Allprep micro kit

Manufactured by Qiagen

Sourced in United States, Germany

The AllPrep Micro Kit is a laboratory equipment product designed for the simultaneous purification of genomic DNA, total RNA, and miRNA from small samples. It is suitable for use with a variety of sample types, including cells, tissues, and body fluids.

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Lab products found in correlation

Rnaprotect, by Qiagen (2 mentions) 2100 bioanalyzer, by Agilent Technologies (2 mentions) High capacity cdna reverse transcription kit, by Thermo Fisher Scientific (2 mentions) Hiseq 2500, by Illumina (1 mentions) Rneasy kit, by Qiagen (1 mentions) Nebnext rna library prep kit, by New England Biolabs (1 mentions) Ovation sp ultralow dr multiplex system, by Tecan (1 mentions) Illuminia truseq stranded total rna kit, by Illumina (1 mentions) Dneasy blood tissue kit, by Qiagen (1 mentions) Bioanalyzer, by Agilent Technologies (1 mentions) Mirneasy mini kit, by Qiagen (1 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (1 mentions) Ez dna methylation kit, by Zymo Research (1 mentions) Topo ta cloning kit for sequencing, by Thermo Fisher Scientific (1 mentions) Rlt plus lysis buffer, by Qiagen (1 mentions) Ampure xp bead, by Beckman Coulter (1 mentions) Infinite 200 pro plate reader, by Tecan (1 mentions) Picogreen dsdna kit, by Thermo Fisher Scientific (1 mentions) Cytoscan hd array kit, by Thermo Fisher Scientific (1 mentions) Nanodrop 2000, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

AllPrep kit (307 citations) AllPrep DNA/RNA Micro Kit (287 citations) Allprep DNA/RNA Plus Micro Kit (3 citations) AllPrep DNA/RNA/Protein Micro Kit (2 citations) AllPrep DNA/RNA mini or micro Kit (2 citations) AllPrep DNA/RNA Micro kit protocol (2 citations) AllPrep DNA/RNA extraction micro kit (2 citations)

29 protocols using allprep micro kit

RNA-seq workflow for LCMV-infected mice

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For LCMV experiments RNA was isolated from sorted cells of LCMV-infected mice with the Qiagen AllPrep Micro Kit. Libraries were prepared and sequenced by the HudsonAlpha Genomic Services Lab (paired-end, 150 bp reads). For all other experiments total RNA was prepared using the RNeasy kit (Qiagen). 500 ng of total RNA was subsequently used to prepare RNA-seq libraries by a combination of NEBNext RNA library prep kit (New England BioLabs) and Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol. The libraries were sequenced for 50 cycles (single read) using the HiSeq 2500 (Illumina).

Petermann F., Pękowska A., Johnson C.A., Jankovic D., Shih H.Y., Jiang K., Hudson W.H., Brooks S.R., Sun H.W., Villarino A.V., Yao C., Singleton K., Akondy R.S., Kanno Y., Sher A., Casellas R., Ahmed R, & O’Shea J.J. (2019). The magnitude of IFN-γ responses is fine-tuned by DNA architecture and the non-coding transcript of Ifng-as1. Molecular cell, 75(6), 1229-1242.e5.

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Transcriptomic Analysis of Aged HSCs

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RNA from transfected CD34+ cells (n=3 biological replicates and 1–3 technical replicates for a total of n=4 sgCTRL and n=4 sgKLF6) was extracted using the Qiagen Allprep Micro kit according to manufacturer’s instructions (Qiagen, #80204). Stranded libraries were prepared by the University of Miami Sequencing Core using the Illuminia TruSeq Stranded Total RNA kit (Illumina, #20020596). Libraries were sequenced on the HiSeq-3000 with 75 bp paired-end sequencing. Data was aligned and processed as described above. For GSEA, the Wald statistic ranked list was used with the top (ranked by log₂FoldChange) 500 genes up- and down-regulated with HSCe aging as gene sets as well as the c2.all.v6.2.symbols gene set using the weighted enrichment score.

Adelman E.R., Huang H.T., Roisman A., Olsson A., Colaprico A., Qin T., Lindsley R.C., Bejar R., Salomonis N., Grimes H.L, & Figueroa M.E. (2019). Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia. Cancer discovery, 9(8), 1080-1101.

