Nuclear RNA was prepared from HEK293T (kidney) cells. Briefly, cells were lysed on ice for 5 min in 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 0.05% NP-40, and nuclei were spun at 2,500g for 3 min and then resuspended in QIAzol for RNA isolation using the miRNeasy kit according to the manufacturer’s instructions (Qiagen). The RNA-seq library was created using the Illumina TruSeq RNA Sample Preparation Kit v2 with the standard protocol, and sequenced on one lane of the HiSeq 2000 platform (100 bp, paired-end). Data are available at NCBI as accession number SRP041943. The database of annotated protein coding and noncoding genes (41,409 genes and 171,904 transcripts in total) was produced by merging all annotated genes from the RefSeq database29 (link), the UCSC Browser24 (link) and the Ensembl database30 (link).
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Standard Preparations
Standard Preparations
Standard Preparations are well-defined, reproducible materials used in research and clinical settings to ensure accuracy and consistency across experiments.
These preparations may include reference substances, calibration standards, or other common reagents that serve as points of comparison.
Utilizing Standard Preparations helps minimize variability and enables reliable, comparable results, supporting the integrity of scientific findings.
Researchers can leverge standardized approaches to optimize their workflows and maximize the impact of their work.
Experencing the power of Standard Preparations can eleviate challenges and bolster confidence in research outcomes.
These preparations may include reference substances, calibration standards, or other common reagents that serve as points of comparison.
Utilizing Standard Preparations helps minimize variability and enables reliable, comparable results, supporting the integrity of scientific findings.
Researchers can leverge standardized approaches to optimize their workflows and maximize the impact of their work.
Experencing the power of Standard Preparations can eleviate challenges and bolster confidence in research outcomes.
Most cited protocols related to «Standard Preparations»
Cell Nucleus
Cells
DNA Library
Edetic Acid
Genes
isolation
Kidney
Nonidet P-40
RNA, Nuclear
RNA-Seq
Sodium Chloride
Standard Preparations
Tromethamine
Total RNAs were extracted using standard hot phenol RNA preparation method (51 (link)). For RT-PCR analysis, 1.5 µg of total RNAs were subjected to reverse transcription (RT) using gene-specific primers, and then the resulting cDNAs were analysed by standard PCR method or qPCR. Primers used are listed in Supplementary Table S3 . The half-life of pre-mRNAs was determined as described previously (52 (link),53 (link)). For northern blotting, the procedures were as previously described (50 (link)) except that total RNAs (10 µg) were separated by 6% acrylamide gels. Sequences of oligonucleotide probes are listed in Supplementary Table S3 . Band intensities were quantified using ImageJ densitometry software.
Acrylamide
Densitometry
DNA, Complementary
Gels
Genes
mRNA Precursor
Oligonucleotide Primers
Oligonucleotide Probes
Phenol
Reverse Transcription
RNA
Standard Preparations
Please refer to the sections “Q-PCR supplies, reagents and stock solutions” and “Preparation of cDNA Standards” in the Supplementary File 1 for the detailed protocols and worksheets for this section.
Total RNA is prepared from cells or frozen tissues with RNA STAT-60 according to the manufacturer′s instructions. For a typical assay, 4µg of total RNA is treated with a 1:5 dilution of RNase-free DNase I in the presence of 4.2mM MgCl2 in a final volume of 20µl. This is performed in 0.2ml thin-walled PCR tubes in a standard thermocycler at 37°C, 30 min., 75°C, 10 min., and 4°C hold. The reverse-transcription mix consisting of 1X First Strand Buffer, 10mM DTT, 200U of SuperScript RTII reverse transcriptase, 2mM dNTPs and 0.08µg/µl random hexamers is then added directly to the tubes with the DNAse-treated RNA for a final volume of 100µl. The cDNA synthesis is carried-out in the thermocycler at 25°C for 10 min., 42°C for 50 min., 72°C for 10 min., and 4°C hold. Following the reverse-transcription, DEPC-treated H2O is added to the unknown samples to bring the volume to 200µl, and the cDNA concentration to 20ng/µl. (Note that samples used as cDNA standards are not diluted prior to making the 5-fold dilution series used in primer validation and standard curve assays.) This will result in enough template cDNA to test approximately 40 QPCR targets.
