Bolton J.L., Noam Y., Simeone K., Cope J., Chen Y., Mortazavi A, & Baram T.Z. (2017). NRSF-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilience. Molecular Psychiatry, 23(3), 648-657.
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7

Histone ChIP-seq Protocol for Epigenomics

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Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated using a Diagenode Bioruptor UCD-300 for 3x 10 min (30 s on; 30 s off). 67 μl of chromatin (1 million cells) was incubated with 229 μl dilution buffer, 3 μl protease inhibitor cocktail and 0.5-1 μg of H3K27ac, H3K4me3, H3K4me1, H3K27me3, H3K9me3 or H3K36me3 antibodies (Diagenode) and incubated overnight at 4°C with rotation. Protein A/G magnetic beads were washed in dilution buffer with 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and rotated for 60 min at 4°C. Beads were washed with 400μl buffer for 5 min at 4°C with five rounds of washes. After washing chromatin was eluted using elution buffer for 20 min. Supernatant was collected, 8 μl 5M NaCl, 3μl proteinase K were added and samples were incubated for 4 hr at 65°C.Finally samples were purified using QIAGEN; Qiaquick MinElute PCR purification Kit and eluted in 20 μl EB. Detailed protocols can be found on the Blueprint website (http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/Histone_ChIP_May2013.pdf).
Novakovic B., Habibi E., Wang S.Y., Arts R.J., Davar R., Megchelenbrink W., Kim B., Kuznetsova T., Kox M., Zwaag J., Matarese F., van Heeringen S.J., Janssen-Megens E.M., Sharifi N., Wang C., Keramati F., Schoonenberg V., Flicek P., Clarke L., Pickkers P., Heath S., Gut I., Netea M.G., Martens J.H., Logie C, & Stunnenberg H.G. (2016). β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance. Cell, 167(5), 1354-1368.e14.
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8

Assay for Transposase-Accessible Chromatin in Hematopoietic Stem Cells

Cited 3 times
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ATAC-seq was performed as previously described with modifications (63 (link)). Briefly, 2 × 104 BM LSK cells were washed twice in PBS and resuspended in 500 μl lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, pH 7.4). Nuclei were harvested by centrifuge at 500 x g for 10 min at 4°C. Nuclei were suspended in 50 μl of tagmentation mix (10 mM TAPS (Sigma), 5 mM MgCl2, pH 8.0 and 2.5 μl Τn5) and incubated at 37°C for 30 min. Tagmentation reaction was terminated by incubating nuclei at room temperature for 2 min followed by incubation at 55°C for 7 min after adding 10 μl of 0.2% SDS. Tn5 transposase-tagged DNA was purified using QIAquick MinElute PCR Purification kit (Qiagen), amplified using KAPA HiFi Hotstart PCR Kit (KAPA), and sequenced on an Illumina Nextseq500 system using the 75 bp high output sequencing kit. ATAC-seq raw reads were trimmed to remove adaptor sequence and aligned to mouse genome assembly (GENCODE Version M9) using Bowtie2 (60 (link)) with default parameters. Only tags that uniquely mapped to the genome were used for further analysis. ATAC-seq peaks were identified using MACS2 (61 (link)). MAnorm (62 (link)) was used to compare ATAC-seq signal intensities between samples, and identify enriched or depleted peaks (|log2 fold change| ≥ 2) between G12D/E2-KO and G12D LSK cells.
Gu Z., Liu Y., Cai F., Patrick M., Zmajkovic J., Cao H., Zhang Y., Tasdogan A., Chen M., Qi L., Liu X., Li K., Lyu J., Dickerson K.E., Chen W., Ni M., Merritt M.E., Morrison S.J., Skoda R.C., DeBerardinis R.J, & Xu J. (2019). Loss of EZH2 Reprograms BCAA Metabolism to Drive Leukemic Transformation. Cancer discovery, 9(9), 1228-1247.
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9

ATAC-seq Protocol for Chromatin Accessibility

Cited 2 times
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ATAC-seq was performed as previously described with modifications (Liu et al., 2017 (link)). Specifically, 5 × 104 cells were washed twice in PBS and resuspended in 500 μL cell lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, pH 7.4). Nuclei were harvested by centrifuge at 500 x g for 10 min at 4°C, resuspended in 50 μL of tagmentation mix (10 mM TAPS (Sigma), 5 mM MgCl2, pH 8.0 and 2.5 μl Tn5), and incubated at 37°C for 30 min. Tagmentation was terminated by incubating nuclei at room temperature for 2 min followed by adding 10 mL of 0.2% SDS and incubating at 55°C for 7 min. Tn5 transposase-tagged DNA was purified using QIA-quick MinElute PCR Purification kit (QIAGEN), amplified using KAPA HiFi Hotstart PCR Kit (KAPA).
ATAC-seq reads were sequenced to 75 base pairs in the single-end mode on the NextSeq500 system and aligned to the mouse genome (mm9) using Bowtie version 1.0.0 (Langmead et al., 2009 (link)) with parameters,–best–strata -k 1 -m 1. PCR duplicates were removed by Picard (https://github.com/broadinstitute/picard) using the default parameter setting. Significantly enriched ATAC-seq peaks were detected by Model-based Analysis of ChIP-seq (MACS) (Zhang et al., 2008 (link)). Genomic track figures of the ATAC-seq peaks (Figures 1B, 3C, 5B, 6A, 7, and S2A) were modified from the visualizations on the UCSC Genome Browser (http://genome.ucsc.edu/).
Liao R., Zheng Y., Liu X., Zhang Y., Seim G., Tanimura N., Wilson G.M., Hematti P., Coon J.J., Fan J., Xu J., Keles S, & Bresnick E.H. (2020). Discovering How Heme Controls Genome Function Through Heme-omics. Cell reports, 31(13), 107832.
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10

ChIP-seq of H3K27ac and H3K4me3

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DNA-histone crosslinking was performed using 1% formaldehyde followed by 1.25 mol/L glycine. Chromatin was sonicated using a Diagenode Bioruptor UCD-300 and immunoprecipitated using H3K27ac or H3K4me3 antibodies (Diagenode) and protein A/G magnetic beads. DNA was purified using QIAGEN Qiaquick MinElute PCR purification Kit. Illumina library preparation was done as previously described [31 ]. Sequencing was performed using Illumina HiSeq 2000.
Badii M., Gaal O.I., Cleophas M.C., Klück V., Davar R., Habibi E., Keating S.T., Novakovic B., Helsen M.M., Dalbeth N., Stamp L.K., Macartney-Coxson D., Phipps-Green A.J., Stunnenberg H.G., Dinarello C.A., Merriman T.R., Netea M.G., Crişan T.O, & Joosten L.A. (2021). Urate-induced epigenetic modifications in myeloid cells. Arthritis Research & Therapy, 23, 202.
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