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Tag: Chromium
Problems rendering a quarto qmd file through jupyter in VS Code – JupyterHub
bj631 January 19, 2024, 10:45pm 1 I’m trying to preview a .qmd file using quarto with jupyter in VS Code. There is a little banner in the bottom right corner that shows up when trying to render the .qmd that says ” command ‘quarto.preview’ not found “. It is a…
Unravelling cell type-specific responses to Parkinson’s Disease at single cell resolution | Molecular Neurodegeneration
Single nucleus RNA-seq reveals cell type heterogeneity in human SNpc We sampled SNpc from post-mortem human brains of 15 sporadic Parkinson’s disease (PD) patients and 14 Control individuals (see Supplementary Table 1 for full pathology reports). Using a 10X Genomics Chromium platform, we performed single nucleus RNA-seq (snRNA-seq) on more than…
State-of-the-art genomic services facility coming to the UK
Scheduled to open in early 2024, Azenta Life Sciences will be locating its GENEWIZ Multiomics and Synthesis Solutions site in Oxford, UK. Drawing upon the experienced team from the former Oxford Genomics Centre (OGC), the new Oxford Genomics Lab will provide fast and reliable genomics services from GENEWIZ to support…
Single-cell RNA-seq workflow
In this tutorial we walk through a typical single-cell RNA-seq analysis using Bioconductor packages. We will try to cover data from different protocols, but some of the EDA/QC steps will be focused on the 10X Genomics Chromium protocol. We start from the output of the Cell Ranger preprocessing software. This…
Arsenic is a potent co-mutagen of ultraviolet light
Barnes, J. L., Zubair, M., John, K., Poirier, M. C. & Martin, F. L. Carcinogens and DNA damage. Biochem. Soc. Trans. 46, 1213–1224 (2018). Article CAS PubMed PubMed Central Google Scholar Ames, B. N., Durston, W. E., Yamasaki, E. & Lee, F. D. Carcinogens are mutagens: a simple test system…
Top 7 Best Fat Burners South Africa
Women have different fat storage patterns than men, so it makes sense that a woman should choose a female fat burner, a supplement that is made for a woman’s fat loss needs. This article gives you information about the 5 best fat burning supplements for women that you can buy…
A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
Animals All experimental procedures were performed in compliance with animal protocols approved by the Institutional Animal Care and Use Committee at Boston Children’s Hospital (Protocol no. 20-05-4165 R). Mice were provided with food and water ad libitum, housed on a 12-hour light/dark schedule (7 a.m.–7 p.m. light period) with no more than five mice…
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Mouse breeding and husbandry All experimental procedures related to the use of mice were approved by the Institutional Animal Care and Use Committee of the AIBS, in accordance with NIH guidelines. Mice were housed in a room with temperature (21–22 °C) and humidity (40–51%) control within the vivarium of the AIBS…
Conserved and divergent gene regulatory programs of the mammalian neocortex
Nucleus preparation from frozen brain tissue for Chromium single-cell multiome ATAC and gene expression analysis M1 tissue was obtained from three human donors (male, aged 42, 29 and 58 years), three macaque donors (male, aged 6 (Macaca mulatta), 6 (M. mulatta) and 14 (Macaca fascicularis) years), three marmoset (Callithrix jacchus)…
Capsiplex Trim Reviews – Will It Make You Stronger?
Capsiplex Trim is a supplement designed exclusively for women to enhance the full athletic performance of the female body. Per the company’s official website, Capsiplex Trim is one of the advanced fat-burning formulas for women. You may come across many Capsiplex Trim reviews by now. If you are wondering why…
Indigenous Australian genomes show deep structure and rich novel variation
Inclusion and ethics The DNA samples analysed in this project form part of a collection of biospecimens, including historically collected samples, maintained under Indigenous governance by the NCIG11 at the John Curtin School of Medical Research at the Australian National University (ANU). NCIG, a statutory body within ANU, was founded…
GlucoTrim Reviews – Should You Buy? Ingredients That Work or Fake Gluco Trim Pills?
Obesity has been a heated topic in recent years, as the statistics suggest that it is the world’s leading cause of death, brought on by the likes of diabetes, heart disease, stroke, and possible cancers. Naturally, so much money is being invested in this research area to tame the risk…
GlucoTrim Reviews – Is It Legit? Negative Gluco Trim Customer Complaints Examined!