Total RNA is prepared from cells or frozen tissues with RNA STAT-60 according to the manufacturer′s instructions. For a typical assay, 4µg of total RNA is treated with a 1:5 dilution of RNase-free DNase I in the presence of 4.2mM MgCl2 in a final volume of 20µl. This is performed in 0.2ml thin-walled PCR tubes in a standard thermocycler at 37°C, 30 min., 75°C, 10 min., and 4°C hold. The reverse-transcription mix consisting of 1X First Strand Buffer, 10mM DTT, 200U of SuperScript RTII reverse transcriptase, 2mM dNTPs and 0.08µg/µl random hexamers is then added directly to the tubes with the DNAse-treated RNA for a final volume of 100µl. The cDNA synthesis is carried-out in the thermocycler at 25°C for 10 min., 42°C for 50 min., 72°C for 10 min., and 4°C hold. Following the reverse-transcription, DEPC-treated H2O is added to the unknown samples to bring the volume to 200µl, and the cDNA concentration to 20ng/µl. (Note that samples used as cDNA standards are not diluted prior to making the 5-fold dilution series used in primer validation and standard curve assays.) This will result in enough template cDNA to test approximately 40 QPCR targets.
Anabolism
angiogenin
Biological Assay
Buffers
Cells
Deoxyribonuclease I
Deoxyribonucleases
DNA, Complementary
Freezing
Magnesium Chloride
Oligonucleotide Primers
Reverse Transcription
RNA-Directed DNA Polymerase
Standard Preparations
Technique, Dilution
Tissues
MRC crystallization plates (Swissci) containing MORPHEUS (85 µl in the main wells) were prepared on a Mosquito (TTP labtech) or ScreenMaker (Innovadyne) nanolitre liquid handler. Our standard setup for initial screens is to mix equal-volume aliquots of the protein and condition at 297 K, with a 200 nl final volume of drops, and to store the plates at 292 K. Final assessments were made after one week by manual inspection using a high-powered Leica MX-12 stereomicroscope. A drop was considered a crystallization hit when it contained protein crystals larger than 20 µm, so that they could be mounted in a cryoloop for X-ray diffraction.
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Crystallization
Culicidae
Proteins
Standard Preparations
X-Ray Diffraction
For immunophenotypic studies, all samples were systematically processed in parallel with the EuroFlow protocol versus the local routine procedures. Accordingly, the EuroFlow standard operating procedures (SOP) for instrument setup, instrument calibration, sample preparation, immunostaining and data acquisition16 were used at individual centers in parallel to the corresponding local protocols and techniques used for routine diagnosis and classification of hematological malignancies according to the WHO criteria. For data analysis, the Infinicyt software (Cytognos SL, Salamanca, Spain) was used in parallel to the local data analysis software programs and procedures.
For multivariate analysis of samples measured with the EuroFlow SOP and antibody panels, the Infinicyt software was used. For this purpose, the merge and calculation functions were applied for multi-tube panels prior to the analysis, as described elsewhere.31 (link), 32 (link) Briefly, prior to multivariate analyses, the populations of interest were selected and stored each in a distinct data file. Data files corresponding to the same cell population from an individual sample but stained with a different antibody tube of a multi-tube panel were merged into a single data file containing all information measured for that specific cell population. In a second step, ‘missing' data in one tube about markers only stained in the other tubes were calculated using previously described algorithms and tools implemented in the Infinicyt software.32 (link) Consequently, the generated final data file contained data about each parameter measured in the multi-tube panel for each of the events composing the cell population in that data file (Figure 2 ). This data file was further merged with the data files of other samples either to create a reference pool of a population of normal, reactive or malignant cells or to compare it with one or more of such reference pool data files, through multivariate analysis, for example, principal component analysis (PCA).31 (link)
