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Tag: hiSeq
A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing
Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…
Red Genes: Assessing WuXi AppTec’s Ties to the Party-Army-State
Executive Summary: WuXi AppTec, a major Chinese biotechnology and pharmaceutical firm, claimed that the company has not, does not, and will not pose a national security risk to any country in response to new legislation introduced in the US Congress. The company’s claims are undermined by WuXi Apptec’s network of…
Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals
The specific environmental/history/collection context The Huseby Klev materials were unearthed and collected by archaeologists (including two of the co-authors of this article) during the excavation of this coastal hunter-fisher-gatherer site in the 90s50. The material assemblage was rich and well preserved: human bones, animal bones, plant remains and pieces of…
LncRNA/circRNA-mRNA networks in CARAS | JIR
Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…
Characteristics of Amorphophallus konjac as indicated by its genome
Genome assembly and annotation The DNA sequencing data (1119.58 Gb, average 110× coverage) of the A. konjac sample were obtained using the Illumina Hiseq 2500 sequencer. A summary of the sequence data used for the assembly is presented in Table S1. The estimated genome size is 4,512,012,462 bp using 19-mer frequency distribution based…
Genomic hypomethylation in cell-free DNA predicts responses to checkpoint blockade in lung and breast cancer
Lung cancer ICB cohort Advanced non-small cell lung carcinoma patients who were treated with anti-PD-1/PD-L1 monotherapy at Samsung Medical Center, Seoul, Republic of Korea were enrolled for this study. The present study has been reviewed and approved by the Institutional Review Board (IRB) of the Samsung Medical Center (IRB no….
Genomic Predictors Associated With Exceptional Response to Systemic Therapy in Advanced Pancreatic Cancer
ABSTRACT Introduction: Exceptional response to therapy is rare in patients with advanced pancreatic cancer. This study explored potential genomic differences between typical and exceptional responses that could confer more favorable biology. Methods: We included exceptional responders and controls with advanced pancreatic cancer from Cleveland Clinic from April 2013 to August…
DNA Sequencing Services Industry Sets Sights on Flourishing Valuation of US$ 2,080.2 Million by 2033-FMI Projection
DNA Sequencing Services Market The DNA sequencing services industry is expected to grow by 8.2% over the course of the forecast year, according to FMI. The industry is projected to be worth US$ 945.6 million on the market by 2023.The DNA Sequencing Services Market is a dynamic sector at the…
Single-cell analysis of chromatin accessibility in the adult mouse brain
Tissue preparation and nucleus isolation All experimental procedures using live animals were approved by the SALK Institute Animal Care and Use Committee under protocol number 18-00006. Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56–63-day-old mice and sectioned into 600 µm coronal sections along the anterior–posterior…
How does sequencing depth affect the identification of bacteria, fungi and viruses?
What are some latest advances in clinical metagenomic diagnostics for pathogen detection using shirt and long read sequencing?5 answersClinical metagenomic diagnostics for pathogen detection using short and long read sequencing have seen several recent advances. Traditional pathogenic diagnosis methods have limitations such as low positivity rates and inability to identify…
Thyroid hormone-regulated chromatin landscape and transcriptional sensitivity of the pituitary gland
Mouse genetic models The ThrbHAB allele expresses TRβ proteins (TRβ1 and TRβ2) fused to a peptide with a hemagglutinin (HAx2) tag and a site for biotinylation by prokaryotic BirA ligase, modified from a published tag30. The tag was inserted at the endogenous Thrb gene by homologous recombination in W9.5 (129/Sv)…
Refurbished DNA Sequencing Platforms Market Insights, Market Players and Forecast Till 2030
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The PacBio RS II sequencer has been effectively utilized to generate a 1.27 Gb genome assembly of Dendrobium officinale [70]. By utilizing advanced sequencing technologies such as Illumina HiSeq, Nanopore, PacBio, and Hi-C, the results have revealed remarkable N50 values of 44 Mb and 65.35 Mb for Gardenia jasminoides and…
Immune-privileged tissues formed from immunologically cloaked mouse embryonic stem cells survive long term in allogeneic hosts
Mice C57BL/6N (strain 005304), C3H/HeJ (strain 000659), FVB/NJ (strain 001800), BALB/cJ (strain 000651) and NSG mice (stock 005557) were purchased from the Jackson Laboratory. CD-1 (stock 022) mice were purchased from Charles River. Mice (6–20-week-old) of each strain/background were used for teratoma assays. Mice were housed in a pathogen-free facility…
Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA
Summary Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY,…
Phenotypic drug-susceptibility profiles and genetic analysis based on whole-genome sequencing of Mycobacterium avium complex isolates in Thailand
Abstract Mycobacterium avium complex (MAC) infections are a significant clinical challenge. Determining drug-susceptibility profiles and the genetic basis of drug resistance is crucial for guiding effective treatment strategies. This study aimed to determine the drug-susceptibility profiles of MAC clinical isolates and to investigate the genetic basis conferring drug resistance using…
Should I remove Kmers identified in FastQC?
