Tag: pbs

In this paper, we present an in vitro and in situ protocol to repair a tendon gap of up to 1.5 cm by filling it with engineered collagen graft. This was performed by developing a modified suture technique to take the mechanical load until the graft matures into the host…

Cell lines and culture Unless stated otherwise, all tumor target cell lines were sourced from the ATCC via LGC Standards. Human endogenous mesothelin (MSLN)-positive target cell lines H-226 (lung carcinoma, MSLN+, ATCC® CRL-5826™) and AsPC-1 (ATCC CRL-1682), and MSLN-negative Raji control cells (ATCC CCL-86) were cultured in RPMI-1640 Glutamax (Life Technologies,…

In this protocol, AAV2 vector is produced by co-culturing Spodoptera frugiperda (Sf9) insect cells with baculovirus (BV)-AAV2-green fluorescent protein (GFP) or therapeutic gene and BV-AAV2-rep-cap infected Sf9 cells in suspension culture. AAV particles are released from the cells using detergent, clarified, purified by affinity column chromatography, and concentrated by tangential…

How to label columns in HTSeq output 0 I’ve been working to process RNAseq data and I’ve used hisat2 to align my reads to the reference genome. When I take those output files and put them into HTSeq-count using the below code, I get a count matrix but the columns…

CD94/KLRD1 Protein, Human, Recombinant (His Tag): 产品信息 纯度 > 95 % as determined by SDS-PAGE 生物活性 Testing in progress 蛋白构建 A DNA sequence encoding the human KLRD1 (Q13241-1) (Lys32-Ile179) was expressed with a polyhistidine tag at the N-terminus. 表达宿主 HEK293 Cells 分子量 The recombinant human KLRD1 consists of…

Running Jobs on Titan Table of Contents Titan’s Job Scheduler – SLURM Documentation Translating to SLURM commands from other workload managers Basic SLURM Commands squeue sinfo scontrol sbatch scancel Titan’s Environment Module System – LMOD Listing all available modules on Titan Loading a module into your environment Listing all modules…

This protocol presents how to quantify AAV transduction efficiency in mouse retina using digital droplet PCR (dd-PCR) together with small scale AAV production, intravitreal injection, retinal imaging, and retinal genomic DNA isolation. In this video, we will show how to quantify AAV transduction in mouse retina using digital droplet PCR…

Significance Interferon (IFN)-mediated antiviral responses serve as the first line of the host innate immune defense against viral infection. Here we identify a previously uncharacterized protein designated phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein (PINLYP), which is essential for embryonic development and plays an important role in type I IFN…

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

How to get normalized count table from DESeq? 1 Hi, I’m using Deseq compare differential abundance. Here is my code: ds.all <- phyloseq_to_deseq2(ps0.infant.pbs, ~ sample_type) geoMeans <- apply(counts(ds.all),1,gm_mean) ds.all <- estimateSizeFactors(ds.all,geoMeans = geoMeans) dds.all <- DESeq(ds.all,fitType = “local”) Then as the results I got 8 ASVs that showed significantly different….

Computational design Protein modeling and design was performed with Rosetta version 3.5 (2015.19.57819)35,37. Python and shell scripts for generating input from Rosetta and analyzing from Rosetta are available at: github.com/raman-lab/biosensor_design The high-resolution TtgR structure co-crystalized with tetracycline was selected as the starting point for computational design (PDB: 2UXH)28. The structure…

Introduction Prostate cancer (PCa) is one of the most common genitourinary system malignant tumor in men worldwide. In Asian countries, many patients with PCa are often diagnosed at an advanced stage maybe mostly because of a large population base with relatively backward economic development and imperfect cancer screening system of…

INTRODUCTION Genomic instability often refers to the existence of a variety of DNA alterations, ranging from single nucleotide changes (such as base substitution, deletion, and insertion) to chromosomal rearrangements (e.g., gain or loss of a segment or the whole chromosome) (1). Loss of genome stability can lead to early onset…

negative PBS values 0 Are negative values for the Population Branch Statistic (from Yi et al. 2010) meaningful? I obtained per SNP pairwise WC Fst from 3 populations of different sizes from Vcftools and calculated PBS. For some SNPs, the PBS is negative for a population and I am not…

Introduction Aural infections are one of the most common diseases of the head and neck and are predominantly caused by bacterial infections of the ear canal. Several studies from different countries have reported that Pseudomonas aeruginosa is the most common pathogen isolated from ear canal secretions, followed by Staphylococcus aureus.1…

Entry EC 1.14.12.17               Enzyme                                  Name nitric oxide dioxygenase Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donorBRITE hierarchy Sysname nitric oxide,NAD(P)H:oxygen oxidoreductase Reaction(IUBMB) 2 nitric oxide + 2 O2 + NAD(P)H =…

Introduction Today, malignant tumors (cancer) still severely imperil human health and cause millions of global mortality rates.1,2 Deep-seated solid tumors are challenging to cure by most therapeutic tools, mainly blamed on the complex tumor microenvironment (TME).3,4 Adoptive cell therapy (ACT), as one of the effective immunotherapeutic means for cancer treatment,…

Hi, I am using PLINK to estimate haplotype blocks using Gabriel’s method. I am using the following command plink –file Chr$PBS_ARRAY_INDEX –noweb –all –blocks –ld-window-kb 500 And it seemed to be working just fine but when job finished no blocks were called at all. The log file does not mention…