For multivariate analysis of samples measured with the EuroFlow SOP and antibody panels, the Infinicyt software was used. For this purpose, the merge and calculation functions were applied for multi-tube panels prior to the analysis, as described elsewhere.31 (link), 32 (link) Briefly, prior to multivariate analyses, the populations of interest were selected and stored each in a distinct data file. Data files corresponding to the same cell population from an individual sample but stained with a different antibody tube of a multi-tube panel were merged into a single data file containing all information measured for that specific cell population. In a second step, ‘missing' data in one tube about markers only stained in the other tubes were calculated using previously described algorithms and tools implemented in the Infinicyt software.32 (link) Consequently, the generated final data file contained data about each parameter measured in the multi-tube panel for each of the events composing the cell population in that data file (
Cells
Diagnosis
Hematologic Neoplasms
Immunoglobulins
Immunophenotyping
Standard Preparations
Most recents protocols related to «Standard Preparations»
Example 4
The ends of the double-stranded nucleic acid can be ligated together via a ligation reaction where the ligation sequence splints the ligation to generate a circularized double-stranded nucleic acid also shown in
The circularized double-stranded nucleic acid can be amplified to generate a linearized double-stranded nucleic acid product, where the orientation of the analyte is reversed such that the 5′ sequence (e.g., 5′ UTR) is brought in closer proximity to the barcode (e.g., a spatial barcode or a cell barcode) (
The resulting double-stranded member of the nucleic acid library including a reversed analyte sequence (e.g., the 5′ end of the analyte sequence is brought in closer proximity to the barcode) can undergo standard library preparation methods, such as library preparation methods used in single-cell or spatial analyses. For example, the double-stranded member of the nucleic acid library lacking all, or a portion of, the sequence encoding the constant region of the analyte can be fragmented, followed by end repair, A-tailing, adaptor ligation, and/or amplification (e.g., PCR) (
As a result of the methods described in this Example, sequences from the 5′ end of an analyte will be included in sequencing libraries (e.g., paired end sequencing libraries). Any type of analyte sequence in a nucleic acid library can be prepared by the methods described in this Example (e.g., reversed).
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5' Untranslated Regions
Cell-Matrix Junction
Cells
DNA Library
Ligation
Nucleic Acids
Oligonucleotide Primers
Splints
Standard Preparations
This study aimed to compare the quality of inpatient (hospitalised) versus outpatient CCE colonic and PIC studies, and to assess factors affecting the outcome.
We performed a retrospective nested case-control study at Tallaght University Hospital, Dublin, Ireland over 1 year. Adult patients who had undergone either an inpatient CCE or PIC were identified from a capsule database. Controls and subjects who had undergone outpatient CCE and PIC procedures during the same period, were sequentially selected, i.e. the next outpatient procedures after the case, in a 1:2 ratio. All participants were ambulatory and able to swallow the capsule. All procedures were performed using PillCam®Colon 2 Capsules (Minneapolis, MN, USA) using a standard bowel preparation and booster regimen. For PIC, the SB sleep mode was manually deselected prior to capsule ingestion. Risk factors for delayed transit were identified at pre-assessment for all outpatients, and if present, patients had a gastric transit assessment at 30 minutes, as per ESGE Technical Review guidance [1 (link), 10 (link)]. Similarly, all inpatients underwent a gastric transit assessment as they are an identified at-risk group. If gastric transit was delayed and in the absence of contra-indications, patients received a prokinetic (metoclopramide 10 mg PO / IV).
Patients took 4 7.5 mg Senna tablets 2 days before the procedure. Then, the evening before the procedure, they ingested the first litre of a two-litre split-dose bowel preparation with Moviprep® (Norgine, Amsterdam, Nederland) a PEG-based solution. The second litre was taken on the morning of the procedure and all procedures were performed before 12:00. The first booster, Moviprep® with 750 ml of water and 15 ml of castor oil, was given when the capsule reached the small bowel. Then, 3 hours later a second booster of Moviprep® with 250 ml of water was given [11 (link)].
All studies were analysed by trained capsule endoscopists using Rapid Reader software version 9.0, and the findings were approved by our institution’s capsule review board. Basic demographics and key outcome measures were identified from the procedure reports and hospital patient records as required. Findings were compared between groups using X [2 (link)] or student t-tests as appropriate, and relevant odds ratio (OR) calculations were performed as indicated. A p-value of < 0.05 was considered significant.
