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Masterpure complete dna extraction kit

Manufactured by Illumina
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The Masterpure Complete DNA Extraction Kit is a laboratory equipment product designed for the purification of high-quality genomic DNA from a variety of sample types, including cells, tissues, and microorganisms. The kit provides all the necessary reagents and protocols to efficiently extract and purify DNA for downstream applications.

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Lab products found in correlation

Facsvantage se w diva cell sorter, by BD (2 mentions) Hiseq 2500 platform, by Illumina (2 mentions) Lcm pen membrane slide, by Thermo Fisher Scientific (2 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (2 mentions) Rneasy mini kit, by Qiagen (1 mentions) Tapestation 2200, by Agilent Technologies (1 mentions) Ack lysing buffer, by Quality Biological (1 mentions)

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DNA extraction kit MasterPure kit

5 protocols using masterpure complete dna extraction kit

1

Particle Sorting for Metagenomic Analysis

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A piece (~1cm3) of fresh Ren-PNG-Bali-16–03 was cut and homogenized gently in calcium-magnesium-free (CMF) artificial seawater (2 mL) using a sterile tissue homogenizer. The resulting suspension was passed through a 70 μm filter and the filtrate was used for cell sorting on a FACSVantage SE w/DiVa cell sorter (BD Biosciences, San Jose, CA USA). Particles were observed on the forward scatter (FSC) and side scatter (SSC) parameters, representing increasing 488 nm laser light scatter due to particle size and granularity, respectively. Eight gates were created along the FSC axis and particles from each were collected into separate tubes, resulting in partitions with increasing particle size composition (Supplementary Fig. 5). Metagenomic DNA was extracted from each using the Masterpure complete DNA extraction kit following manufacturer’s protocol (Epicenter, Madison, WI, USA). The DNA obtained was used for both 16S rRNA gene amplicon sequencing (1.5 K reads on average) and shotgun metagenomic sequencing (an average of 7 M single-end reads of 75 bps per sample) on an Illumina HiSeq 2500 platform as described above (Supplementary Table 1). 16S rRNA gene sequencing data were processed using Qiime as described above, and metagenomic data were assembled using SPAdes and processed as described below.
Tianero-McIntosh M.D., Balaich J.N, & Donia M.S. (2019). Localized production of defense chemicals by intracellular symbionts of Haliclona sponges. Nature microbiology, 4(7), 1149-1159.
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2

Metagenomic Analysis of Sponge Bacteriocytes

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A small cube (~0.5 cm3) of RNALater preserved sample was washed in sterile water three times to reduce salt crystals. The tissue was then crushed gently on a 70 μm filter which was then washed with sterile water (500 μL). The filtrate was centrifuged at 500 × g for 5 min at 4 °C to pellet larger sponge cells and particles. The resulting pellet was then suspended in water (100 μL) and a 10% dilution (50 μL) was spread on an LCM PEN membrane slide (ThermoFisher Scientific, USA) and allowed to air dry. Chemobacteriocytes were identified as distinct round particles with diameter of 15–25 μm and isolated by laser microdissection on an MMI Cell Cut LCM system (mmi). 100 bacteriocytes were collected and 50 background membrane cuts were further collected as a negative control. DNA was extracted from both the cells and negative control using the Masterpure complete DNA extraction kit following manufacturer’s protocol (Epicenter, Madison, WI, USA) and used for Illumina library preparation and metagenomic sequencing as described above (Supplementary Table 1). BLASTn (e-value cutoff of 1 × 10−20) was used to assign metagenomic reads to the Ca. E. renieramycinifaciens chromosome, p-ren, and sponge mitochondrion.
Tianero-McIntosh M.D., Balaich J.N, & Donia M.S. (2019). Localized production of defense chemicals by intracellular symbionts of Haliclona sponges. Nature microbiology, 4(7), 1149-1159.
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3