Are you struggling with pre-diabetes or type-2 diabetes and want to take charge of your blood sugar health? Introducing GlucoTrim, a supplement that stabilizes your blood sugar levels without painful injections or side effects. It promotes healthy metabolism, supports weight management, and promotes vitality. A detailed GlucoTrim review will help…
Gluco Trim Reviews – Does It Work? GlucoTrim Official Website Investigation
Gluco Trim is a blood sugar support supplement created by an ex-pharma scientist. Marketed as an alternative to Ozempic, Gluco Trim purportedly “slashes high blood sugar numbers and burns fat” without injections, prescriptions, or expensive drugs. Does Gluco Trim work? How does Gluco Trim mimic the effects of Ozempic? Please…
GlucoTrim Reviews – Scam or Safe Gluco Trim Glucose Modulator Formula for High Blood Sugar?
One of the biggest viral trends of 2023 was women displaying their weight loss results with Ozempic on TikTok. If you aren’t up to speed, Ozempic is Eli Lilly’s new “wonder drug” that promises to make fat people thin again. While the marketing is great, the reality of using the…
Optimal Fat Sugar Trim Formula
Learn About Turn Fats and Sugars into Useful Energy Metabolic Machine Uses lipase, a patented form of chromium, rosemary, and other herbs to help metabolize fat and sugar as energy. Stop the Spikes Contains ingredients specifically tailored to lower and stabilize blood sugar levels. Break it Down Properly breaks down…
Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cell Ranger.
Looks like 10x has example datasets on their web site. Will take a look to see what these BC sequences look in reality. Should be possible to bin them using seal.sh from BBMap. Edit: From one of the test datasets it is possible to see these BC barcodes in Read…
Greenphire, Florence Healthcare Team Up; Illumina Partnerships; Oxford Nanopore Develops New Data Technology
November 29, 2023 | Greenphire and Florence Healthcare announce a technology partnership; Illumina and Veracyte join together in a multi-year agreement; Oxford Nanopore Technologies collaborates with Fabric Genomics and Saphetor to develop data technology for research; more. Greenphire and Florence Healthcare announced a technology partnership that integrates two of the…
Reviewing Revvity (NYSE:RVTY) and 10x Genomics (NASDAQ:TXG)
10x Genomics (NASDAQ:TXG – Get Free Report) and Revvity (NYSE:RVTY – Get Free Report) are both medical companies, but which is the better investment? We will contrast the two companies based on the strength of their dividends, risk, analyst recommendations, valuation, institutional ownership, profitability and earnings. Volatility and Risk 10x…
Senior Research Technician (Fixed Term) at University of Cambridge
We are seeking to recruit a Senior Research Technician to join us at the Genomics & Bioinformatics Core (GBC) at Wellcome-MRC Institute of Metabolic Science. This is an exciting opportunity for someone who is passionate about genomics, next-generation (high-throughput) DNA sequencing and laboratory automation The GBC has, over the last…
Elevated stress response marks deeply quiescent reserve cells of gastric chief cells
Generation of inducible H2b-GFP knock-in mice Generation of inducible H2b-GFP knock-in mice was performed by using CRISPR/Cas943. In brief, a mixture containing a sgRosa26-1 crRNA43 (8.7 ng/μl, Fasmac, Japan), a tracrRNA (14.3 ng/μl, Fasmac, Japan), a single strand oligo donor nucleotide (ssODN) composed of 5′ arm, adenovirus splicing acceptor, SV40 pA, TRE3G…
Insects | Free Full-Text | Novel Insights into the circRNA-Modulated Developmental Mechanism of Western Honey Bee Larval Guts
1. Introduction As a representative social insect with crucial ecological, economic and scientific value, the western honey bee (Apis mellifera) is widely reared and applied in the apicultural industry in considerable countries around the world [1]. In addition, A. mellifera has been applied as a research model for development, social…
visual studio code – JupyterHub vscode extension Error: Unable to determine base url of Jupyter Hub Server
I want to access jupyterHub from my vscode. I have my URL like this: <my-hub-url>/user/<my-hub-user-name>/?token=<my-token>. This URL works just fine in Chrome if I click on it and the connection between VSCode & the hub is also working using other computer but on mine computer I got : Here are…
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer
Mice The research conducted in this study complied with all of the relevant ethical regulations. The animal protocols were approved by and performed in accordance with the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. C57BL/6, OT-I50, pmel51 and Rosa26-Cas9 knock-in52 mice were purchased from The…
5 Best Genome Sequencing Companies
The Genomic And Multi-omic Revolution The first human genome decoding started in 1990 and was first achieved in 2003. It also cost a staggering $3B. Fast forward 20 years, and the cost of genome sequencing has fallen to $600/genome. Or a 5,000,000x reduction in cost! And it could fall to…
Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer | Military Medical Research
Zhu J, Ke Y, Liu Q, Yang J, Liu F, Xu R, et al. Engineered Lactococcus lactis secreting Flt3L and OX40 ligand for in situ vaccination-based cancer immunotherapy. Nat Commun. 2022;13(1):7466. Article CAS PubMed PubMed Central Google Scholar Evans ER, Bugga P, Asthana V, Drezek R. Metallic nanoparticles for cancer…
Proteintech Genomics Launches First Commercially Available Solution for the Detection of Intracellular Proteins for Single-Cell RNAseq Experiments
SAN DIEGO–(BUSINESS WIRE)– Proteintech Genomics, a subsidiary of Proteintech Group, Inc., and a provider of multiomic solutions for single-cell and spatial analysis, announced the launch of the MultiPro™ Human Fixed Cell Immune Profiling Antibody Cocktail. This cocktail contains 53 antibodies against intracellular and cell surface proteins, plus 5 isotype controls….