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DNA Extraction from Tumor and Germline

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Tumour DNA was extracted using the Allprep Micro Kit (Qiagen, CA) and germline DNA extracted with the DNeasy Blood & Tissue Kit (Qiagen, MD) following the manufacturer’s instructions. Further details are contained in the supplementary data, available at Annals of Oncology online.

Linch M., Goh G., Hiley C., Shanmugabavan Y., McGranahan N., Rowan A., Wong Y.N., King H., Furness A., Freeman A., Linares J., Akarca A., Herrero J., Rosenthal R., Harder N., Schmidt G., Wilson G.A., Birkbak N.J., Mitter R., Dentro S., Cathcart P., Arya M., Johnston E., Scott R., Hung M., Emberton M., Attard G., Szallasi Z., Punwani S., Quezada S.A., Marafioti T., Gerlinger M., Ahmed H.U, & Swanton C. (2017). Intratumoural evolutionary landscape of high-risk prostate cancer: the PROGENY study of genomic and immune parameters. Annals of Oncology, 28(10), 2472-2480.

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Profiling B cell subsets

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Naïve (CD19⁺PNA⁻FAS⁻CD11b⁻CD11c⁻), CD19⁺PNA⁺FAS⁺ GC, and CD19⁺CD11b⁺CD11c⁺ ABC B cells were sorted and total DNA was isolated using an AllPrep Micro kit (Qiagen). Replication history of sorted B cell subsets was subsequently determined by KREC analysis, as previously described (21 (link)).

Du S.W., Arkatkar T., Al Qureshah F., Jacobs H.M., Thouvenel C.D., Chiang K., Largent A.D., Li Q.Z., Hou B., Rawlings D.J, & Jackson S.W. (2019). Functional characterization of CD11c+ age-associated B cells as memory B cells. Journal of immunology (Baltimore, Md. : 1950), 203(11), 2817-2826.

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Optimized Sample Extraction for Tissue Biopsies

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Freshly collected biopsy samples were placed into sample tubes containing an RNA preservative (RNAprotect; Qiagen, Germantown, MD, USA) ahead of shipping to the laboratory at refrigerated temperatures (2–8 °C), where they were frozen prior to processing. Sample extraction methods were developed and optimized for each biopsy and tissue type, as described previously [12 (link),13 (link),16 (link),24 (link),25 (link)]. Briefly, RNA from thyroid nodule FNAs, lung nodule TBNAs, lung nodule TBBs, lung TBBs, and lung tissue were extracted with the AllPrep Micro Kit (Qiagen, Germantown, MD, USA). RNA was extracted from bronchial brushes of upper airway and nasal swabs using Qiazol and the miRNeasy Mini kit (Qiagen, Germantown, MD, USA). RNA was quantitated using the Promega Quantifluor kit (Promega, Madison, WI, USA) and a Tecan fluorometer (Tecan, San Jose, CA, USA). RNA quality was assessed by Bioanalyzer (Agilent, Santa Clara, CA, USA).

Walsh P.S., Hao Y., Ding J., Qu J., Wilde J., Jiang R., Kloos R.T., Huang J, & Kennedy G.C. (2022). Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies. Journal of Personalized Medicine, 13(1), 24.

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LCMV-Infected Mouse T Cell Isolation

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CD101⁻Tim3⁻, CD101⁻Tim3⁺, and CD101⁺Tim3⁺ PD-1⁺CD8⁺ T cells were isolated by FACS from three pools of ten mice each infected with LCMV clone 13 15 or >45 days prior to the sort (Figure S1). In each case, naive CD8⁺ T cells from three age-matched uninfected mice were also isolated by FACS. RNA was isolated using the Qiagen AllPrep Micro kit according to the manufacturer’s protocols. RNA sequencing with poly(A) selection was performed at the Yerkes Nonhuman Primate Genomics Core.

Hudson W.H., Gensheimer J., Hashimoto M., Wieland A., Valanparambil R.M., Li P., Lin J.X., Konieczny B.T., Im S.J., Freeman G.J., Leonard W.J., Kissick H.T, & Ahmed R. (2019). Proliferating transitory T cells with an effector-like transcriptional signature emerge from PD-1+ stem-like CD8+ T cells during chronic infection. Immunity, 51(6), 1043-1058.e4.

