DNA was collected from untreated and DAC-treated cells using the PureLink DNA kit (Invitrogen). Methylation analyses using the HM450 array (Illumina) was performed by the Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Ontario, Canada) including bisulfite conversion, hybridization, background subtraction, and normalization (Geo Series Accession #GSE78875; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78875 ). β-values for Illumina probes near RARRES1 were extracted from the data, and locations determined relative to the protein-coding regions.
Purelink dna kit
Manufactured by Thermo Fisher Scientific
Sourced in United States
The PureLink DNA kit is a product designed for the purification of DNA from various sample types. It utilizes a simple and efficient silica-based membrane technology to capture and purify DNA, making it suitable for downstream applications such as PCR, sequencing, and cloning.
Automatically generated - may contain errors
Lab products found in correlation
Hm450 array, by Illumina (1 mentions)
Hm450 beadchip array, by Illumina (1 mentions)
Epic array, by Illumina (1 mentions)
Hugene 2.0 st array, by Thermo Fisher Scientific (1 mentions)
Purelink rna kit, by Thermo Fisher Scientific (1 mentions)
Lightcycler 480, by Roche (1 mentions)
Qubit 3.0 fluorometer, by Thermo Fisher Scientific (1 mentions)
7 protocols using purelink dna kit
1
Methylation Analysis of RARRES1 in Cells
2
LINE-1 Repeat Amplification from Fibroblasts
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA extraction from the fibroblast cell lines was performed using the Pure Link DNA kit (Invitrogen, Waltham, MA, USA) according to the basic DNA extraction protocol. LINE-1-like repeat sequences called LINE-1 have been amplified by polymerase chain reaction (PCR); each probe was amplified from the species own DNA; the universal set of primers, developed for the PCR of LINE-1 repeats in mammals, have been used: L1R, 5′-ATTCTRTTC CAT TGG TCT A-3′ and L1F 5′-CCA TGC TCATSGAT TGG -3′ [40 (link),41 (link)].
Genomic DNA was amplified in 50 μL PCR-reactions: five units of Taq GOLD DNA Polymerase (Invitrogen), the template DNA, 500 nM of each primer, 200 μM each of dATP, dCTP, dTTP, and dGTP in 10 mM TRIS-HCl, pH 8.3, 1.5 mM MgCl2, 50 mM KCl. PCR reactions were performed using an Applied biosystems SimplyAmp (Thermo Fisher Scientific, Waltham, MA, USA) with the following cycling parameters: 30 cycles each of 94 °C, 30 s; 52.5 °C, 30 s; 72 °C, 30 s, following a 2 min denaturation at 94 °C. A bright band of about 400 pb was visualised on 1% agarose gel. The PCR products were directly labelled through nick translation using 11-dUTP-Fluorescein (green) (Invitrogen) for H. sapiens and dUTP-cy5 (red) (Amersham) for the Cebidae species.
Genomic DNA was amplified in 50 μL PCR-reactions: five units of Taq GOLD DNA Polymerase (Invitrogen), the template DNA, 500 nM of each primer, 200 μM each of dATP, dCTP, dTTP, and dGTP in 10 mM TRIS-HCl, pH 8.3, 1.5 mM MgCl2, 50 mM KCl. PCR reactions were performed using an Applied biosystems SimplyAmp (Thermo Fisher Scientific, Waltham, MA, USA) with the following cycling parameters: 30 cycles each of 94 °C, 30 s; 52.5 °C, 30 s; 72 °C, 30 s, following a 2 min denaturation at 94 °C. A bright band of about 400 pb was visualised on 1% agarose gel. The PCR products were directly labelled through nick translation using 11-dUTP-Fluorescein (green) (Invitrogen) for H. sapiens and dUTP-cy5 (red) (Amersham) for the Cebidae species.
3
DNA Methylation Analysis of TNBC Cells
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA was collected from untreated and DAC-treated MDA-MB-231 and MDA-MB-468 cells using the PureLink DNA kit (Invitrogen). Methylation analyses using the HM450 bead chip array (Illumina) was performed by The Centre for Applied Genomics including bisulfite conversion, hybridization, background subtraction, and normalization (Geo Accession GSE103425). β-values for Illumina probes near each gene of interest were extracted from the data, and location determined relative to the transcription start site (TSS).
4
Genomic DNA Extraction Protocol
5
PDX Epigenomic and Transcriptomic Profiling
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA was extracted from human cells of PDXs using the PureLink DNA kit (Thermo Fisher Scientific), according to manufacturer’s instructions. Sample preparation, bisulfite conversion, hybridization to the Illumina EPIC array (PDX C and D), and data collection were performed by The Centre for Applied Genomics (TCAG) at the Hospital for Sick Children (Toronto, ON, Canada). Data can be accessed through the GEO repository (GSE117926). HM450 data (PDX A and B) was obtained from GSE78875 [41 (link)]. HM450 and EPIC data was analyzed in the R environment using the minfi package with Swan normalization [64 (link),65 (link)]. Cross-reactive and SNP-associated probes were removed.
RNA was extracted from all cells of PDXs using Trizol reagent and the PureLink RNA kit (Invitrogen) with DNase treatment. Sample preparation, labelling, and hybridization to the Affymetrix HuGene 2.0ST array was performed by TCAG and data can be accessed through the GEO repository (PDX A and B, GSE117579; PDX C and D, GSE118002).
RNA was extracted from all cells of PDXs using Trizol reagent and the PureLink RNA kit (Invitrogen) with DNase treatment. Sample preparation, labelling, and hybridization to the Affymetrix HuGene 2.0ST array was performed by TCAG and data can be accessed through the GEO repository (PDX A and B, GSE117579; PDX C and D, GSE118002).
6
Mitochondrial DNA Quantification via qRT-PCR
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total DNA including mtDNA was extracted from cells using the PureLink DNA kit (ThermoFisher), and DNA purity and quantity were determined using a spectrophotometer. To determine the ratio between mitochondrial and nuclear DNA, qRT-PCR was performed on a Roche Lightcycler 480 using SYBR Green dye. Mitochondrial gene expression was corrected for nuclear gene expression values, and normalized to the value of the control group for each experiment as described before. Forward and reverse primer sequences are as follows: UUR forward, CAC CCA AGA ACA GGG TTT GT; UUR reverse, TGG CCA TGG GTA TGT TGT TA for mt DNA; B2-microglobulin forward, TGC TGT CTC CAT GTT TGA TGT ATC T; and B2-microglobulin reverse, TCT CTG CTC CCC ACC TCT AAG T.
7
Sediment Microbial Community Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
From 2017–2020, sediment samples were collected using a Van Veen grab from the surficial benthic layer (top 20 cm at the water column interface). The surficial layer at the sediment-water interface represents the more recent microbial community12 ,28 . During the summer season, we sampled sites 1 (2017, 2019) 2 (2017), 3(2017,2018,2019,2020), 4 (2018), 5 (2018), 6 (2019), and 7 (2019). One sediment grab from each site was collected and measured for grain size by particle sieve analysis. From each grab collected across the seven geographic sites, a total of 14 sediment samples were analyzed. Approximately 30 g of sediment were transferred from the grab to a sterile 50 mL Falcon™ tube. The collection tubes were immediately placed on ice in a container onboard until returned to the laboratory. DNA was then extracted from 0.30 g of sediment samples using a PureLink® DNA kit (Thermo Fisher Scientific™). The DNA extract was pooled based on sample replicates, and concentrations were quantified using a Qubit 3.0 fluorometer (Thermo Fisher Scientific). The sample DNA was stored at − 20 °C until sequencing.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!