Single-cell transcriptomics reveals the brain evolution of web-building spiders
Animals for single-cell sequencing Adult samples of the aerial web-building spider (Hylyphantes graminicola) were collected from Anci district, Langfang, Hebei, China (39° 31.90’ N, 116° 38.15’ E) between September and October 2020. Collected spiders used for brain dissection were housed individually in a glass tube (Φ12 mm × 80 mm) at temperature- and humidity-controlled condition (24–26 °C and 50–60%…
Jupyterhub with AzureAD – JupyterHub
Hello, I’m trying to create docker image with azure ad login im able to login with my account after login in webpage i get Unhandled error starting server Username You can try restarting your server from the [home page]( Log D 2023-11-01 14:34:46.657 JupyterHub base:961] Initiating spawn for USER.Ext [D…
Epigenetic regulation during cancer transitions across 11 tumour types
Specimen data All samples for MM, OV, BRCA, PDAC, UCEC, CRC, CESC/AD, SKCM and HNSCC, as well as 2 NATs for GBM and 1 NAT for ccRCC were collected with informed consent in concordance with Institutional Review Board (IRB) approval at the School of Medicine at Washington University in St…
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…
DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages
Parasite culture, maintenance, synchronization and transfection The DiCre-expressing P. falciparum clone II3 (ref. 10) was maintained in human A+ erythrocytes at 37 °C in Roswell Park Memorial Institute 1640 medium containing AlbumaxII (Invitrogen) supplemented with 2 mM l-glutamine. Parasites were either synchronized by sorbitol treatment or by purifying mature schizont stages using…
Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility
Abstract Shotgun metagenomes is a repository of all the genes present in an environmental sample. With recent advancements in bioinformatic techniques, it is now possible to in-silico retrieve sequences that belong to specific taxa, followed by assembly and annotation and the obtained sequences are called as metagenome-assembled genome (MAG), which…
Comment: Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cel
I was only referring to `mkfastq` part to demultiplex the samples (step 1 in the process). Going by this line in link above > but the 10x Sample Index name (i.e. SI-TS-A1) is needed for > demultiplexing sequencing runs when running more than one sample per > lane. The relevant…
Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice
Mouse strains All mouse procedures were approved by the Institutional Animal Care and Use Committees at Binghamton or Stanford University; and were conducted in accordance with the National Institute of Health Guide for Care and Use of Laboratory Animals, Eighth Edition. All mice were originally obtained from Jackson Laboratories, and…
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…
Apoptotic stress causes mtDNA release during senescence and drives the SASP
Cell culture and treatments Human embryonic lung MRC5 fibroblasts (ATCC) and IMR90 fibroblasts (ATCC) were grown in Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, D5796) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U ml−1 penicillin, 100 μg ml−1 streptomycin and 2 mM l-glutamine and maintained at 37 °C under 5% CO2. MRC5 fibroblasts were cultured in…
AMD acquires open-source AI software developer Nod.ai
Advanced Micro Devices Inc. today announced that it has acquired Nod.ai, a startup that develops open-source software for speeding up artificial intelligence models, for undisclosed financial terms. Nod.ai, officially Nod Inc., is the developer of an open-source AI tool called SHARK. It’s a so-called runtime system designed to increase the…
Create seurat inputs without cellranger
Create seurat inputs without cellranger 1 “Hey there! I’m really curious about creating Seurat inputs without using Cell Ranger, as we’ve got our own sequencer and have done the sequencing in-house. Has anyone else tried this approach or can offer some guidance on how to go about it? Any help…
INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution
Anderson, N. M. & Simon, M. C. The tumor microenvironment. Curr. Biol. 30, R921–R925 (2020). Article CAS PubMed PubMed Central Google Scholar Kostic, A. D. et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14, 207–215 (2013). Article CAS PubMed PubMed Central Google Scholar …
Associate DSI device lifetime with auxiliary device
[PATCH] drm/bridge: ti-sn65dsi86: Associate DSI device lifetime with auxiliary device * [PATCH] drm/bridge: ti-sn65dsi86: Associate DSI device lifetime with auxiliary device @ 2023-10-02 23:54 ` Stephen Boyd 0 siblings, 0 replies; 4+ messages in thread From: Stephen Boyd @ 2023-10-02 23:54 UTC (permalink / raw) To: Andrzej Hajda, Neil Armstrong,…
Is APAC Edging Closer to Clinical Application of Single-cell Tech?