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Gastric Biopsy Collection and DNA Extraction

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Gastric mucosal biopsies from the antrum, proximal body and fundus were acquired for each enrolled patient and those with gastric carcinoma had additional biopsies taken at the tumor site as well as adjacent normal tissue. Biopsies were obtained using the Bard Precisor EXL coated disposable biopsy forceps (Bard International, Murray Hill, NJ, USA) and were immediately placed into individual sterile cryovials on dry ice and flash frozen while still in the endoscopic suite. The samples were then transferred to liquid nitrogen for prolonged storage. Genomic DNA was extracted from each gastric biopsy using an AllPrep micro kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Samples were homogenized using a rotor stator homogenizer for less than 30 seconds. DNA concentration was measured for each sample using a Qubit® 2.0 Fluorometer (Life Technologies, Grand Island, NY, USA) and DNA quality was checked on a 1 % agarose gel stained with ethidium bromide. Samples were run alongside a 1-kb DNA Extension Ladder (Life Technologies, Grand Island, NY, USA).

Zhang C., Cleveland K., Schnoll-Sussman F., McClure B., Bigg M., Thakkar P., Schultz N., Shah M.A, & Betel D. (2015). Identification of low abundance microbiome in clinical samples using whole genome sequencing. Genome Biology, 16, 265.

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Bisulfite sequencing of Spry2 in mouse models

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DNA was extracted from whole splenic cells derived from WT, Tet2^−/−, Nras^G12D, Tet2^−/−Nras^G12D and Tet2^−/−Flt3^ITD mice at 6 months from PIPC injection or whole splenic cells from Tet2^−/−Nras^G12D transplant leukemia mice treated with vehicle or 5-Aza 5 mg/kg IP using All Prep micro kit (Qiagen). DNA was subjected to bisulfite conversion with the EZ DNA Methylation Kit (Zymo Research) and PCR amplified. The primers used for the amplification of bisulfite converted DNA are as follows: mouse Spry2 (Forward primer 5’-GTTGGCGAGTTTTTTTTTTTTTTGG-3’, Reverse primer 5’-CGCCTACCTCCACTTAAAAACAAC-3’). PCR amplified products were subcloned into pCR4-TOPO vector with the TOPO TA Cloning Kit for Sequencing (Invitrogen) and sequenced by Sanger method.

Kunimoto H., Meydan C., Nazir A., Whitfield J., Shank K., Rapaport F., Maher R., Pronier E., Meyer S.C., Garrett-Bakelman F.E., Tallman M., Melnick A., Levine R.L, & Shih A.H. (2017). Cooperative Epigenetic Remodeling by TET2 Loss and NRAS Mutation Drives Myeloid Transformation and MEK Inhibitor Sensitivity. Cancer cell, 33(1), 44-59.e8.

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Single-cell RNA-seq Library Preparation

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For RNA-seq analysis, cells were sorted directly into RLT Plus lysis buffer (QIAGEN). Isolation of RNA was carried out according to the manufacturer’s instruction using the AllPrep Micro Kit (QIAGEN). Subsequently, isolated RNA was used for generation of sequencing libraries with the NuGEN Ovation SoLo Kit (Tecan). Size selection was carried out using AMPure XP Beads (Beckman Coulter, 0.8× beads). Qualitative assessment of the resulting libraries was performed using the Bioanalyzer High Sensitivity Assay (Agilent).

Deng L., Pollmeier L., Bednarz R., Cao C., Laurette P., Wirth L., Mamazhakypov A., Bode C., Hein L., Gilsbach R, & Lother A. (2024). Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression. Science Advances, 10(10), eadj5101.

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Thyroid Tissue DNA Profiling

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Thyroid tissue DNA was extracted with the AllPrep Micro kit (Qiagen, Hilden, Germany) and quantitated with the Pico Green dsDNA kit (Thermo Fisher) on a Tecan Infinite Pro 200 plate reader (Tecan, Männedorf, Switzerland). DNA (125 ng) was used as input into the CytoScan HD array kit (Affymetrix, Santa Clara, CA) and the samples were processed according to the manufacturer’s protocol. Cel files were input into the Affymetrix Chromosome Analysis Software (ChAS) and Copy Number and SNP outputs were analyzed for LOH and other CNVs.

Hao Y., Duh Q.Y., Kloos R.T., Babiarz J., Harrell R.M., Traweek S.T., Kim S.Y., Fedorowicz G., Walsh P.S., Sadow P.M., Huang J, & Kennedy G.C. (2019). Identification of Hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms. BMC Systems Biology, 13(Suppl 2), 27.

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