Should I remove Kmers identified in FastQC? 2 Hi, apologies for this basic questions, I new in NGS quality control. I have been check my NGS data (Illumina – HiSeq 2500 2*100pb) using FastQC after trimming Nextera Adaptater with bbduck (BBTool package) using trimming overlap (ktrim=r k=25 mink=11 hdist=1 tpe…
an extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input
error while running cellranger: an extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input 1 Hi, I’m quite new to scRNA-seq and I got an error as below while trying to run cellranger (version 7.2.0) for public human brain cortex data. [error]…
Primate-specific ZNF808 is essential for pancreatic development in humans
Subjects The study was conducted in accordance with the Declaration of Helsinki and all subjects or their parents/guardian gave informed written consent for genetic testing. DNA testing and storage in the Beta Cell Research Bank was approved by the Wales Research Ethics Committee 5 Bangor (REC 17/WA/0327, IRAS project ID…
Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo
Introduction The non-random packaging of chromatin within the nucleus is a universal feature of eukaryotic genomes. The three-dimensional (3D) spatial organization of chromatin could be partitioned at different levels based on the interaction frequency between two given loci in the genome. Advances in sequencing technologies have led to the identification…
Quantification of rare somatic single nucleotide variants by droplet digital PCR using SuperSelective primers
Primary samples and nucleic acid extraction A cohort of 48 patients diagnosed with advanced adenoma (AAD), defined by size > 20 mm, or colorectal carcinoma (CRC) were collected between 2013 and 2016. The study was approved by the institutional ethics committee of Hospital General Universitario de Alicante (Ref. CEICPI2013/01), and written informed consent…
Metagenomic Data of Bacterial 16S rRNA in the Cemetery Soil Samples in Surakarta City, Indonesia by Triastuti Rahayu, Erma Musbita Tyastuti, Ambarwati Ambarwati, Lina Agustina, Noor Alis Setiyadi, Nazia Jamil, Yasir Sidiq :: SSRN
10 Pages Posted: 1 Nov 2023 See all articles by Triastuti Rahayu Universitas Muhammadiyah Surakarta Universitas Muhammadiyah Surakarta Universitas Muhammadiyah Surakarta Universitas Muhammadiyah Surakarta Universitas Muhammadiyah Surakarta University of the Punjab (PU) Universitas Muhammadiyah Surakarta Abstract Cemetery soils most likely contain…
What is FastQC | 5 Answers from Research papers
FastQC is a software tool used for quality control in sequencing data analysis. It is commonly used in standard pipelines at sequencing centers. The tool provides computations to assess the quality of sequencing data, such as per base sequence content and per tile sequence quality. It generates HTML reports with…
From 9 patients undergoing hip joint replacement surgery for osteoarthritis, we collected 3 cartilage samples each: a low-grade sample (no obvious evidence of damage or fibrillation); a high-grade sample (damaged and fibrillated cartilage); an osteophytic sample (overlaid bony protrusions mainly around the margins of the articular surface). Multiplexed libraries were sequenced on Illumina HiSeq 2000 (75bp paired-end read length) and a cram file was produced for each sample. This dataset contains all the data available for this study on 2017-06-09.