Asia Pacific (APAC) is expected to be a major contributor to the growth of single cell technology as the market is driven by factors such as the growing demand for personalised medicine, advancements in sequencing technologies, and the increasing use of single cell analysis in drug discovery. While Japan is…
Do you wonder what 10X data looks like on the newest Illumina sequencer?
in Industry News, Information 18 hours ago 626 Views Single-cell analysis can help tease apart heterogeneity in complex cell populations, distinguishing cell types and revealing dynamic cell states. The 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression prepares sequencing-ready libraries to simultaneously profile gene expression and chromatin accessibility from the…
Chan Zuckerberg Life Sciences Computing System, Microsoft and Paige AI Partnership, Rehm Takes Chair of GA4GH
September 28, 2023 | Paige and Microsoft aim to build the world’s largest image-based AI models for digital pathology and oncology; Flatiron Health and FDA partner; HHS extends partnership with Regeneron; the GA4GH Board of Directors has elected Heidi Rehm to succeed Ewan Birney; and more. Paige has joined forces…
Transcriptional linkage analysis with in vivo AAV-Perturb-seq
Experimental procedures Plasmid design and cloning AAV genome plasmids (Fig. 1a and Extended Data Figs. 1a,g,h and 5a) were based on Addgene plasmid 60231 (ref. 12). To achieve widespread transgene expression, the hSyn promoter was replaced by the ubiquitous CBh promoter (pAS088). For the triple-colour experiments (Extended Data Fig. 1a),…
Node.js 2023 Edition Available
The Node.js team has recently released version 20.6.0, which brings improvements in environment variable configuration, module resolution, module customization, and experimental support for C++ garbage collection. In this patch, developers gain a new feature: built-in support for `.env` files. These files, following the INI file format, offer a simplified approach…
Genome of the southern giant petrel assembled using third-generation dna sequencing and linked reads reveals evolutionary traits of southern avian
@article{35c896a0cb2a48eab59dd587594ac6d2, title = “Genome of the southern giant petrel assembled using third-generation dna sequencing and linked reads reveals evolutionary traits of southern avian”, abstract = “The southern giant petrel Macronectes giganteus, a large seabird of the southern oceans, is one of only two members of the genus Macronectes and is…
Bioconductor – WeberDivechaLCdata
DOI: 10.18129/B9.bioc.WeberDivechaLCdata This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see WeberDivechaLCdata. Spatially-resolved transcriptomics and single-nucleus RNA-sequencing data from the locus coeruleus (LC) in postmortem human brain samples Bioconductor version: 3.16 Spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from the locus coeruleus…
Single-cell brain organoid screening identifies developmental defects in autism
Stem cell and cerebral organoid culture conditions Feeder-free hES cells or iPS cells were cultured on hES cell-qualified Matrigel (Corning, catalogue no. 354277)-coated plates with Essential8 stem cell medium supplemented with bovine serum albumin (BSA). H9 embryonic stem cells were obtained from WiCell. Cells were maintained in a 5% CO2 incubator at 37 °C….
