Pcr cleanup kit

Manufactured by Illumina

The PCR cleanup kit is a laboratory tool designed to remove unwanted compounds, such as primers, nucleotides, and salts, from polymerase chain reaction (PCR) products. The kit provides a simple and efficient way to purify PCR amplicons, enabling further downstream applications.

Automatically generated - may contain errors

Lab products found in correlation

Hiseq 2500, by Illumina (3 mentions) Minelute kit, by Qiagen (3 mentions) Nextera dna sample prep kit, by Illumina (2 mentions) Nextera indexing primers, by Illumina (1 mentions) Tn5 transposes, by Illumina (1 mentions) Mrna purification kit, by Thermo Fisher Scientific (1 mentions) Phusion dna polymerase, by Qiagen (1 mentions) Pcr cleanup kit, by Qiagen (1 mentions) Superscript 2, by Thermo Fisher Scientific (1 mentions) Vahts universal pro dna library prep kit, by Vazyme (1 mentions)

6 protocols using pcr cleanup kit

Lentiviral Inserts Sequencing Protocol

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Lentiviral inserts were PCR amplified from genomic DNA using a nested PCR protocol with outer primers targeting the virus backbone^{16 (link)} and custom inner primers with binding sequences for Illumina Nextera adaptor read1 and read2 attached to the 5′-ends. After product purification using a PCR cleanup kit (Macherey and Nagel), a third PCR using Illumina Nextera indexing primers (N7xx and S5xx) produced the final sequencing libraries that were diluted, pooled, and sequenced on a HiSeq2500 (Illumina) with paired-end 125 bp read length, and v4 sequencing chemistry. The sequencing was done at the SciLife core facility at Uppsala University. The primers are listed in Supplementary Table 1.

Gul N., Karlsson J., Tängemo C., Linsefors S., Tuyizere S., Perkins R., Ala C., Zou Z., Larsson E., Bergö M.O, & Lindahl P. (2019). The MTH1 inhibitor TH588 is a microtubule-modulating agent that eliminates cancer cells by activating the mitotic surveillance pathway. Scientific Reports, 9, 14667.

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ATAC-seq Protocol for Chromatin Profiling

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ATAC-seq was performed as previously described^{30 (link)}. 20,000 unfixed nuclei were tagged using Tn5 transposase (Nextera DNA sample prep kit; Illumina) for 30 min at 37°C, and the resulting library fragments were purified using a Qiagen MinElute kit. Libraries were amplified by 10–12 PCR cycles, purified using a Qiagen PCR cleanup kit, and finally sequenced on an Illumina HiSeq 2500 with 75 bp paired-end reads to a minimum depth of 30 million reads per sample. At least two technical replicates were processed per biological sample.

Caielli S., Troggian Veiga D., Balasubramanian P., Athale S., Domic B., Murat E., Banchereau R., Xu Z., Chandra M., Chung C.H., Walters L., Baisch J., Wright T., Punaro M., Nassi L., Stewart K., Fuller J., Ucar D., Ueno H., Zhou J., Banchereau J, & Pascual V. (2018). A CD4+ T cell population expanded in Lupus blood provides B cell help through IL10 and succinate. Nature medicine, 25(1), 75-81.

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ATAC-seq Protocol for Chromatin Profiling

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ATAC-seq Profiling of Human AML Cells

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Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed on MOLM-13 human AML cells as described(Buenrostro et al., 2013 (link)).Briefly, MOLM-13 cells were subjected to cell lysis in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Following 30 seconds of lysis, cells were centrifuged at 500 ×g for 10 minutes, 4°C. Lysed cell pellets were then subjected to the transposition reaction at 37°C for 30 minutes using Tn5 Transposes (Illumina Cat #FC-121–1030), followed by purification of transposed DNA using the Qiagen MinElute Kit. Transposed DNA fragment were amplified using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs Cat #M0541) and Customized Nextera PCR primers under the following conditions: (Step 1) 72°C for 5 minutes, (Step 2) 98°C for 30 seconds, (Step 3) 98°C for 30 seconds, (Step 4) 63°C for 30 seconds, (Step 5) 72°C for 1 minute, and (Step 6) 4°C hold, with amplified library purified using Qiagen PCR Cleanup Kit prior to Illumina Sequencing. For PCR steps 3–5, transposed library was amplified with number of cycles based on quantitative PCR in order to stop amplification prior to saturation, thus reducing GC and size bias in PCR.

Wang E., Zhou H., Nadorp B., Cayanan G., Chen X., Yeaton A.H., Nomikou S., Witkowski M.T., Narang S., Kloetgen A., Thandapani P., Ravn-Boess N., Tsirigos A, & Aifantis I. (2021). Surface Antigen-Guided CRISPR Screens Identify Regulators of Myeloid Leukemia Differentiation. Cell stem cell, 28(4), 718-731.e6.

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PAS-seq Protocol for Transcriptome Profiling

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PAS-seq was performed as described previously (Zhang et al., 2015) . Briefly, poly(A) + RNAs from 12-day-seedlings were purified using an mRNA purification kit (Invitrogen) and fragmented by heating at 95 C for 25 min. Reverse transcription (Superscript II, Invitrogen) was carried out using our modified HITS-3 0 adaptor at 42 C for 30 min, then the HITS-5 0 adaptor (an SMART oligo) was added and the sample incubated for an additional 30 min. The cDNAs were purified using a Qiagen PCR Cleanup kit and the second-strand cDNAs were synthesized by three cycles of PCR using Phusion DNA polymerase (NEB) and the PE1.0 and PE2.0 primers. PCR products were separated in a 2.5% agarose gel and 200to 300-base pair (bp) bands were excised and purified. Gel-extracted DNAs were amplified for an additional 13 cycles. PCR products were purified using a Qiagen PCR Cleanup kit and sequenced by Illumina. Oligos for PAS-seq are listed in the Supplemental information, Supplemental Table 6.

Hou Y., Sun J., Wu B., Gao Y., Nie H., Nie Z., Quan S., Wang Y., Cao X, & Li S. (2021). CPSF30-L-mediated recognition of mRNA m⁶A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis. Molecular plant, 14(4).

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Mutation Identification via PCR and NGS

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After virus infection and puromycin selection, we extracted genomic DNA from each cell line. PCR primers were designed via NCBI Primer BLAST, and then PCR was conducted with Q5 Hot Start High-Fidelity 2× Mix (NEB, M0494) (Supplementary Table S11). The PCR product was purified via a QIAquick PCR Clean-up Kit and was constructed into an Illumina sequencing library via a VAHTS Universal Pro DNA Library Prep Kit (Vazyme, ND608) for NGS. We extracted reads with primer sequences and integrated them by the types of mutation. Alignment results were built by BLAST software.

Pan C., Li R., Shui L., Xiao Z., Wang Y., Zhu J., Wu C., Zhang L., Jia J, & Zheng M. (2023). A new method to synthesize multiple gRNA libraries and functional mapping of mammalian H3K4me3 regions. Nucleic Acids Research, 51(9), e50.

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