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BP protocol

BP protocol: A comprehensive, AI-driven platform that empowers researchers to streamline their biopharmaceutical (BP) research.
Discover and compare BP protocols from literature, preprints, and patents, leveraging cutting-edge AI technology to identify the most effective approaches.
Optimize your BP studies and take your research to new heights with the power of PubCompare.ai.
Convinient and user-friendly, this platform helps you navigate the complexities of BP protocol selection, saving time and guiding you towards the best possible outcomes.

Most cited protocols related to «BP protocol»

Comparative Genomic Sequencing of Salmonella and Staphylococcus

Cited 170 times

Three different datasets were used for evaluation in the present study, comprising selected Salmonella Montevideo [17] (link), Staphylococcus aureus CC398 [5] , and Salmonella Typhimurium DT104 [18] (link) from previous studies.
For S. Montevideo 12 closely related outbreak strains where sequenced once by US Food and Drug Administration using Roche Genome sequencer FLX system, Illumina MiSeq and Life Technologies Ion Torrent and made publicly available (Table S1), although only the MiSeq data was used in the original study [16] (link). The raw data were downloaded from the Sequence Read Archive (SRA). For Staphylococcus aureus CC398, the completely sequenced and annotated strain SO385 (AM990992.1) as well as four additional strains were selected from a previously published study [5] and sequenced twice using both MiSeq and Ion Torrent. HiSeq was used in the original study for sequencing. All the strains except for the reference strain were chosen from the same clade, named IIa1i in the original study. The strains are not epidemiologically related but have all been isolated from Danish Pigs and are shown to be closely related in the original study. For S. Typhimurium DT104 the reference strain NCTC 13348 (HF937208.1) and an additional three isolates from the same outbreak [18] (link) were sequenced twice on both MiSeq and Ion Torrent.
Genomic DNA (gDNA) was purified from the isolates using the Easy-DNA extraction kit (Invitrogen) and DNA concentrations determined using the Qubit dsDNA BR Assay Kit (Invitrogen). The isolates were sequenced twice on the MiSeq platform (Illumina) and Ion Torrent PGM (Life Technologies).
For Ion Torrent the isolates were sequenced following the manufacturer’s protocols for 200 bp gDNA fragment library preparation (Ion Xpress Plus gDNA and Amplicon Library 96 Preparation), template preparation (Ion OneTouch System), and sequencing (Ion PGM 200 Sequencing kit) using the 316 chip. For MiSeq the isolates chromosomal DNA of the isolates was used to create genomic libraries using the Nextera XT DNA sample preparation kit (Illumina, cat. No. FC-131-1024) and sequenced using v2, 2×250 bp chemistry on the Illumina MiSeq platform (Illumina, Inc., San Diego, CA).

Kaas R.S., Leekitcharoenphon P., Aarestrup F.M, & Lund O. (2014). Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms. PLoS ONE, 9(8), e104984.

Publication 2014

Biological Assay BP protocol Chromosomes cyclo(D-tyrosyl-arginyl-arginyl-3-(2-naphthyl)alanyl-glycyl) DNA, Double-Stranded DNA Chips DNA Library Genome Genomic Library Salmonella Salmonella typhimurium Staphylococcus aureus Strains Sus scrofa

Isolation and Sequencing of Immune Cell Chromatin

Cited 47 times

Neutrophil granulocytes, CD4+ and CD8+ T-cells were isolated from donor blood using Histopaque density gradients and Ig-coupled beads against blood cell surface makers (pan T and CD4+ microbeads, Miltenyi Biotec). Nucleosome cores were prepared as previously described⁷; cells were snap-frozen and crushed to release chromatin, followed by micrococcal nuclease treatment. In vitro nucleosomes were prepared by combining human genomic DNA with recombinantly-derived histone octamers at an average ratio of 1 octamer per 850 bps. Unbound DNA was then digested using micrococcal nuclease. After digestion, reactions were stopped with EDTA, samples were treated with proteinase K, and nucleosome-bound DNA was extracted with phenol-chloroform and precipitated with ethanol (Supplementary methods). Purified DNA was size-selected (120–180 bp) on agarose to obtain mononucleosome cores, followed by sequencing library construction. RNA was isolated by homogenizing purified cells in Trizol, poly-A RNA was purified using Qiagen Oligotex kit and RNA-seq libraries were constructed using SOLiD Whole Transcriptome Analysis kit. All sequence data was obtained using SOLiD 35 bp protocol and aligned using the SOLiD pipeline against the human hg18 reference genome. Downstream analyses were all conducted using custom scripts (supplementary methods).