Dataset Description From 9 patients undergoing hip joint replacement surgery for osteoarthritis, we collected 3 cartilage samples each: a low-grade sample (no obvious evidence of damage or fibrillation); a high-grade sample (damaged and fibrillated cartilage); an osteophytic sample (overlaid bony protrusions mainly around the margins of the articular surface). Multiplexed…
TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells
Animal models Animal studies were approved by the Institutional Animal Care Use Committee of the Institute of Biosciences and Technology, Texas A&M University (AUP 2020-0195). Most mouse strains bear a C57BL/6 genetic background unless otherwise noted. All the animals were housed in a certified animal facility with a standard dark/light…
Effect of Spaceflight and Simulated Microgravity on Plant Defense Responses (Plant Habitat-06)
Upon sample return to Earth, next-generation sequencing is performed to identify genome-wide transcriptional defense responses. In addition, next-generation sequencing is used to examine the transcriptional response to spaceflight in immune-deficient tomatoes. Total RNA is extracted from each sample using TRIZOL. At approximately three-weeks post germination, RNA yields of more than…
Transcriptome analysis of Haemaphysalis flava female using Illumina HiSeq 4000 sequencing: de novo assembly, functional annotation and discovery of SSR markers | Parasites & Vectors
Machado-Ferreira E, Vizzoni VF, Balsemao-Pires E, Moerbeck L, Gazeta GS, Piesman J, et al. Coxiella symbionts are widespread into hard ticks. Parasitol Res. 2016;115:4691–9. doi.org/10.1007/s00436-016-5230-z. Article PubMed Google Scholar Jung M, Kho JW, Lee WG, Roh JY, Lee DH. Seasonal occurrence of Haemaphysalis longicornis (Acari: Ixodidae) and Haemaphysalis flava, vectors…
Genomic Characteristics of Carbapenem-Resistant Klebsiella pneumoniae
Introduction Klebsiella pneumoniae (K. pneumoniae), which belongs to the family Enterobacteriaceae, is a common nosocomial pathogen that causes a variety of human infections, including bloodstream infection, respiratory tract infection, urinary tract infection, and abdominal infection.1,2 Carbapenems are generally considered to be a last choice for the treatment of multi-drug resistant…
OmicsSuite: Tailored Pipeline for Multi-Omics Big Data Analysis
Abstract: With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems, however it is challenging…
The mutational signature of hypertrophic cardiomyopathy
Introduction Hypertrophic cardiomyopathy (HCM), characterized by asymmetric hypertrophy of the ventricular wall, is a condition where the heart becomes thickened without a distinct inducement.1,2 Epidemiological investigation shows that the estimated prevalence rate of HCM in the general population is 1:500.3,4 The clinical manifestations vary greatly, with no symptoms and mild…
New deep screening technique enables rapid discovery of high-affinity antibodies to clinically relevant drug targets
Published on 9 October, 2023 Leveraging next generation sequencing technology, deep screening promises to accelerate antibody discovery for a wide range of targets by generating sequence-function correlation data on an unprecedented scale Deep screening builds upon the HiSeq next generation sequencing platform, where on a microfludic flow cell, billions of DNA…
Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening
Construct design To transcribe and translate sequenced DNA clusters on an Illumina flow cell, our DNA constructs contained the following elements: a P5 adaptor, followed by a 28 nt unique barcode, a 27 nt unstructured spacer (5p UNS v2), a ribosome binding site, start codon, protein coding region, TolAk short linker, 2×…
Phylogenomics reveals the history of host use in mosquitoes
Taxon sampling and specimen collection All samples were collected legally following local requirements and our research complies with all relevant ethical regulations. Insect specimens were received at NC State University’s Insect Museum, pursuant to CITES permit 08US827653 (GRSCICOLL URI: grbio.org/cool/ij62-iybb). Our dataset contains representatives of 268 species from nine tribes,…
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…
Draft genome sequencing of Tilletia caries inciting common bunt of wheat provides pathogenicity-related genes
1Indian Agricultural Research Institute (ICAR), India 2Uttarakhand University of Horticulture and Forestry, India The final, formatted version of the article will be published soon. Notify me Receive an email when it is updated You just subscribed to receive the final version of…
Broken String Biosciences strengthens senior leadership team to accelerate product development and commercialization