We performed a retrospective nested case-control study at Tallaght University Hospital, Dublin, Ireland over 1 year. Adult patients who had undergone either an inpatient CCE or PIC were identified from a capsule database. Controls and subjects who had undergone outpatient CCE and PIC procedures during the same period, were sequentially selected, i.e. the next outpatient procedures after the case, in a 1:2 ratio. All participants were ambulatory and able to swallow the capsule. All procedures were performed using PillCam®Colon 2 Capsules (Minneapolis, MN, USA) using a standard bowel preparation and booster regimen. For PIC, the SB sleep mode was manually deselected prior to capsule ingestion. Risk factors for delayed transit were identified at pre-assessment for all outpatients, and if present, patients had a gastric transit assessment at 30 minutes, as per ESGE Technical Review guidance [1 (link), 10 (link)]. Similarly, all inpatients underwent a gastric transit assessment as they are an identified at-risk group. If gastric transit was delayed and in the absence of contra-indications, patients received a prokinetic (metoclopramide 10 mg PO / IV).
Patients took 4 7.5 mg Senna tablets 2 days before the procedure. Then, the evening before the procedure, they ingested the first litre of a two-litre split-dose bowel preparation with Moviprep® (Norgine, Amsterdam, Nederland) a PEG-based solution. The second litre was taken on the morning of the procedure and all procedures were performed before 12:00. The first booster, Moviprep® with 750 ml of water and 15 ml of castor oil, was given when the capsule reached the small bowel. Then, 3 hours later a second booster of Moviprep® with 250 ml of water was given [11 (link)].
All studies were analysed by trained capsule endoscopists using Rapid Reader software version 9.0, and the findings were approved by our institution’s capsule review board. Basic demographics and key outcome measures were identified from the procedure reports and hospital patient records as required. Findings were compared between groups using X [2 (link)] or student t-tests as appropriate, and relevant odds ratio (OR) calculations were performed as indicated. A p-value of < 0.05 was considered significant.
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Adult
Capsule
Castor oil
Colon
Ethics Committees, Research
Inpatient
Intestines
Intestines, Small
Metoclopramide
MoviPrep
Outpatients
Patients
Population at Risk
Secondary Immunization
Senna Plant
Sleep
Standard Preparations
Stomach
Student
Treatment Protocols
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Adult
Asepsis
COVID-19 Vaccines
COVID 19
Mental Recall
Nursing Staff
Personnel, Hospital
Pharmacy Student
Pressure
Standard Preparations
Sterility, Reproductive
Student
Vaccination
Vaccines
A blood sample was collected from the male proband and a lymphoblast line was set up according to standard practices. A skin biopsy was obtained from the proband and a fibroblast culture was established according to standard practices. All patient and control human cell lines receive authentication by genotyping and chromosomal microarray prior to freezing large stocks. All cell lines are tested monthly for mycoplasma contamination.
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Biopsy
BLOOD
Cell Lines
Chromosomes
Fibroblasts
Homo sapiens
Males
Microarray Analysis
Mycoplasma
Patients
Skin
Standard Preparations
Total RNA was isolated using the Qiagen RNeasy Kit (Qiagen, Germantown, MD) and treated with DNase I (New England Biolabs). Total DNA was extracted using the QIAamp DNA Mini Kit (Qiagen, Germantown, MD). The concentration was quantified by the NanoDrop One (Thermo Fisher Scientific, MA, USA), and the RNA quality was analyzed by the 2100 Agilent Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). Libraries were generated using a standard library preparation kit (KAPA) according to the manufacturer’s instructions. Libraries were quantified on the Qubit4 (Thermo Fisher Scientific, MA, USA) with the High Sensitivity DNA Assay (Thermo Fisher Scientific, MA, USA). Samples were equimolar pooled and sequenced on the Illumina NovaSeq (Illumina, San Diego, CA, USA) in 150-bp paired-end mode.
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Biological Assay
Deoxyribonuclease I
DNA Library
Hypersensitivity
Standard Preparations
Top products related to «Standard Preparations»
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The HiSeq 2000 is a high-throughput DNA sequencing system designed by Illumina. It utilizes sequencing-by-synthesis technology to generate large volumes of sequence data. The HiSeq 2000 is capable of producing up to 600 gigabases of sequence data per run.
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The HiSeq 2500 is a high-throughput DNA sequencing system designed for a wide range of applications, including whole-genome sequencing, targeted sequencing, and transcriptome analysis. The system utilizes Illumina's proprietary sequencing-by-synthesis technology to generate high-quality sequencing data with speed and accuracy.