Valouev A., Johnson S.M., Boyd S.D., Smith C.L., Fire A.Z, & Sidow A. (2011). Determinants of nucleosome organization in primary human cells. Nature, 474(7352), 516-520.

Publication 2011

Blood Cells BP protocol CD8-Positive T-Lymphocytes Cells Chloroform Chromatin Digestion DNA Library Donor, Blood Edetic Acid Endopeptidase K Ethanol Freezing Gene Expression Profiling Genome, Human Histones histopaque Micrococcal Nuclease Microspheres Neutrophil Nucleosomes Phenol Receptors, Antigen, B-Cell RNA, Polyadenylated RNA-Seq Sepharose trizol

Nextera-based Library Preparation for Sequencing

Cited 19 times

For the 500 pg and 100 pg E. coli (CC118) libraries and 10 pg human library (NA18507, Coriell), genomic DNA (in 1 μl volume) was incubated with 1 μl Nextera Illumina-compatible transposomes (Epicentre) at a 1 to 50 dilution (1 μl Nextera enzyme, 24 μl TE, 25 μl 100% glycerol), 1 μl 5× Nextera HMW buffer, and 2 μl nuclease-free water (Ambion). To avoid contamination, all dilutions and reaction preparation was carried out in a PCR hood. Reactions were incubated at 55°C for 5 min followed by addition of 25 μl 2× Nextera PCR buffer, 0.5 μl SYBR Green, 1 μl 50× Nextera primer cocktail, and 1 μl 0.5 μM barcode adaptor 2 (barcodes A6, A9, or A4 for 500 pg and 100 pg E. coli DNA, or 10 pg human DNA, respectively) and cycled under standard Nextera conditions in a MiniOpticon (Bio-Rad) real-time PCR thermocycler. Both reactions were removed after 20 cycles and cleaned up using Qiaquick MinElute columns, eluting in 20 μl EB. Libraries were run on a 6% Novex TBE PAGE gel (Invitrogen) for size verification and sequenced as barcoded spike-ins as per standard Illumina GAIIx protocol as a paired-end 101 bp (plus 9 bp barcode) run for E. coli libraries and a paired-end 36 bp (plus 9 bp barcode) run for human.

Adey A., Morrison H.G., A.s.a.n., Xun X., Kitzman J.O., Turner E.H., Stackhouse B., MacKenzie A.P., Caruccio N.C., Zhang X, & Shendure J. (2010). Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biology, 11(12), R119.

Publication 2010

BP protocol Buffers DNA Library Enzymes Escherichia coli Genome Glycerin Homo sapiens Oligonucleotide Primers Real-Time Polymerase Chain Reaction SYBR Green I Technique, Dilution