Broken String Biosciences (“Broken String”), a genomics company building a technology platform to drive the development of cell and gene therapies that are safer by design, today announced the expansion of its senior leadership team with the appointments of Vincent Smith, Ph.D., as Chief Technology Officer and Jessica Rich as…
Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny
Chloroplast genome features of four Polygonatum species In this phase of our study, we pursued the sequencing of four Polygonatum species namely P. filipes, P. cyrtonema, P. zanlanscianense and P. odoratum, using the Illumina HiSeq 2500 sequencing platform. This endeavour yielded a corpus of Illumina reads ranging from 15,915,998 to…
Purpose, Types, Applications, Bioinformatics and more
Next-Generation Sequencing (NGS), also known as high-throughput sequencing, is a revolutionary technology used for determining the sequence of DNA or RNA molecules. It has significantly advanced the field of genomics and has numerous applications in various biological and medical fields. Key Points of Next-Generation Sequencing (NGS): Revolutionary Technology: NGS represents…
Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease
Samples for H3K27ac ChIP–seq Samples were collected by the GTEx Consortium. The donor enrollment and consent, informed consent approval, histopathological review procedures, and biospecimen procurement methods and fixation were the same as previously described22. No compensation was provided to the families of participants. Massachusetts Institute of Technology Committee on the…
The Genomic Renaissance: Recent Whole Exome Sequencing Market Changes
(MENAFN– EIN Presswire) Whole Exome Sequencing Market Size Exome sequencing is a technique for sequencing all of the exome and protein-coding genes in a genome. PORTLAND, OREGON, UNITED STATES, September 28, 2023 /EINPresswire/ — Allied Market Research added new research on Whole Exome Sequencing Market – Opportunity Analysis and Industry…
DNA Sequencing Instruments Market Size, Share and Forecast 2031
The GlobalDNA Sequencing Instruments Market is poised to value USD 26 billion in 2027 end at a CAGR of 20% during the forecast period 2023 to 2031. DNA Sequencing Instruments Market DNA sequencing has revolutionized the field of genomics, enabling scientists to decode the genetic information present in an organism’s…
Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast
Rubin, S., Parr, T., Da Costa, L. & Friston, K. Future climates: Markov blankets and active inference in the biosphere. J. R. Soc. Interface 17, 20200503 (2020). Article CAS PubMed PubMed Central Google Scholar Cantonati, M. et al. Characteristics, main impacts, and stewardship of natural and artificial freshwater environments: Consequences…
DNA-bridging by an archaeal histone variant via a unique tetramerisation interface
Chromatin isolation and MNase digestion M. jannaschii DSM 2661 cells were grown in 100 l fermenters in minimal medium containing 0.3 mM K2HPO4, 0.4 mM KH2PO4, 3.6 mM KCl, 0.4 M NaCl, 10 mM NaHCO3, 2.5 mM CaCl2, 38 mM MgCl2, 22 mM NH4Cl, 31 µM Fe(NH4)2(SO4)2, 1 mM C6H9NO6, 1.2 µM MgSO4, 0.4 mM CuSO4, 0.3 µM MnSO4, 36 nM FeSO4, 36 nM CoSO4, 3.5 nM…
Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect
Yeast strain and growth conditions S. cerevisiae strain BY4741 was grown in YPD media at 30 °C. Saturated cultures were diluted into 300 ml YPD medium with an optical density at 660 nm (OD660) of approximately 0.1 and then grown at 30°C with shaking at 250 rpm until mid-log phase with an OD660 of…
Association analysis of agronomic traits and construction of genetic networks by resequencing of 306 sugar beet (Beta vulgaris L.) lines
Genome resequencing approach for genotyping 306 sugar beet germplasm resources In this study, we performed high-depth genome-wide resequencing of 306 sugar beet accessions using an Illumina HiSeq 2000 sequencer, obtaining 1977.12 Gb of sequencing data. This collection included 72 endemic accessions from Northeast China (Harbin), 114 endemic accessions from North China…
Illumina: The Measurement Monopoly – by Elliot Hershberg
Welcome to The Century of Biology! This newsletter explores data, companies, and ideas from the frontier of biology. You can subscribe for free to have the next post delivered to your inbox: Enjoy! 🧬 No technology has ever improved more rapidly than DNA sequencing. The resulting explosion of genomic data…
Genome-wide identification of lncRNA & mRNA for T2DM
Department of Biotechnology, College of Science, Taif University, Taif, 21944, Saudi Arabia Correspondence: Sarah Albogami, Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia, Email [email protected] Purpose: According to the World Health Organization, Saudi Arabia ranks seventh worldwide in the number of patients with…
Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety
Study design We set up a prospective, double-blinded, randomised, placebo-controlled intervention study that was performed in our academic hospital, the Amsterdam University Medical Centres location AMC in the Netherlands. After passing screening, 24 subjects with MetSyn were randomised to receive a sterile FFT from a lean healthy donor or a…
RNA-sequencing and bioinformatics analysis | COPD
Introduction COPD, a common preventable and treatable disease characterized by persistent airflow limitation and respiratory symptoms, is associated with exposure to harmful environments. COPD is currently the third leading cause of death globally. The high incidence and mortality of COPD, which seriously threaten human health, represent a public health problem…
DNA Sequencing Services Market: Genomic Discoveries Await, Targeting US$ 2,080.2 Million by 2033
According to FMI’s analysis, the DNA Sequencing Services Market will grow by 8.2% over the forecast period. The industry is expected to grow to a market value of US$ 945.6 million by 2023. Surges in DNA sequencing services are expected to drive industry growth during the assessment period. For example,…
DNA Sequencing Equipment market research report provides critical insights that can help shape business development by providing a CAGR of 7.3% from 2023 to 2030
This “DNA Sequencing Equipment Market” highlights key external drivers that affect the industry and assesses the current performance and revenue growth of the industry. This report helps to collect industry information for target audiences before commencing any advertising campaign. The DNA Sequencing Equipment market is expected to grow annually by…
An analysis of the demand for the Automated DNA Sequencers market, key suppliers, and significant geographic regions from 2023 to 2030, with a projected CAGR of 4.7%, is presented in this report.
This market research report shows the present level and the future prospects of the “Automated DNA Sequencers Market” from 2023 to 2030. This entire report is of 147 pages. The Automated DNA Sequencers market is expected to grow annually by 4.7% (CAGR 2023 – 2030). Automated DNA Sequencers Market Outlook…
One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade
Isolation and microscopy of Mantamonas sphyraenae sp. nov Mantamonas sphyraenae SRT-306 was collected on 26 Sep. 2013 from the surface of a barracuda caught in a lagoon on Iriomote Island, Taketomi, Okinawa Prefecture, Japan (24° 23′ 36.762″ N, 123° 45′ 22.572″ E). It was isolated manually from the rough sample…
Single-cell transcriptomes reveal a molecular link between diabetic kidney and retinal lesions
Animals The animal experiments were approved by the Institutional Animal Care and Use Committee of Jinling Hospital (Nanjing, China), in accordance with the approved guidelines of the Institutional Animal Care and Use Committee of Jinling Hospital. 7 weeks old male wild-type (wt) and leptin receptor-deficient (db/db) mice on the C57BLKS/J…
Functional conservation of microbial communities determines composition predictability in anaerobic digestion
Lin Q, De Vrieze J, Li C, Li J, Li J, Yao M, et al. Temperature regulates deterministic processes and the succession of microbial interactions in anaerobic digestion process. Water Res. 2017;123:134–43. Article CAS PubMed Google Scholar Coban O, De Deyn GB, van der Ploeg M. Soil microbiota as game-changers…
Gut microbial carbohydrate metabolism contributes to insulin resistance
Study participants and data collection The study participants were recruited from 2014 to 2016 during their annual health check-ups at the University of Tokyo Hospital. The individuals included both male and female Japanese individuals aged from 20 to 75 years. The exclusion criteria were as follows: established diagnosis of diabetes,…
Iso-Seq method outperforms other long-read methods in benchmarking consortium study
A benchmarking of long-read RNA sequencing methods and analysis tools The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) consortium, an initiative to systematically evaluate methods for transcript identification and quantification, recently released their final assessment of long-read sequencing technologies and tools in the preprint “Systematic assessment of long-read RNA-seq methods…
DNA Sequencing Services Market is expected to hit US$
NEWARK, Del, Aug. 28, 2023 (GLOBE NEWSWIRE) — The DNA Sequencing Services Market is forecast to experience a growth of 8.2% over the estimated time, as per FMI’s analysis. The industry’s size is predicted to reach a market value of US$ 945.6 million in 2023. Surging advancements in DNA sequencing services…