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…
Symmetric inheritance of parental histones governs epigenome maintenance and embryonic stem cell identity
The research in this study was conducted under the ethical approval of the Danish Regulatory Authority under project license 2018-15-0201-01520. Cell culture and differentiation assays WT, MCM2-2A, MCM2-R and POLE4-KO mouse ESCs used in this study were derived from the male, E14JU cell line with a 129/Ola background81. Genome editing…
Mission Accomplished, India Puts Moon Rover to ‘Sleep’ for 14 Days
To complete one full rotation around its axis it takes the moon 655 hours. So a single “lunar day” is 13.64 earth days. But sunset has finally come for India’s Chandrayaan-3 spacecraft and its Pragyan rover, writes long-time Slashdot reader Geoffrey.landis , and the rover has switched off for the…
Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution
Consensus MTG taxonomy across primates The BRAIN Initiative Cell Census Network26 generated high-resolution transcriptomic maps of the MTG in human, chimpanzee, gorilla, macaque and marmoset by applying single-nucleus transcriptomic (snRNA-seq) assays to samples isolated from between three and seven donor brains in each species (plate-based SMART-seq v4 (SSv4) for great…
Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection
Bacterial strains and growth conditions for eBW1 B. subtilis 168 and E. coli (MG1655) were streaked out from a frozen glycerol stock onto an LB plate and grown overnight at 37 °C. Following a night of growth, a single colony was picked and inoculated into 5 ml of LB broth and grown…
Postdoctoral Research Associate in Bioinformatics – University of Oxford – job portal
UK date and time: 29-August-2023 17:47   Applicant Options New Search Login Job Details Help Terms of Use & Privacy Policy   Job Details Postdoctoral Research Associate in Bioinformatics Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, Roosevelt Drive, Headington, Oxford OX3 7FY. The Kennedy Institute…
Non-cell-autonomous cancer progression from chromosomal instability
Cell culture IMR90, 4T1, CT26, RAW264.7 and B16F10 cell lines were purchased from the American Type Culture Collection and cultured in MEM (IMR90), DMEM (B16F10, RAW264.7) or RPMI (4T1, IMR90, CT26) supplemented with 10% FBS in the presence of penicillin (50 U ml−1) and streptomycin (50 μg ml−1). All cells were found to be…
Creating custom GTF file for use with Cellranger with barcode sequences
Creating custom GTF file for use with Cellranger with barcode sequences 0 Hello all I am working with 3′ single cell expression data that has been generated on the 10x Chromium platform. The starting material is human cells that have been labeled with an RFP expressing lentiviral vector which also…
Transient naive reprogramming corrects hiPS cells functionally and epigenetically
Cell culture All cell lines used and derived by different approaches in this study are listed in Supplementary Table 1. Detailed information about the experimental design, materials and reagents is presented in the Reporting Summary. Primary human adult dermal fibroblasts (HDFa) from three different female donors were obtained from Gibco…
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…
Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers
Pan-cancer WGS data sources GrCh37/hg19 BAM alignments for 2,489 primary tumour and matched normal whole-genome sequencing data were obtained as previously described18. In brief, 989 tumour–normal (T/N) pairs were obtained from The Cancer Genome Atlas (TCGA) Research Network (Genomic Data Commons at portal.gdc.cancer.gov/, accession: phs000178.v11.p8). Additional WGS data were obtained for 874 T/N pairs…
In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis
Mouse models C57BL/6J (strain 000664, The Jackson Laboratory) and B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*/-EGFP)Fezh/J (strain no. 026179, The Jackson Laboratory) were used for all experimental procedures. The Npm1c/Flt3-ITD/Cas9 model has been extensively described previously31,57,58. The maximal tumor size allowed by the Home Office license for this project and authorized by the Animal Welfare Ethical…
Comparative analysis of carbapenem-resistant K. pneumoniae
Introduction The worldwide spread of Klebsiella pneumoniae is a major global public health threat.1,2 K. pneumoniae is an opportunistic pathogen that colonizes the human gut and respiratory tract and possibly causes infection in immunocompromised hosts. Gut colonized K. pneumoniae is one of the important pathogens causing nosocomial infections, although the…
Dissecting human population variation in single-cell responses to SARS-CoV-2
Sample collection The individuals of self-reported African (AFB) and European (EUB) descent studied are part of the EVOIMMUNOPOP cohort18. In brief, 390 healthy male donors (188 AFB and 202 EUB) were recruited between 2012 and 2013 in Ghent (Belgium), thus, before the COVID-19 pandemic. Blood was obtained from the healthy…
Cas9-mediated knockout of Ndrg2 enhances the regenerative potential of dendritic cells for wound healing
Ndrg2 expression is reduced in tolerogenic DCs To identify potential targets for gene editing in DCs, we compared transcriptomic profiles of treatment induced tolerogenic DCs, which confer a variety of clinical benefits11,12,13,14,15,16,17 with untreated DCs. Bone marrow-derived DCs were cultivated from wild-type (WT) mice (C57/BL6) according to standard protocols25. Vitamin…
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,…
Organization of the human intestine at single-cell resolution
Tissue collection and processing This study complies with all relevant ethical regulations and was approved by the Washington University Institutional Review Board and the Stanford University Institutional Review Board. Human bowel tissues were procured from deceased organ donors. Written informed consent was obtained from the next-of-kin for all donor participants….