Standardized Auscultatory Blood Pressure Measurement Protocol

Cited 12 times

CKiD participants have casual BP measurements obtained in the right arm by auscultation at study entry (baseline), then annually thereafter. All participating sites have been provided the same aneroid sphygmomanometer (Mabis MedicKit 5, Mabis Healthcare, Waukegan, IL) by the CKiD Clinical Coordinating Centers (CCC's). The CCC's also provide standardized training and certification in the auscultatory BP measurement protocol described below to all study personnel responsible for casual BP measurement. Recertification in auscultatory BP measurement technique and calibration of each center's aneroid device takes place annually.
At each study visit, prior to BP determination, arm circumference is measured (in centimeters) with a plastic measuring tape at the midpoint of the upper arm between the amicron and olecranon and a cuff is then selected so that the length of the cuff bladder is equal to 80-100% of the arm circumference^{6 (link)}. Following cuff selection, the peak inflation pressure is determined by inflating the cuff to 60 mmHg and then gradually continuing to inflate in increments of 10 mmHg until the radial pulse is no longer felt – thereby determining the pulse obliteration pressure. An additional 30 mmHg is added to this value and recorded as the peak inflation pressure. The cuff is then inflated to this value for all BP measurements at that study visit.
After 5 minutes of rest, BP measurement begins. Participants are instructed to refrain from caffeine intake, smoking, and exercise at least one half hour prior to and until completion of BP measurement. They are also instructed to refrain from playing video games, using a cell phone, or other activities that may affect BP until all measurements are obtained. First, pulse is measured by palpation of the radial artery. Then three BP measurements at 30-second intervals are obtained by auscultation of the brachial artery, using the first Korotkoff sound for systolic BP (SBP) and the fifth Korotkoff sound for diastolic BP (DBP). The average of the 3 BP measurements is recorded as the participant's BP for the study visit. Participants' BP's so obtained at the baseline visit are included in the present study.

Flynn J.T., Mitsnefes M., Pierce C., Cole S.R., Parekh R.S., Furth S.L, & Warady B.A. (2008). Blood Pressure in Children with Chronic Kidney Disease: A Report from the Chronic Kidney Disease in Children Study. Hypertension, 52(4), 631-637.

Publication 2008

Arteries, Radial Auscultation BP protocol Brachial Artery Caffeine Feelings Medical Devices methyl 4-azidobenzimidate Olecranon Process Palpation Pressure Pressure, Diastolic Pulse Pressure Pulse Rate Sound Sphygmomanometers Systolic Pressure Urinary Bladder

Barcoded Sequencing of Herpes Simplex Virus

Cited 10 times

Barcoded sequencing libraries for each virus were prepared following the manufacturer’s protocol for sequencing of genomic DNA (Illumina TruSeq DNA sample preparation kit). Viral nucleocapsid DNA (1 to 5 µg) was used as the input for library preparation. Five to six libraries were multiplexed per flow cell lane; the DNA fragment size selected for each library was centered at 550 bp. Libraries of HSV-1 KOS and F subclones were sequenced at the Sequencing Core Facility of the Lewis-Sigler Institute for Integrative Genomics (Princeton University), using paired-end, 100-bp sequencing protocols on an Illumina HiSeq2000 with version 2 chemistry. Illumina real-time analysis (RTA 1.12.4.2) software provided image analysis and base calling under default settings. Libraries of HSV-1 H166 and H166_Syncytial strains were sequenced on an Illumina MiSeq at Pennsylvania State University, using 300-bp paired-end, version 3 sequencing chemistry. Image analysis and base calling were done under default settings with MiSeq Control software (MCS) version 2.3.0.

Parsons L.R., Tafuri Y.R., Shreve J.T., Bowen C.D., Shipley M.M., Enquist L.W, & Szpara M.L. (2015). Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses. mBio, 6(2), e02213-14.

Publication 2015

BP protocol Cells DNA, Viral DNA Library Genome Human Herpesvirus 1 Nucleocapsid Strains Virus

Most recents protocols related to «BP protocol»

Whole Exome Sequencing for Genetic Diagnosis

WES was performed on genomic DNA isolated from the peripheral blood of the proband, his parents, and his unaffected brother to identify the pathogenic gene mutation. The SureSelectXT Reagent kit was used to hybridise the SureSelectXT Human All Exon V6 (both from Agilent Technologies, Santa Clara, CA, USA) with the DNA library for WES capture. Polymerase Chain Reaction (PCR) was used to amplify the exon DNA library. High-throughput sequencing was performed on the Hiseq/NovaSeq platform (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions with a 2 × 150 bp sequencing protocol. Reads were mapped to the human reference genome (GRCH38/hg38). Variants were annotated with Annovar (https://annovar.openbioinformatics.org/en/latest/) [14 (link)] and allele frequency, pathogenicity, and protein function were evaluated.