The Key to Unlocking Our Genetic Heritage
Exploring the Future: DNA Sequencing Technologies and Our Genetic Heritage DNA sequencing technologies are revolutionizing our understanding of the human genome, offering unprecedented insights into our genetic heritage and potential. These technologies, which decode the order of nucleotides in a DNA molecule, are unlocking the secrets of our genetic makeup,…
A highly efficient scheme for library preparation from single-stranded DNA
Vector construction The gene encoding VTopoI (GenBank: L13447.1) was synthesized by Eurofins Genomics Inc (Tokyo, Japan), with codon optimization for Escherichia coli K-12, exclusion of internal BamHI and EcoRI sites, and their inclusion at the 5′- and 3′-ends of the DNA, respectively (Supplementary Sequences). The BamHI-EcoRI fragment of the gene…
FastQC duplicates questions
FastQC duplicates questions 0 Hi all, I’m trying to analyze a quality of some open RNA-seq data from the granulosa cells, and I’m dealing with some weird QC problems in 2 separate study data. Study 1 : a lot of duplicate reads with the polyT overrepresented sequence (sample treatment: RNA-seq…
Platelet factors attenuate inflammation and rescue cognition in ageing
Animal models The C57BL/6 mouse line was used for all of the experiments (The Jackson Laboratory and National Institutes of Aging). Homozygous Pf4-KO mice were previously generated and characterized as described48. Pf4-KO mice were a gift from M. Anna Kowalska. Heterozygous mice were bred to generate Pf4-KO and WT littermate…
Metagenomes Assembles Genomes from cultivated freshwater bacterial communities
This dataset represents 122 Metagenomes-Assembled Genomes (MAGs) that were reconstructed from 20 individual microcosms in the context of understanding microbial community assembly processes. The cultivation media consisted in Artificial Lake Water (ALW) enriched with glucose and cellobiose (See details in Le Moigne et al., 2023, Ecology). The microcosms (200 mL)…
AAV-mediated base-editing therapy ameliorates the disease phenotypes in a mouse model of retinitis pigmentosa
Ethics statement This study did not involve human data. All animal procedures were approved by the Institutional Review Board of Shanghai Jiao Tong University and were conducted in accordance with the Association for Research in Vision and Ophthalmology Statement for the Use of Animals in Ophthalmic and Visual Research. Animals…
Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica
Genome assembly, annotation, and overview We assembled a chromosome-scale genome of a GS E. indica plant using PacBio Sequel II and long-range interaction (Hi-C) datasets. The assembly consists of nine chromosomes spanning 509,878,742 base pairs estimated to be ~97.8% complete by Benchmarking Universal Single-Copy Orthologs (BUSCO)28 analysis with an LTR…
DNA Sequencing Services Market Set
DNA Sequencing Services Market According to FMI’s analysis, the DNA Sequencing Services Market will grow by 8.2% over the forecast period. The industry is expected to grow to a market value of US$ 945.6 million by 2023. Surges in DNA sequencing services are expected to drive industry growth during the…
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE? 2 Hey namhaesly, You need to create segmentation files for your data. You can use VarScan2 (the copynumber) function, or any other program that computes copy number information. My tool of choice is ExomeCNV though I don’t…
Evolutionary genomics of camouflage innovation in the orchid mantis
Sample collection Captive breeding individuals of H. coronatus (Mantodea, Hymenopodidae) hatched from the same ootheca that was collected from the Xishuangbanna rainforest, Yunnan Province, China in 2018. Individuals of D. lobata (Mantodea, Deroplatyidae) were collected from a captive breeding center in Beijing, China in 2018. All individuals were housed in semitransparent…
Ngs-Based Rna-Sequencing Market Size & Share Analysis – Growth Trends & Forecasts (2023 – 2028)
(MENAFN– GlobeNewsWire – Nasdaq) New York, Aug. 09, 2023 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “NGS-Based RNA-Sequencing Market Size & Share Analysis – Growth Trends & Forecasts (2023 – 2028)” – The NGS-Based RNA-Sequencing Market size is expected to grow from USD 3.09 billion in 2023…
MPs | Free Full-Text | Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies
1. Introduction Microbiota are found in many habitats but are poorly characterized due to a high proportion of unnamed species-level taxa [1,2]. However, the human oral bacterial community is relatively well characterized at the species level and boasts many types of microbiota. In fact, the oral cavity is second only…
