Tag: DMSO

Abstract The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals…

RNAi screens identify senolytic targets. a, Experimental design for the RNAi screens to identify senolytic targets. b, Right: quantification of cell survival of senescent (4OHT) and control (DMSO) IMR90 ER:RAS cells three days post-transfection with BCL2L1 siRNA (n = 3). Left: representative DAPI-stained immunofluorescence (IF) images. Scale bar, 100 µm. c, Results of…

In a recent study published in Cell Reports, researchers demonstrated clustered regularly interspersed short palindromic repeats (CRISPR)-mediated elimination of glioblastoma (GBM) cells. Study: Targeting the non-coding genome and temozolomide signature enables CRISPR-mediated glioma oncolysis. Image Credit: ART-ur/Shutterstock.com Background Primary GBM is an aggressive tumor that is challenging to treat. The…

Introduction During each heartbeat, the intracellular calcium concentration ([Ca2+]i) cycles dynamically between low resting diastolic and high active systolic levels within cardiomyocytes (Bers, 2002; Eisner et al, 2017; Sankaranarayanan et al, 2017): upon electrical excitation, Ca2+ influx via voltage-gated CaV1.2 channels activates Ca2+-induced Ca2+ release via SR ryanodine receptor type…

A. Bioinformatics analyzes Search strategy and study selection From April to June 2021, we read relevant and related publications in Medline, EMBASE, Web of Science, and Wanfang. The search term “NOX4” have been used. The articles that fit specified criteria were all added at once: (1) Participants were split into…

Plasmid construction All the constructs used in this study were generated with standard cloning strategies, including PCR, overlapping PCR, oligo annealing, digestion and ligation. Primers were purchased from Genewiz. The plasmid sequence was verified by Sanger sequencing. The pCAG-spike(D614G)-GFP11-mCherry plasmid was modified from Addgene plasmid 158761. Briefly, GFP11 and mCherry…

Introduction Proper functioning of all living organisms depends on the faithful maintenance and transmission of genomic information stored in the molecule of DNA. However, DNA integrity is continuously challenged by a variety of endogenous and exogenous agents causing DNA lesions which have a critical impact on cellular activities and homeostasis….

Introduction Host defence against infection relies on two important systems: the immune and the coagulation systems. Platelets are anucleate cells produced by megakaryocytes and are responsible for blood clotting and haemostasis (Lefrancais et al, 2017). They are also very abundant and play unexpected roles in immune responses (Maouia et al,…

Cell growth and transfections Procyclic form (PCF) T. brucei, strain 29-1354, which carries integrated genes for the T7 polymerase and the tetracycline repressor, was grown in SDM-79 medium supplemented with 10% fetal calf serum, in the presence of 50 μg/ml hygromycin. Cells were grown in the presence of 15 μg/ml G418 for…

UCSC Genome Browser Custom Track Blank 0 Hello, I have a bigwig (.bw) file which I can properly view on IGV. IGV makes it very difficult to edit the figure nicely so I am trying to view it in the UCSC genome browser. I uploaded my data to cyverse and…

Introduction Microbial resistance has become a problem in the contemporary medical environment due to the inadequate development of new antibiotics and the asinine prescription of antibiotics in both developed and developing nations. Antimicrobial resistance (AMR), which affects wealthy and developing nations, is a global concern.1 AMR is a problem for…

(A) Stability assays of HEK293 cells expressing wild-type ROMK, or ROMK carrying the G228E, L320P, or N377K mutation. HEK293 cells transfected with the indicated expression vector were treated with MG-132 or the equivalent volume of DMSO for 30 min, at which point cycloheximide was added. Cells were next processed as…

DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment 0 Hello, I have RNAseq coming from CDX models that were treated with DMSO and another compound (condition). I have 12 CDX models in total, 6 were implanted with cell1 (4 DMSO, 2 treated) and 6 with cell2 (3DMSO, 3 treated). I would…

journal contribution posted on 2023-11-12, 04:20 authored by Rebecca J. Stevick, Bianca Audrain, Sébastien Bedu, Nicolas Dray, Jean-Marc Ghigo, David Pérez-Pascual Additional file 1: Supplementary figures: Fig. S1. Sequencing depth and coverage for 16S rRNA gene amplicon data from conventional zebrafish larvae. (A) Number of quality-controlled bacterial sequences per sample. (B)….

