Tissue from 28 patients with confirmed HCC undergoing resection at the Department of Surgery, University of Mainz, Germany were collected following patient informed consent and local ethics committee approval. Validation cohort of 20 patients was obtained from the Institute of Pathology, University of Basel, Switzerland. Clinicopatholigical details are provided in Supplementary Table S1 . Tissue was macroscopically dissected into tumor tissue (T), tumor margin/ border (B) (approximately 2-4mm from each region) and peri-tumoral tissue (SL) (Supplementary Figure S1 ). Total RNA was extracted using the Qiagen RNEasy mini Kit (Qiagen GMBH, Hilden, Germany) following the manufacturer's instructions. RNA quantity and purity were estimated using a Nanodrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and integrity was assessed by Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). DNA was extracted using Qiagen Qiamp DNA Kit (Qiagen GMBH, Hilden, Germany) following the manufacturer's instructions.
Qiamp dna kit
Manufactured by Qiagen
Sourced in Germany, United States, Spain
The QIAamp DNA kit is a DNA extraction and purification kit designed for the isolation of genomic DNA from a variety of sample types, including tissue, blood, and body fluids. The kit utilizes a silica-based membrane technology to efficiently bind, wash, and elute DNA, providing a reliable and consistent method for DNA extraction.
Automatically generated - may contain errors
Lab products found in correlation
Pinpoint reagents, by Zymo Research (4 mentions)
Nextflex 16s v4 amplicon seq kit, by PSC Biotech (4 mentions)
Rneasy mini kit, by Qiagen (3 mentions)
Hiseq system, by Illumina (3 mentions)
Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (2 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (2 mentions)
Rnase a, by Thermo Fisher Scientific (2 mentions)
Truxtrac ffpe microtube dna kit column purification kit, by Covaris (2 mentions)
Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (2 mentions)
Hybond, by Cytiva (2 mentions)
Qubit fluorometer, by Thermo Fisher Scientific (2 mentions)
Qubit 2.0 fluorometer, by Thermo Fisher Scientific (2 mentions)
Miseq 300, by Illumina (2 mentions)
Tissuelyser lt, by Qiagen (2 mentions)
Ribolyser resin, by MP Biomedicals (2 mentions)
Nanodrop nd 1000, by Thermo Fisher Scientific (1 mentions)
Epitect bisulfite kit, by Qiagen (1 mentions)
Qiacube, by Qiagen (1 mentions)
Mj mini personal thermal cycler, by Bio-Rad (1 mentions)
Mirnaeasy ffpe kit, by Qiagen (1 mentions)
59 protocols using qiamp dna kit
1
Tissue Sampling for HCC Analysis
2
Liver Cancer Tissue Profiling
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Tissue from 34 patients with confirmed HCC undergoing resection at the Department of Surgery, University of Mainz, Germany were collected following patient informed consent and local ethics committee approval. This research has been approved by the ethic committee of the Landesärztekammer Rheinland-Pfalz on 05/15/13 (ethic code: 837.199.10 (7208). Detailed description of the cohort can be found [33 (link)]. Total RNA was extracted using the Qiagen RNEasy mini Kit (Qiagen GMBH, Hilden, Germany) following the manufacturer’s instructions. RNA quantity and purity were estimated using a Nanodrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), and integrity was assessed by Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA). DNA was extracted using Qiagen Qiamp DNA Kit (Qiagen GMBH, Hilden, Germany) following the manufacturer’s instructions.
3
DNA Extraction and Bisulfite Conversion
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA from the cancer cell lines and from the colorectal and gastric tissue samples was isolated using either a standard phenol/chloroform extraction protocol or magnetic beads. DNA from the formalin-fixed paraffin embedded pancreatic cancers was extracted using the QIAmp DNA kit (Qiagen, Qiagen Inc., Valencia, CA), and the ND-1000 Nanodrop (NanoDrop Technologies, Wilmington, DE) was used to measure DNA quantity and quality. DNA (1.3 µg) was bisulfite treated using the EpiTect Bisulfite Kit (Qiagen) according to the manufacturer's protocol. Following the conversion reaction, which was performed in an MJ Mini Personal Thermal Cycler (Bio-Rad, Hercules, CA), bisulfite converted DNA was purified using the QIAcube (Qiagen) automated pipetting system, and eluted in 40 µl elution buffer.
4
DNA Extraction from FFPE and Blood Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For germline, DNA was isolated from thawed buffy coat or mouth rinse samples using a QIAmp DNA kit (QIAGEN). For tumors, DNA for whole exome sequencing (WES) was purified with the truXTRAC FFPE microTUBE DNA Kit-Column Purification kit (Covaris). In brief, tumor tissues were scraped from 1–5 of 10 mm FFPE sections, deparaffinized using xylene, and lysed in an optimized lysis buffer that contains proteinase K. Following the proteinase K digestion to release DNA from the tissue, a higher temperature was used incubation to reverse formalin crosslinking alongside RNase treatment using RNase A (Thermo Fisher). The DNA and RNA samples were stored at −80°C before being used for assays.