Mei Y., Jiang Y., Zhang Z, & Zhang H. (2023). Muscle and bone characteristics of a Chinese family with spinal muscular atrophy, lower extremity predominant 1 (SMALED1) caused by a novel missense DYNC1H1 mutation. BMC Medical Genomics, 16, 47.

Publication 2023

BLOOD BP protocol Brothers DNA Library Exons Genome Genome, Human Homo sapiens Mutation Parent Pathogenicity Polymerase Chain Reaction Proteins

16S rRNA Amplicon Sequencing Protocol

A total of 224 16S V3-V4 amplicon libraries (112 samples per each sampling site) were prepared following the Illumina metagenomic sequencing library construction workflow. The metagenome sequencing platform of the Illumina targeted a partial area containing the V3-V4 hypervariable region of the bacterial 16S rRNA gene. PCR for amplifying the target region was performed using the KAPA HiFi Hot Start Ready Mix (2×) (Roche, Mannheim, Germany), and a pair of 16S V3-V4 target-specific primer recommended by Illumina. The primer sequences were as follows: 16S 341F forward primer is 5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG-3“ and 16S 805 R reverse primer is 5”-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC-3’. After the PCR amplification, the purification process of all PCR amplicon products was conducted using the AMPure XP beads (Beckman Coulter, USA). Then, additional PCR amplification was performed using Nextera XT Index Kit (Illumina, USA), which included Illumina multiplexing dual index barcode and sequencing adapter sequence. The final PCR products were then purified once again using the AMPure XP beads. After the amplicon library construction, the 16S metagenome sequencing was performed using the paired-end 2 × 300 bp Illumina MiSeq^TM protocol (Illumina Miseq, USA).

Jeong J., Ahn K., Mun S., Yun K., Kim Y.T., Jung W., Lee K.E., Kim M.Y., Ahn Y, & Han K. (2023). Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans. Journal of Oral Microbiology, 15(1), 2186591.

Publication 2023

BP protocol DNA Library Genes, Bacterial Metagenome Oligonucleotide Primers RNA, Ribosomal, 16S

16S rRNA Gene Sequencing of Microbiome

DNA samples were submitted for 16S rRNA gene sequencing at the Integrated Microbiome Resource (IMR) at Dalhousie University (Halifax, Canada). Variable regions V3-V4 of the bacterial 16S rRNA gene were amplified from all purified DNA samples using a set of primers 341F: 5'- CCTACGGGNGGCWGCAG -3' and 805R: 5'- GACTACHVGGGTATCTAATCC -3' [21 (link)] and sequenced on an Illumina MiSeq using paired-end 300 bp sequencing [22 , 23 (link)].
The 16S fusion primers were added to the multiplexed samples in equal amounts. Illumina Nextera adapters and barcodes were included in the fusion primers for dual-labeling at both ends of the amplicons. The reaction mixture of 25 µL contained 5 µL of 5 × HF buffer, 0.5 µL dNTPs (40 mM), 5 µL forward and 5 µL reverse primer (1 µM), 0.25 µL Phusion polymerase (2 U/µL; Thermo Scientific), 2 µL template and 7.25 µL water. The reaction conditions started with denaturation at 98 °C (30 s), followed by 30 cycles of 98 °C (10 s), 55 °C (30 s), and 72 °C (30 s). The final extension was performed for 4.5 min at 72 °C. The samples and negative controls were combined to form a single library and then applied to the Illumina MiSeq platform using 2 × 300 bp Pair-End v3 chemistry according to the manufacturer's protocol.

Mahdy M.S., Azmy A.F., Dishisha T., Mohamed W.R., Ahmed K.A., Hassan A., Aidy S.E, & El-Gendy A.O. (2023). Irinotecan-gut microbiota interactions and the capability of probiotics to mitigate Irinotecan-associated toxicity. BMC Microbiology, 23, 53.