Circadian Rhythm-Aware Blood Collection for FKBP5 Analysis

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Blood samples for RNA on visit 2 were collected between 11am-2pm to minimize the effect of the circadian rhythm on plasma cortisol levels and FKBP5 expression. Immediately after blood collection, red blood cells were lysed using 3.5 times the volume of ACK Lysing Buffer (Quality Biological, Gaithersburg, MD). Remaining white blood cells were pelleted by centrifugation at 300 x g for 5 minutes, resuspended in ice cold PBS, and separated into two equal aliquots. Genomic DNA was extracted from the other aliquot using the MasterPure Complete DNA Extraction kit (Epicentre, Madison, WI) according to the manufacturer’s protocol. DNA concentrations were determined by Qubit 2.0 Fluorometer (ThermoFisher, Waltham, MA). Messenger RNA was extracted from one aliquot of white blood cells using the RNeasy Mini Kit (Qiagen, Germantown, MD) according to the manufacturer’s protocol. Concentrations and RNA integrity numbers (RIN) were determined from each mRNA sample by TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN<8.0 were excluded.
Lee R.S., Mahon P.B., Zandi P.P., McCaul M.E., Yang X., Bali U, & Wand G.S. (2018). DNA methylation and sex-specific expression of FKBP5 as correlates of one-month bedtime cortisol levels in healthy individuals. Psychoneuroendocrinology, 97, 164-173.
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4

Particle Sorting for Metagenomic Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
A piece (~1cm3) of fresh Ren-PNG-Bali-16–03 was cut and homogenized gently in calcium-magnesium-free (CMF) artificial seawater (2 mL) using a sterile tissue homogenizer. The resulting suspension was passed through a 70 μm filter and the filtrate was used for cell sorting on a FACSVantage SE w/DiVa cell sorter (BD Biosciences, San Jose, CA USA). Particles were observed on the forward scatter (FSC) and side scatter (SSC) parameters, representing increasing 488 nm laser light scatter due to particle size and granularity, respectively. Eight gates were created along the FSC axis and particles from each were collected into separate tubes, resulting in partitions with increasing particle size composition (Supplementary Fig. 5). Metagenomic DNA was extracted from each using the Masterpure complete DNA extraction kit following manufacturer’s protocol (Epicenter, Madison, WI, USA). The DNA obtained was used for both 16S rRNA gene amplicon sequencing (1.5 K reads on average) and shotgun metagenomic sequencing (an average of 7 M single-end reads of 75 bps per sample) on an Illumina HiSeq 2500 platform as described above (Supplementary Table 1). 16S rRNA gene sequencing data were processed using Qiime as described above, and metagenomic data were assembled using SPAdes and processed as described below.
Tianero-McIntosh M.D., Balaich J.N, & Donia M.S. (2019). Localized production of defense chemicals by intracellular symbionts of Haliclona sponges. Nature microbiology, 4(7), 1149-1159.
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5

Metagenomic Analysis of Sponge Bacteriocytes

Check if the same lab product or an alternative is used in the 5 most similar protocols
A small cube (~0.5 cm3) of RNALater preserved sample was washed in sterile water three times to reduce salt crystals. The tissue was then crushed gently on a 70 μm filter which was then washed with sterile water (500 μL). The filtrate was centrifuged at 500 × g for 5 min at 4 °C to pellet larger sponge cells and particles. The resulting pellet was then suspended in water (100 μL) and a 10% dilution (50 μL) was spread on an LCM PEN membrane slide (ThermoFisher Scientific, USA) and allowed to air dry. Chemobacteriocytes were identified as distinct round particles with diameter of 15–25 μm and isolated by laser microdissection on an MMI Cell Cut LCM system (mmi). 100 bacteriocytes were collected and 50 background membrane cuts were further collected as a negative control. DNA was extracted from both the cells and negative control using the Masterpure complete DNA extraction kit following manufacturer’s protocol (Epicenter, Madison, WI, USA) and used for Illumina library preparation and metagenomic sequencing as described above (Supplementary Table 1). BLASTn (e-value cutoff of 1 × 10−20) was used to assign metagenomic reads to the Ca. E. renieramycinifaciens chromosome, p-ren, and sponge mitochondrion.
Tianero-McIntosh M.D., Balaich J.N, & Donia M.S. (2019). Localized production of defense chemicals by intracellular symbionts of Haliclona sponges. Nature microbiology, 4(7), 1149-1159.
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