Statistical methods Statistical tests, test statistics and P values are indicated where appropriate in the main text. Categorical associations were established using the chi-squared test of independence if n > 5 for all categories and Fisherʼs exact test otherwise. For both tests, the Python package scipy.stats v1.5.3 implementation was used64. Multiple hypothesis corrections…

Introduction The innate immune system represents the host´s first-line defense against viral infections (Koyama et al, 2008). In this context, IFN-I are produced by all nucleated cells and represent the principal cytokines that counteract viral replication (Ivashkiv & Donlin, 2014). In fact, several receptors of the infected cell can recognize…

Statistics and reproducibility Anti-AMP IP for LC-MS/MS analysis was performed in three independent biological replicates (n = 3). TSA assay data represents technical triplicates. Time-resolved (de)AMPylation analyzed by LC-MS was performed as biological triplicates. CD measurements were performed in technical triplicates. Anisotropy data is shown as technical triplicates. Anisotropy measurements were repeated…

Fig 3. Concentration-dependent transcriptional activation by corticosteroids and progesterone of FLAG-tagged wild-type and mutated elephant shark MR. Plasmids for FLAG-tagged wild-type elephant shark MR and mutated elephant shark MR (with a TRQG insert) were expressed in HEK293 cells with either an MMTV-luciferase promoter or a TAT3-luciferase promoter. Cells were treated…

List of reagents Chloramine-T trihydrate (Merck, Darmstadt, Germany), Copper(II)Sulphate, Penicillin, Streptomycin, RPMI-1640 (Sigma-Aldrich, Burlington, MA, USA), RPMI-1640 (Euroclone, Pero, Italy), DMEM low glucose (Sigma-Aldrich), Trypsin–EDTA (Sigma-Aldrich), Blasticidin hydrochloride (Sigma-Aldrich), Trichloroacetic acid (Merck), Fetal Bovine Serum (Merck, Darmstadt, Germany), Iodine 125 Radionuclide (Perkin Elmer, Waltham, Mass., USA), Iodogen™ iodination reagent (Pierce,…

Fasting-mimicking diet (FMD) is emerging as an effective dietary intervention with the potential to prolong life span in healthy people and boost antitumor immunity in patients with cancer. FMD refers to a medically designed fasting-like state that allows periodic consumption of a very-low-calorie and low-protein diet (1, 2). Compared with…

Kanoktip Petcharat,1 Narongsuk Munkong,2 Rungthip Thongboontho,1 Widsanusan Chartarrayawadee,3 Arthid Thim-Uam1 1Division of Biochemistry, School of Medical Sciences, University of Phayao, Phayao, 56000, Thailand; 2Department of Pathology, School of Medicine, University of Phayao, Phayao, 56000, Thailand; 3Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand Correspondence: Arthid Thim-Uam,…

The study was approved by The Central Denmark Region Committees on Health Research Ethics (1-10-72-269-20), and it was prospectively registered with ClinicalTrials.gov (ClinicalTrials.gov identifier: NCT05185557). The research was carried out according to the principles set out in the Declaration of Helsinki 1964 and all subsequent revisions. Written and orally informed…

A recent case study published by AMSBIO highlights ground-breaking research in neuromuscular diseases. Led by Dr Roger Kamm at the Massachusetts Institute of Technology (MIT), this project focuses on developing a 3D microfluidic neuromuscular platform for modelling Motor Neuron Diseases (MNDs). MNDs, particularly amyotrophic lateral sclerosis (ALS), remain a significant…

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…

Cells and viruses Haploid mSCs AN3–12 are a feeder independent clonal derivative of HMSc2 isolated from mice oocyte and maintained at IMBA52. The AN3–12 library and knocked out cells used for the haploid screening was obtained from IMBA (Austria)14,52. AN3–12 cells were validated by STR analysis. Haploid mES cells were…

Reagents and chemicals pFastBac Dual His6 MBP N10 TEV LIC cloning vector (5 C) was purchased from Addgene (Addgene plasmid no. 30123; www.addgene.org/30123). All restriction enzymes, the pFastBac1 vector, and DH10Bac cells were purchased from Thermo Fisher Scientific. Sf9 cells were purchased from ATCC. Q5® High-Fidelity DNA Polymerase, the Monarch® DNA…

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…

Normalizing Chip seq data using fruit fly genome 0 Hello I have the human chip seq data on which I want to perform the chip seqanalysis. In many papers it has been referred to normalize the data using the spike in method. I have done the alignment of the data…

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×…

Rab8A and Rab41 are required for xenophagy of GAS For comprehensive screening of Rab GTPases involved in xenophagy against GAS infection, we first knocked down the expression of Rab GTPases in HeLa cells. We examined bacterial survival in cells at 6 h post-infection (hpi) compared with that at 2 hpi because…

Photocontrolled, biologically active compounds contain reversibly photoisomerizable fragments, photoswitches in their molecules. Compounds are cyclic peptides modified by a diarylethene fragment that undergoes reversible light-induced electrocyclic transformations. They can photoswitch, that is, toggle between a UV-generated, biologically inactive form and a red light-generated, biologically active form. It is believed that…

Design of arabinose-inducible artificial transcription factors A core objective of our work was to develop inducible, heterologous regulators capable of genetically reprogramming gene regulatory networks in Enterobacteriaceae, specifically Salmonella and E. coli. To achieve this, we designed arabinose-inducible ATFs incorporating diverse DBDs originating from CRISPR/dCas9 and plant heterologous TFs (Fig. 1)….