Publication 2023

Adjustment Disorders BP protocol Buffers DNA Library Genes Genes, Bacterial Microbiome Oligonucleotide Primers RNA, Ribosomal, 16S

Generating Inducible GNAS R201C Mutant

The GNAS active mutant was previously generated by site-directed mutagenesis of R201 to cysteine^{56 (link)}. GNAS^R201C cDNA was cloned into the pENTR backbone (pDONR221; ThermoFisher Scientific, 12536017) using the Gateway cloning BP reaction according to the manufacturer’s protocols (Invitrogen, 11789020). Activity of the GNAS^R201C active mutant was confirmed by cAMP-responsive element (CRE) luciferase assay (Dual-Glo Luciferase Assay System; Promega, E2920) or cAMP immunoassay (R&D Systems, KGE002B). The GNAS^R201C-pENTR vector was then recombined with the lentiviral vector pLVX-TetOne FLAG Puro (provided by the Krogan group, UCSF) using the Gateway LR reaction according to the manufacturer’s protocol (Invitrogen, 11791020). Viral particles were collected from HEK293T17 cells and concentrated by ultracentrifugation. Cells were transduced two times for 48 h and then selected with 1 μg ml^–1 puromycin for 5 d. Expression of GNAS^R201C was induced by adding 1 μg ml^–1 doxycycline.

Ruiz-Saenz A., Atreya C.E., Wang C., Pan B., Dreyer C.A., Brunen D., Prahallad A., Muñoz D.P., Ramms D.J., Burghi V., Spassov D.S., Fewings E., Hwang Y.C., Cowdrey C., Moelders C., Schwarzer C., Wolf D.M., Hann B., VandenBerg S.R., Shokat K., Moasser M.M., Bernards R., Gutkind J.S., van ‘t Veer L.J, & Coppé J.P. (2023). A reversible SRC-relayed COX2 inflammatory program drives resistance to BRAF and EGFR inhibition in BRAFV600E colorectal tumors. Nature Cancer, 4(2), 240-256.

Publication 2023

Biological Assay BP protocol Cells Cloning Vectors DNA, Complementary Doxycycline Immunoassay Luciferases Mutagenesis, Site-Directed Promega Puromycin Ultracentrifugation Vertebral Column Virion

Illumina-based 16S rRNA Sequencing

For the library PCR step in combination with sample-specific barcoded primers, purified PCR products were shipped to BaseClear BV (Leiden, The Netherlands). PCR products were purified, checked on a Bioanalyzer (Agilent), and quantified. This was followed by multiplexing, clustering, and sequencing on an Illumina MiSeq with the paired-end (2×) 300 bp protocol and indexing. The sequencing run was analysed with the Illumina CASAVA pipeline (v1.8.3) by demultiplexing based on sample-specific barcodes. From the raw sequencing data, low quality of sequence reads, reads containing adaptor sequences, or PhiX control with an in-house filtering protocol were discarded and only “passing filter” reads were selected. On the remaining reads, we performed a quality assessment using the FASTQC quality control tool version 0.10.0. (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, accessed on 8 February 2022).
Sequences of the 16S rRNA gene were analysed using a workflow based on QIIME 1.8 [20 (link)]. On average, 23,918 (range 11,071–36,288) 16S rRNA gene sequences per sample were analysed. We performed operational taxonomic unit (OTU) clustering (open reference), taxonomic assignment and reference alignment with the pick_open_reference_otus.py workflow script of QIIME, using uclust as clustering method (97% identity) and GreenGenes v13.8 [21 ,22 (link),23 (link)] as reference database for taxonomic assignment. Reference-based chimera removal was performed with Uchime [24 (link)]. The RDP classifier version 2.2 was performed for taxonomic classification [25 (link)].

Olga L., van Diepen J.A., Chichlowski M., Petry C.J., Vervoort J., Dunger D.B., Kortman G.A., Gross G, & Ong K.K. (2023). Butyrate in Human Milk: Associations with Milk Microbiota, Milk Intake Volume, and Infant Growth. Nutrients, 15(4), 916.

Publication 2023

BP protocol Chimera DNA Library Genes Oligonucleotide Primers RNA, Ribosomal, 16S

Top products related to «BP protocol»

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Miseq platform by Illumina

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What is a BP protocol and how can it help my research?