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
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The Agilent 2100 Bioanalyzer is a lab instrument that provides automated analysis of DNA, RNA, and protein samples. It uses microfluidic technology to separate and detect these biomolecules with high sensitivity and resolution.
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The RNeasy Mini Kit is a laboratory equipment designed for the purification of total RNA from a variety of sample types, including animal cells, tissues, and other biological materials. The kit utilizes a silica-based membrane technology to selectively bind and isolate RNA molecules, allowing for efficient extraction and recovery of high-quality RNA.
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The Protein Preparation Wizard is a laboratory tool designed to automate the process of preparing protein samples for analysis. It streamlines the various steps involved in protein preparation, including solubilization, purification, and buffer exchange, to ensure consistent and reliable results. The core function of the Protein Preparation Wizard is to simplify and standardize the protein preparation workflow, enabling researchers to focus on their core research objectives.
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The MiSeq platform is a benchtop sequencing system designed for targeted, amplicon-based sequencing applications. The system uses Illumina's proprietary sequencing-by-synthesis technology to generate sequencing data. The MiSeq platform is capable of generating up to 15 gigabases of sequencing data per run.
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The NovaSeq 6000 is a high-throughput sequencing system designed for large-scale genomic projects. It utilizes Illumina's sequencing by synthesis (SBS) technology to generate high-quality sequencing data. The NovaSeq 6000 can process multiple samples simultaneously and is capable of producing up to 6 Tb of data per run, making it suitable for a wide range of applications, including whole-genome sequencing, exome sequencing, and RNA sequencing.
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The HiSeq 2500 platform is a high-throughput DNA sequencing system designed for a wide range of genomic applications. It utilizes sequencing-by-synthesis technology to generate high-quality sequence data. The HiSeq 2500 platform is capable of producing up to 1 billion sequencing reads per run, making it a powerful tool for researchers and clinicians working in the field of genomics.
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The QIAamp DNA Mini Kit is a laboratory equipment product designed for the purification of genomic DNA from a variety of sample types. It utilizes a silica-membrane-based technology to efficiently capture and purify DNA, which can then be used for various downstream applications.
More about "Standard Preparations"
Standard preparations, also known as reference materials or calibration standards, are well-defined, reproducible substances used in research and clinical settings to ensure accuracy, consistency, and reliability across experiments.
These preparations serve as points of comparison, helping to minimize variability and enabling researchers to obtain reliable, comparable results.
Leveraging standardized approaches, such as the use of the HiSeq 2000, HiSeq 2500, MiSeq, and NovaSeq 6000 platforms, as well as reagents like TRIzol, the RNeasy Mini Kit, and the Protein Preparation Wizard, researchers can optimize their workflows and maximize the impact of their work.
By utilizing the Agilent 2100 Bioanalyzer and the QIAamp DNA Mini Kit, researchers can further enhance the quality and integrity of their scientific findings.
Experiencing the power of standard preparations can alleviate challenges and bolster confidence in research outcomes, supporting the overall integrity of the scientific process.
Researchers can leverage the insights and tools provided by resources like PubCompare.ai to easily locate the best protocols from literature, pre-prints, and patents, ensuring they are utilizing the most effective and reproducible approaches in their work.
These preparations serve as points of comparison, helping to minimize variability and enabling researchers to obtain reliable, comparable results.
Leveraging standardized approaches, such as the use of the HiSeq 2000, HiSeq 2500, MiSeq, and NovaSeq 6000 platforms, as well as reagents like TRIzol, the RNeasy Mini Kit, and the Protein Preparation Wizard, researchers can optimize their workflows and maximize the impact of their work.
By utilizing the Agilent 2100 Bioanalyzer and the QIAamp DNA Mini Kit, researchers can further enhance the quality and integrity of their scientific findings.
Experiencing the power of standard preparations can alleviate challenges and bolster confidence in research outcomes, supporting the overall integrity of the scientific process.
Researchers can leverage the insights and tools provided by resources like PubCompare.ai to easily locate the best protocols from literature, pre-prints, and patents, ensuring they are utilizing the most effective and reproducible approaches in their work.