5
DNA Extraction from FFPE and Blood Samples
6
Genetic Sample Collection and Extraction
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
During routine care, peripheral blood, chorionic villi, or amniotic fluid were collected from the proband and peripheral blood from their parents (when available). DNA was extracted using the QIAmp DNA Kit (QIAGEN) manually or using the QIAcube instrument according to the manufacturer’s instructions.
7
Characterization of iPSCs Harboring AK2 Mutations
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
iPSCs were maintained on irradiated mouse embryonic fibroblasts (Global Stem) in hESC medium containing DMEM, 20% KOSR, 10 ng/ml bFGF,1 mmol/liter l -Glutamine, 100 mmol/liter nonessential amino acids, 100 mmol/liter 2-b-Mercaptoethanol, and 100 mg/liter Primocin as previously described (Park et al., 2008b (link)). Karyotype analysis was performed by Cell Line Genetics. Genomic DNA was isolated using the QiAMP DNA kit (QIAGEN), and the genomic regions flanking the reported mutations were PCR amplified using primers AK2 M13 F (5′-ACAGCATCCTGGGCAGAATG-3′) and AK2 M13 R (5′-ATTCCCACCCATTGCCCTAC-3′) and sequenced in a commercial core facility (Eton Bioscience).
8
Mitochondrial DNA Copy Number Determination
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The total DNA was isolated from liver tissues using a QIAmp DNA kit (Qiagen, Germantown, MD) and was stored at −80 °C until further use. The mitochondrial DNA copy number was assessed as previously described [18 (link)]. The quantitative Real-Time PCR (qPCR) was performed with 1:100 of diluted DNA templates for mitochondrially encoded cytochrome c oxidase 1, 2, and 3. The PCR conditions were as follows: 3 min at 95 °C for initial denaturing, followed by 15 s at 95 °C, 30 s at 60 °C for annealing, and 15 s at 72 °C for an extension for 40 cycles, followed by a melt curve analysis. All of the samples were run in triplicate. Details of the primers are provided in Table 1 .
9
Extraction and Quantification of DNA and miRNA from Glioblastoma Cells and Tissues
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA from HBT-14 (U-87 MG) cells was extracted using the QIAmp DNA kit (Qiagen™) according to the manufacturer’s recommendation.
The miRNAs from HBT-14 (U-87 MG) cells were extracted using miRNAeasy (Qiagen™). The miRNAs from the 97 FFPE (formalin-fixed paraffin-embedded) surgically resected tumor specimens or the 8 non-tumoral brain tissues were extracted on 3 adjacent 15 μm cuts using the miRNAeasy-FFPE kit (Qiagen™, Hilden, Germany). For the tumoral specimens, morphological control was systematically carried out beforehand by a neuropathologist (ELZ) in order to guarantee that the percentage of tumor cells was greater than 70% and the absence of areas of necrosis or hemorrhage. When this was not the case, a macro-dissection of the samples was performed to determine these quality criteria. miRNAs were extracted from the seven plasma samples using NucleoSpin miRNA Plasma (Macherey-Nagel™, Düren, Luxembourg). For each sample, miRNA extraction was carried out according to the respective manufacturer’s instructions.
The integrity and quality of the purified DNA were assessed by 1% agarose gel electrophoresis, and the DNA/miRNA concentration was measured with the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Asnières-sur-Seine, France).
The miRNAs from HBT-14 (U-87 MG) cells were extracted using miRNAeasy (Qiagen™). The miRNAs from the 97 FFPE (formalin-fixed paraffin-embedded) surgically resected tumor specimens or the 8 non-tumoral brain tissues were extracted on 3 adjacent 15 μm cuts using the miRNAeasy-FFPE kit (Qiagen™, Hilden, Germany). For the tumoral specimens, morphological control was systematically carried out beforehand by a neuropathologist (ELZ) in order to guarantee that the percentage of tumor cells was greater than 70% and the absence of areas of necrosis or hemorrhage. When this was not the case, a macro-dissection of the samples was performed to determine these quality criteria. miRNAs were extracted from the seven plasma samples using NucleoSpin miRNA Plasma (Macherey-Nagel™, Düren, Luxembourg). For each sample, miRNA extraction was carried out according to the respective manufacturer’s instructions.
The integrity and quality of the purified DNA were assessed by 1% agarose gel electrophoresis, and the DNA/miRNA concentration was measured with the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Asnières-sur-Seine, France).
10
DNA Extraction and Genotyping from Blood Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA extraction from blood samples for the MEC‐APS participants was performed using the Qiagen QIAmp DNA kit (Qiagen Inc., Valencia, CA). DNA samples were genotyped by the Illumina MEGAEX array. Single‐nucleotide polymorphisms (SNPs) with a call rate <0.95, a replicate concordance <1.00% based on 39 QC replicate samples, and those with poor clustering after visual inspection were removed. Problematic samples with a call rate <0.95 or gender/sex mismatches were removed. From an initial 2,046,060 genotyped SNPs, there were 1,847,764 genotyped SNPs available.
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!