A BP protocol is a comprehensive, AI-driven platform that empowers researchers to streamline their biopharmaceutical (BP) research. It allows you to discover and compare BP protocols from literature, preprints, and patents, leveraging cutting-edge AI technology to identify the most effective approaches. By optimizing your BP studies with the help of PubCompare.ai, you can take your research to new heights and achieve better outcomes.

How can PubCompare.ai assist in the optimal use and comparison of BP protocols?

PubCompare.ai allows you to screen protocol literature more efficiently and leverage AI to pinpoint critical insights. The platform's AI-driven analysis can help researchers identify the most effective protocols related to BP protocol for their specific research goals, highlighting key differences in protocol effectiveness. This enables you to choose the best option for reproducibility and accuracy, saving time and guiding you towards the best possible outcomes.

What are the different variations or types of BP protocols, and how can I determine the best one for my research?

BP protocols can vary in terms of their methodologies, target applications, and underlying technologies. PubCompare.ai makes it easy to navigate this complexity by providing a convenient and user-friendly platform to compare and contrast different BP protocol options. The AI-driven insights offered by the platform can help you identify the most suitable protocol variation for your specific research needs, ensuring that you achieve the best possible results.

How can I use PubCompare.ai to address common challenges in BP protocol usage?

One of the key challenges in using BP protocols is ensuring that you select the most effective and reproducible approach for your research. PubCompare.ai addresses this by providing AI-driven comparisons that highlight the critical differences between various BP protocols. This allows you to make informed decisions and avoid potential pitfalls, saving time and resources. The platofrm also helps you navigate the complexities of BP protocol selection, guiding you towards the best possible outcomes.

What are some specific applications of BP protocols, and how can PubCompare.ai assist in these use cases?

BP protocols have a wide range of applications, from drug discovery and development to biomarker identification and therapeutic optimization. PubCompare.ai can help you in all of these use cases by providing a comprehensive platform to discover, compare, and select the most effective BP protocols. Whether you're working on novel therapeutics, investigating disease mechanisms, or optimizing existing treatments, the platform's AI-driven insights can be invaluable in streamlining your research and achieving your goals more efficiently.

More about "BP protocol"

Biopharmaceutical (BP) research is a rapidly evolving field that requires efficient and effective protocols to drive innovation and advance scientific discoveries.
The PubCompare.ai platform is an AI-driven solution that empowers researchers to streamline their BP studies by providing access to a comprehensive database of protocols from literature, preprints, and patents.
Leveraging cutting-edge AI technology, PubCompare.ai helps researchers identify the most effective BP protocols by enabling them to discover and compare a wide range of approaches.
This convenient and user-friendly platform saves time and guides users towards the best possible outcomes for their research.
Key capabilities of the PubCompare.ai platform include: - Accessing a vast repository of BP protocols from various sources, including published literature, preprints, and patents - Utilizing AI-powered comparisons to identify the most effective and relevant protocols for your specific research needs - Optimizing BP studies by selecting the most appropriate protocols, which can lead to improved efficiency and better research outcomes - Navigating the complexities of BP protocol selection with the help of the platform's intuitive interface and advanced features The PubCompare.ai platform is designed to be a valuable tool for researchers working in the biopharmaceutical field.
By leveraging the power of AI and providing access to a wealth of protocol information, the platform helps users streamline their research and take their BP studies to new heights.
In addition to the PubCompare.ai platform, researchers in the biopharmaceutical field may also find value in other technologies and tools, such as the HiSeq 2500, HiSeq 2000, MiSeq, NovaSeq 6000, HiSeq 4000, NextSeq 500, TRIzol reagent, Bioanalyzer, RNeasy Mini Kit, and Agilent 2100 Bioanalyzer.
These technologies can provide valuable data and insights that complement the capabilities of the PubCompare.ai platform.
Overall, the PubCompare.ai platform is a compelling solution for researchers looking to optimize their biopharmaceutical research, streamline their workflows, and unlock new possibilities in their BP studies.