4.0.1: context menu for notebook tabs not working – JupyterHub
Hi,I was sent here by the bot after it closed my bug report as being a support request… This is a GUI bug in 4.0.1 which does not exist in 3.x, so I’m not sure why it is considered not a bug report, but anwyay, here it is Right-clicking on…
CIMB | Free Full-Text | A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseumonadota
1. Introduction One characteristic of many geothermal fields is the presence of steam vents, i.e., fumaroles, that consist of permanent emissions of steam and gases from the subsoil due to magmatic activity or groundwater geothermal heating [1]. Consequently, the steam has temperatures above 70 °C, wet conditions, and a concentration…
Spatially resolved multiomics of human cardiac niches
Research ethics for donor tissues All heart tissue samples were obtained from transplant donors after Research Ethics Committee approval and written informed consent from donor families as previously described2. The following ethics approvals for donors of additional heart tissue were obtained: D8 and A61 (REC reference 15/EE/0152, East of England…
CAR T-Cell Study Enabled by 10x Genomics Single Cell Technology Published in Nature Medicine
Data Uncovers New Gene Signature to Help Understand Persistence in CAR T-cells PLEASANTON, Calif., July 5, 2023 /PRNewswire/ — 10x Genomics, Inc. (Nasdaq: TXG), a leader in single cell and spatial biology, announced today that its single-cell genomic technologies were used in a study published in the journal Nature Medicine…
Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development
BACKGROUND Accumulating evidence suggests that the maxillary process, to which cranial crest cells migrate, is essential to tooth development. Emerging studies indicate that Cd271 plays an essential role in odontogenesis. However, the underlying mechanisms have yet to be elucidated. AIM To establish the functionally heterogeneous population in the maxillary process,…
LKML: Benjamin Bara: Re: [PATCH v2 1/3] usb: misc: onboard-hub: support multiple power supplies
From Benjamin Bara <> Subject Re: [PATCH v2 1/3] usb: misc: onboard-hub: support multiple power supplies Date Wed, 21 Jun 2023 17:45:05 +0200 Hi,thanks for the feedback!On Wed, 21 Jun 2023 at 16:57, Matthias Kaehlcke <mka@chromium.org> wrote:> On Wed, Jun 21, 2023 at 04:26:27PM +0200, Benjamin Bara wrote:> > +…
Adipogenic and SWAT cells separate from a common progenitor in human brown and white adipose depots
Human samples Human adipogenic progenitor cells were isolated from the stromal vascular fraction of adipose tissue samples on the day they were obtained (surgery or biopsy) from four regions: (1) visceral adipose tissue (obtained during gallbladder surgery); (2) perirenal adipose tissue (obtained during nephrectomy surgery); (3) abdominal subcutaneous adipose tissue…
Allow the video BIOS to work in SPL with QEMU
QEMU emulates two common machines (Q35 and i440fx) which use mapping to determine whether RAM is present below 1MB. In order to copy the video BIOS to c0000 we need to flip this mapping over to RAM. This does not happen automatically until SPL has finished running. Switch in RAM…
10x Genomics Stock: The Illumina of Single-Cell Analysis?