RNA Sequencing- Definition, Principle, Steps, Types, Uses
RNA sequencing is the molecular technique used to identify the order of nucleotide bases (adenine, uracil, guanine, and cytosine) in an RNA molecule. RNA sequencing (RNA-Seq) is a newly developed next-generation sequencing approach to the transcriptome (a complete set of RNA content within a cell including both coding and non-coding…
Whole genomic analysis of Mycobacterium tuberculosis
Introduction Tuberculosis (TB), caused by etiological Mycobacterium tuberculosis (Mtb), remains a public health worldwide and the leading cause of death from a single infectious agent until the COVID-19 pandemic.1 Previous studies revealed that M. tuberculosis originated in Africa and spread with human migration worldwide, it developed to a contemporary phylogeny…
An electrogenetic interface to program mammalian gene expression by direct current
Key plasmids used in this study Construction details for all vectors are provided in Supplementary Table 1. Key plasmids included (1) a constitutive KEAP1 expression vector (pJH1004, PhCMV-KEAP1-pA) and the corresponding vector containing inverted terminal repeats (ITRs) of Sleeping Beauty (SB) transposase (pJH1054, ITR-PhCMV-KEAP1-P2A-BlastR-pA-ITR) for stable cell line generation; (2)…
A diverse ancestrally-matched reference panel increases genotype imputation accuracy in a underrepresented population
In the present study, we enrolled 412 participants from the Southeast Asian Brugada syndrome cohort (ClinicalTrials.gov number, NCT04232787). The study was approved by the Institutional Review Board (IRB) of the Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (IRB No. 431/58). All methods were performed in accordance with relevant guidelines/regulations. Informed…
Bacterial Genome Sequencing in Bengaluru
Bacterial Genome Sequencing in Bengaluru | ID: 23080056348 Product Specification Service Location Bangalore Minimum Order Quantity 1 Product Description Preparation of gDNA Library, 2×150 PEIllumina Hiseq sequencing to generate 1GBData. Additional Information Item Code 9992 Delivery Time 5-7 days Interested in this service?Get Latest Price from the seller Contact Seller…
Rapid gene content turnover on the germline-restricted chromosome in songbirds
This work was carried out in accordance with ethical animal research requirements of Poland according to Polish law (the Act On the Protection of Animals used for Scientific or Educational Purposes, 15.01.2015, item 266, implementing Directive 2010/63/EU of the European Parliament and of the European Council of 22.09.2010). Experiments on…
On-Demand DNA Synthesis in High Demand
The state of DNA synthesis is a bit like humanity’s journey to the moon—just because something has been achieved before doesn’t mean we should cease figuring out how to do it better.” That is how Harold P. de Vladar, CEO and founder of long-synthetic DNA service provider Ribbon Biolabs, sees…
Illumina short-read genome sequencing of knockout mutants in Streptococcus suis strain P1/7 constructed using pSStarget, a novel plasmid-based CRISPR/Cas9 genome editing system
Description: This dataset contains sequencing reads of the wild type strain S. suis P1/7 and two knockout mutants constructed using a novel CRISPR-Cas9 genome editing system for S. suis. Our data shows that our laboratory stock of strain P1/7 has 2 SNPs and one 5bp deletion relative to the reference…
Agrigenomics Market Is Booming Worldwide : Illumina, LGC, Eurofins USA
This press release was orginally distributed by SBWire NJ New Jersey, USA — (SBWIRE) — 07/25/2023 — Advance Market Analytics added research publication document on Worldwide Agrigenomics Market breaking major business segments and highlighting wider level geographies to get deep dive analysis on market data. The study is a perfect…
RARRES2 regulates lipid metabolic reprogramming to mediate the development of brain metastasis in triple negative breast cancer | Military Medical Research
Tumor samples from patients Biopsies of primary breast tumors and breast tumors that had metastasized to the brain were obtained from patients with TNBC at the National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital of the Chinese Academy of Medical Sciences and Peking Union Medical College. Single-cell RNA sequencing…
Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodeling
Coil implantation in fetal lambs We have complied with all relevant ethical regulations for animal testing. All procedures followed the Canadian Council on Animal Care guidelines and were approved by the University of Western Ontario Council on Animal Care (protocol 2010-257). Time-dated pregnant Dorset × Rideau Arcott ewes (gestational age 76 days,…