Soil incubation and cell extraction Approximately 3 kg of unmanaged marginal soil (pH 8) was collected from the Pacific Northwest National Laboratory field site in Prosser, Washington (46° 15′ 04″ N and 119° 43′ 43″ W) [23], homogenized, sieved (4 mm mesh size), and stored at 4 °C until further processing. Probe specific…

Introduction Protein levels are regulated at several nodes. One mode of protein level regulation acts through enhancing or reducing gene transcription. Gene transcription can be stimulated by binding transcription factors to promoters or enhancers of target genes and by posttranslational modifications of transcription factors and histones. Such modifications can be…

DeSeq2 design fails (full model matrix is less than full rank) 1 @theodoregeorgomanolis-7993 Last seen 16 hours ago Germany Hi all, I am trying to create a design to compansate for different DMSO concetrations in an experiment using same cell but different inhibitors. the sampleTable looks like sampleTable$group <- factor(sampleTable$group)…

Datasets The gene expression data, mutation data, CRISPR, and drug perturbation data sets used in this study were obtained from the Depmap project depmap.org/portal/download/all/. The gene expression data set consists of the log2 transformed transcript per million (TPM) values of 19,221 protein-coding genes from 1406 cell lines across 33 cancer…

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…

Generation and characterization of Ago2 knockout mutants To demonstrate the essential function of Ago2 in the Ae. aegypti siRNA pathway, we used CRISPR/Cas9 to knock out Ago2 and then investigated its role in defending against arbovirus infection (Fig. 1a). Ae. aegypti Ago2 (AeAgo2) has four exons and four predicated functional domains,…

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…

ATXN3 mRNA For hit validation SK-N-SH wildtype cells were treated at effective concentrations of 10 µM for 2 h in 24 well plate format and triplicates. Total RNA was extracted with the RNeasy Mini kit (Qiagen). RT-qPCR reactions were performed with the QuantiTect SYBR Green RT-PCR Kit (Qiagen) in a 96 well…

AuNP production Fusarium oxysporum was used for the extracellular production of AuNP. The fungus was acquired from the Culture Collection of Fungi of the Charles University (CCF 3732, Czech Republic). After cultivation in Sabouraud Dextrose Broth (SDB, Sigma Aldrich, Prague, Czech Republic) at 30 °C and 150 rpm for 4 days, the supernatant…

This protocol presents an automated, image-based high-throughput technique to identify compounds modulating natural killer cell-mediated breast cancer cell killing in the presence of a therapeutic anti-HER-2 antibody. Antibody-dependent cellular cytotoxicity, or ADCC for short, can be mediated by natural killer cells, which we refer to as NK cells, granulocytes and…

Directed differentiation of hiPSCs (SBAD2) towards cardiomyocytes after exposure to teratogens and non-teratogens To study the early events of the process of cardiomyogenesis, we used a cell monolayer-based directed hiPSC differentiation protocol, designated as the UKK2 cardiotoxicity test (UKK2-CTT), which is based on the sequential activation and inhibition of Wnt/β-catenin…

KDM6A inactivation in an autochthonous SCLC mouse model promotes NEUROD1 expression leading to SCLC tumors that express both ASCL1 and NEUROD1. a, Schematic of the adenovirus used for IT injection into the lungs of LSL-Cas9 mice to generate autochthonous SCLC tumors that are Kdm6a inactivated or Kdm6a WT. RPP: sgRb1,…

Transcript To apply compounds to the plants using the Novel 3D-Printed Direct Plant Infusion, or DPI device, ensure the device is properly fitted to the plants. When assembled properly, the plastisol ring should be flush against the DPI device and the spout should line up with the hole drilled in…

1. Introduction Diffuse large B-cell lymphoma (DLBCL) is an aggressive malignant lymphoid neoplasm, which accounts for 40% of all malignant lymphoid neoplasms and includes morphologically and molecularly heterogeneous disease subtypes [1,2]. According to gene expression profiling, different forms of DLBCL are subdivided into germinal center B-cell-like (GCB-DLBCL) and activated B-cell-like…