The United States is famously the most litigious society in the world. One statistic we’ve come across is that the country spends about $310 billion a year on litigation. One particularly well-known American has been involved in some 3,500 lawsuits, perhaps skewing the statistics a bit. However, our particular interest…
Development of Specialized Microelectrode Arrays with Local Electroporation Functionality
Fabrication and Encapsulation of MEAs Borosilicate glass wafers with 100 mm (4ʺ) diameter were used as substrates for the MEA structures. For a lift-off process (Fig. 2a-1 and a-2), AZ5215E photoresist (MicroChemicals GmbH, Ulm, Germany) was spin-coated and patterned by an image reversal UV photolithography step. Then, 10 nm titanium was deposited…
DNA Sequencing Market to Surpass US$ 14,755.5 Million by 2030, Says Coherent Market Insights (CMI)
CMI Next-Gen DNA Sequencing Solutions: Empowering Precision Medicine & Genetic Research for Advancements in Healthcare & Biotechnology Burlingame, June 07, 2023 (GLOBE NEWSWIRE) — According to Coherent Market Insights, Global DNA Sequencing Market is estimated to be valued at US$ 6,802.2 million in 2023 and is expected to exhibit a CAGR…
DNA Sequencing Market to Surpass US$ 14,755.5 Million by
Burlingame, June 07, 2023 (GLOBE NEWSWIRE) — According to Coherent Market Insights, Global DNA Sequencing Market is estimated to be valued at US$ 6,802.2 million in 2023 and is expected to exhibit a CAGR of 11.7% during the forecast period (2023-2030). Analysts’ Views on Global DNA Sequencing Market: Rising demand for…
Quantification and statistical modeling of droplet-based single-nucleus RNA-sequencing data
doi: 10.1093/biostatistics/kxad010. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA. 2 Department of Genetic Medicine, Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA. Item in Clipboard Albert Kuo et…
Problem with RStudio update – General
Hi everyone, I’m running RStudio on a Ubuntu 18.04.6, my R version is 4.3.0 (2023-04-21) — “Already Tomorrow”.After updating RStudio to the latest version with the installer rstudio-2023.03.1-446-amd64.deb, I am no longer able to run RStudio. Opening it from the GUI doesn’t work. When trying to open it from the…
High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq
Overview of the droplet-based snRandom-seq method for FFPE tissues The main workflow of snRandom-seq is shown in Fig. 1. For single nucleus isolation of FFPE tissues, the areas of interest of banked FFPE tissue block were first selected and placed into tubes. Deparaffinization and rehydration were carried out with standard xylene…
r – pdftools working on Task Scheduler but not on RStudio IDE
I have a script that reads this pdf www.bls.gov/news.release/pdf/cpi.pdf and it has been working perfectly when running it through my scheduled task in the Windows Task Scheduler. Recently, I was planning on adding some extra things to it but when I tried to read the pdf using pdftools::pdf_text(‘https://www.bls.gov/news.release/pdf/cpi.pdf’) it returned…
Drug discovery through Covid-19 genome sequencing with siamese graph convolutional neural network
Abdel-Basset M, Hawash H, Elhoseny M, Chakrabortty RK, Ryan M (2020) DeepH-DTA: deep learning for predicting drug-target interactions: a case study of COVID-19 drug repurposing. IEEE Access 8:170433–170451 Article Google Scholar Abdulrahman SA, Salem ABM (2020) A efficient deep belief network for Detection of Corona Virus Disease COVID-19. Fusion Pract,…
New Age Metals Completes Phase 3 Rhodium Geochemistry Study of the River Valley Palladium Project
Rhodium (Rh) (~US$ 7,950/ ounce, dated 9st May 2023) is the most valuable platinum group metal (PGM), with recent spot price highs of 5 times higher than Pd and 7 times higher than Pt 552 Rh new assay results for the Dana and Lismer Zones of the River Valley Palladium Deposit…
Spontaneous tumor regression mediated by human T cells in a humanized immune system mouse model
Human CD34+ cell isolation Human fetal liver (FL) samples were obtained from Advanced Biosciences Resources (Alameda, CA) with proper consent. FL samples were cut in small fragments, treated for 25 min at 37 °C with Collagenase D (100 ng/mL; Roche). The cell suspension was prepared, and the human CD34+ cells were separated by…
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes
Blume-Werry G, Krab EJ, Olofsson J, Sundqvist MK, Väisänen M, Klaminder J. Invasive earthworms unlock arctic plant nitrogen limitation. Nat Commun. 2020;11:1766. Article CAS PubMed PubMed Central Google Scholar Xing Y, Meng X, Wang L, Zhang J, Wu Z, Gong X, et al. Effects of benzotriazole on copper accumulation and…
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting
Handa IT, Aerts R, Berendse F, Berg MP, Bruder A, Butenschoen O, et al. Consequences of biodiversity loss for litter decomposition across biomes. Nature. 2014;509:218–21. Article CAS PubMed Google Scholar Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus…