Upcycling rice yield trial data using a weather-driven crop growth model
Phenotype data We obtained yield datasets for rice (Oryza sativa L.) from 207,331 trials with 8524 cultivars during the 38 years from 1980 to 2017. The data were obtained from field trials at 110 public agricultural experimental stations in Japan conducted by the Institute of Crop Science of the National…
Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
Ethics We confirm our research complies with all relevant ethical regulations and was approved by the animal ethics committee of the School of Biology at the University of St Andrews on 26 July 2018 www.st-andrews.ac.uk/research/environment/committees/awerb/. The three new contemporary dolphin samples analysed in this study were collected under the relevant…
Acquisition, co-option, and duplication of the rtx toxin system and the emergence of virulence in Kingella
A common ancestor of pathogenic Kingella species acquired the RTX toxin Consistent with existing literature, when the five Kingella species were assessed for β-hemolysis on BHI plates supplemented with 10% sheep blood, only K. kingae and K. negevensis were hemolytic (Fig. 1A), suggesting that the two pathogenic Kingella species produce the…
A framework for individualized splice-switching oligonucleotide therapy
Patients The WGS and clinical data of 235 patients with A-T were provided by the Global A-T Family Data Platform of ATCP. Our access to the data was approved by the Data Access Committee of ATCP. Selected patients with A-T enrolled at the Manton Center for Orphan Disease Research under…
ResR/McdR-regulated protein translation machinery contributes to drug resilience in Mycobacterium tuberculosis
Bacterial strains and culture conditions Escherichia coli strain DH5α (Thermo Fisher) was used for the propagation of plasmids, whereas E. coli BL21 DE3 (Novagen) was used for the expression and purification of ResR/McdR protein. Mtb Erdman was obtained from Dr. Ramandeep Singh at THSTI, India, and Mtb H37Rv mc2 790242…
Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group
Isolate storage, growth, and identification Historical BFG isolates originally cultured from clinical material between 1973 and 2018 were stored either lyophilized or frozen in skim milk media at the National Institutes of Health Clinical Center Department of Laboratory Medicine (Bethesda, MD). Isolates were de-identified and metadata including year and source/site…
hypervariable region of 16s rrna
The mock community was created from pure cultures, whose 16S rRNA genes were determined through Sanger sequencing to be >3% different (Table S1). Bartram, Andrea. WebWhile 16S hypervariable region analysis is a powerful tool for bacterial taxonomic studies, it struggles to differentiate between closely related species. Limited by sequencing Rarefaction…
First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome [PeerJ]
Introduction Vultures are obligate scavengers, birds of prey that provide several ecological services such as nutrient recycling or avoiding soil contamination by carcass feeding, which help to reduce the spread of diseases in their habitats (Ogada, Keesing & Virani, 2012; Chung et al., 2015; Buechley & Şekercioğlu, 2016). Vultures are…
bbmap split paired-end reads back into separated fastq files?
bbmap split paired-end reads back into separated fastq files? 1 Hi, I am trying to remove human reads from my metagenomic sequences (skin samples). I have used the command recommended in the bbmap documentation: bbmap.sh minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/path/to/hg19masked/ qtrim=rl trimq=10 untrim -ea -Xmx100g in=reads.fq outu=clean.fq…
Mitochondrial DNA is a target of HBV integration
Patients Tumour tissues from seven HBsAg-positive patients (6 men, 1 woman; mean age 66.7 ± 8 years) with HBV-related HCC and paired adjacent non-tumour tissues from six of them were studied. The clinical, histological, and virologic characteristics of the patients are summarised in Table 1. Two normal liver samples from HBV-negative patients who…
The performance of whole genome bisulfite sequencing on DNBSEQ-Tx platform examined by different library preparation strategies
Background: Whole-genome bisulfite sequencing (WGBS) technology can provide comprehensive DNA methylation at a single-base resolution on a genome-wide scale, and is considered to be the gold standard for the detection of 5-methylcytosine (5 mC). However, the International Human Epigenome Consortium propose a full DNA methylome should have at least 30…