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters
Ethics statement In vitro and animal work were conducted under appropriate biosafety conditions in a BSL-3 facility at the Institut für Virologie, Freie Universität Berlin, Germany. All animal experiments were performed in compliance with relevant institutional, national and international guidelines for the care and humane use of animals and approved…
Spatial multiomics map of trophoblast development in early pregnancy
Human samples Placental and decidual samples used for the in vivo and in vitro profiling were obtained from elective terminations from: The MRC and Wellcome-funded Human Developmental Biology Resource (HDBR, www.hdbr.org), with appropriate maternal written consent and approval from the Fulham Research Ethics Committee (REC reference 18/LO/0822) and Newcastle and…
Single-Cell RNA Isoform Sequencing Picks up Steam as Long-Read Technologies Improve
NEW YORK – Riding the wave of recent technological advancements in long-read sequencing, single-cell RNA isoform analysis has not only become feasible but is snowballing into a thriving field. The approach, based on the ability of long-read platforms to capture full-length transcriptomes, allows scientists to take a closer looker at…
Clustering with monocle 3
Clustering with monocle 3 0 Hello everyone, I was trying to analyze a scRNA dataset (chromium 10x) using monocle 3. I realized that changing the resolution parameter when applying modularity maximization did not change the capacity to discriminate subpopulations. The number of cells is 2k and UMAP visualization separates the…
RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding
RevGel-seq sample preparation workflow Experiments were performed with the RevGel-seq protocol, capable of analyzing 10,000 input cells per sample with the specially designed gelation device (Fig. S3). The individual steps shown in Fig. 1A, from cell-barcoded bead coupling to library preparation for sequencing, are more fully described below: Cell labeling Cells…
Bioinformatician IRCCS Regina Elena National Cancer Institute, Italy
The Fanciulli Lab at IRCCS Regina Elena National Cancer Institute is seeking a highly motivated Bioinformatician with expertise in Scientific Computing Support. The selected candidate will play a key role in the development, implementation, and maintenance of various IT systems, with a primary focus on scientific software and services. Additionally,…
Whole-genome doubling drives oncogenic loss of chromatin segregation
Cell culture hTERT-RPE-1 WT and hTERT RPE-1 TP53−/− (46, XX)27 cells were a gift from J. Korbel. The cells were grown in DMEM/F-12, GlutaMAX (10565018) supplemented with 10% FBS (Thermo Fisher Scientific, 10270106) and 1% antibiotic–antimycotic (Thermo Fisher Scientific, 15240062). CP-A (KR-42421) (47, XY) cells were purchased from the American Type…
STAR solo segmentation fault after ‘started Solo counting’
STAR solo segmentation fault after ‘started Solo counting’ 1 Dear all, I have some 10x v3 single cell rna seq fastq files that I am trying to map to hg38 human genome using STAR aligner and generate read counts. However, I am getting the following error and hope that some…
Bipotent transitional liver progenitor cells contribute to liver regeneration
Mice All mice experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) at the Center for Excellence in Molecular Cell Science, Shanghai Institutes of Biological Sciences, Chinese Academy of Science. The approved animal protocol number is SIBCB-S374-1702-001-C1. The CK19-CreER, HNF4α-DreER, R26-tdTomato (R26-tdT),…
10x 3′ library creates R1 and R2 fastq files with the same read length
Let me show you an example: trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR16093385&display=metadata This data contains two reads, R1 and R2. The read length of R1 and R2 are the same 150bp. However, this experiment is performed following 10x 3’library protocol. In the method section, it described as below: The scRNA-seq libraries were generated using the…
updt / node-jira / issues / #4922 – Aloha browser
Aloha Browser features powerful downloads manager. You can download videos directly from the media player while watching them online or download music, videos and files as you do on desktop. ABOUT. ➤ ► 👉 Download here – tinyurl.com/ykvzju5w?8850583 ➤ ► 👉 Download tool – tinyurl.com/ykvzju5w?3191796 ..Aloha Browser is coming to…
fastq file for GSE151671
fastq file for GSE151671 1 Hello everyone, I am attempting to download the fastq file for GSE151671 from SRA explore. However, this dataset seems a little unusual. For the Native kidney sample, there is only one sample, but there are two fastq files. It is not clear from the filename…