Creation and sequencing of epigenetically diverse plant populations To induce epigenetic variation, A. thaliana seeds were treated with three different concentrations of zebularine. We will describe these three different zebularine concentration groups, and our water and DMSO controls as “populations” throughout the remainder of this paper. Plants displayed stunted vegetative…

No statistical methods were used to predetermine sample size. The experiments were not randomized and investigators were not blinded to allocation during experiments and outcome assessment. Expression constructs The coding sequence of mouse PIEZO1 (E2JF22, UniprotKB entry) was codon-optimized, synthesized and cloned into the pcDNA3.1 plasmid. An amber stop codon…

All experimental protocols were approved by Dali University. All methods were performed in accordance with relevant guidelines and regulations. Reagents and chemicals MEM medium, RPMI-1640 medium, fetal bovine serum (FBS), phosphate-buffered saline (PBS), and penicillin–streptomycin (Pen Strep) were purchased from Biological Industries (Israel). CCK-8 reagent was purchased from Proteintech (Wuhan,…

Establishment of the klf1 mutant and klf1–klf17 double mutant and phenotypic analysis of these mutants in zebrafish haematopoietic development Both the klf1 and klf17 genes are specifically expressed in the blood island/ICM during zebrafish embryogenesis9,13. The expression of klf1 was maintained in the CHT, whereas the expression of klf17 was…

MACS2 peak calling and drug treatment 1 Hello, I have called peak for a transcription factor (say TF1) using MACS2 on a cell line with DMSO treated with two replicates and the same cell line was treated with a drug that is supposed to degrade the TF1. In DMSO treated…

Human study The study was approved by the institutional review boards (Ethics Commission of the Medical Faculty of Technical University Munich (protocol 193/17S) and Ethics Committee of the Medical Faculty of Heidelberg University (protocol S-206/2011)) and all patients provided written informed consent under these protocols. The study was conducted in…

SF3B1 MUT cells show selective sensitivity to PARP inhibitors To identify candidate therapeutic targets for cancers with SF3B1 hotspot mutations, we utilized the leukemia K562K700E (SF3B1K700E) and parental (SF3B1WT) isogenic cells1, to model one of the most prevalent SF3B1 hotspot mutations seen in patients8,19,20 (Fig. 1a,b and Supplementary Fig. 1a)….

Development and validation of a senescence CyTOF antibody panel We constructed and validated a comprehensive CyTOF antibody panel to include markers for both cell identity and senescent phenotype (Table 1). A defining characteristic of senescent cells is expression of cell cycle inhibitors, in particular p16 or p2129, so we carefully validated…

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,…

Identifying Drug hits for a Group of cell Lines 0 Hey guys, I have two groups of cell lines from CCLE, each made of around 40 cell lines. I am using the PRISM Repurposing drug dataset and would like to identify drugs that are sensitive for group A cell lines…

Statement of ethics and regulations Our clinical data collection was approved by the Research Ethics Committee of the Affiliated Hospital of Southwest Medical University (KY 2021010). The animal study was conducted according to the guidelines of the Institutional Animal Care and Use Committee of Macau University of Science and Technology…

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…

Aim, design and setting of the study We aim to address our research question – how does microbial diversity affect PD pathology with ageing at the molecular level and can early intervention in the microbiome modulate the disease course? Herein, we have studied longitudinally the gut microbiome dynamics with ageing and report that with ageing,…

Molecular biology A two-color intramolecular human SERCA2a (2CS) biosensor, based on human cardiac SERCA2a fused to green fluorescent protein (eGFP) and red fluorescent protein (tagRFP) was developed to detect structural changes that are related to the functional changes of SERCA20,22,25. Briefly, tagRFP was genetically fused to the N-terminus of SERCA…

Phytocannabinoids (pCBs) refer to compounds from the cannabis plant (Cannabis sativa), also known as cannabinoids , we found that pCBs can be differentially metabolized by different cytochrome P450 (CYP) and different polymorphisms of human CYP2D6, In addition, inhibition or activation of enzymes involved in drug metabolism by pCB will in…

Sample collection Sampling kits were sent out to various bat rehabilitators in the UK, as described previously56, for the collection of faeces from bats. These faecal samples (0.02–1 g) were immediately stored in 5 ml of RNAlater solution to prevent degradation of RNA. The geographical locations and collection dates for all samples…

Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases. sFluorescence images of Calcein AM/PI staining in the CsA- or DMSO-treated NPCs. NPC pyroptosis mechanism via mtDNA mediated TLR9-NF-B-NLRP3 axis activation is unclear. In addition, we found that TLR9 recognized and bound mtDNA, which is critical for NF-B and the NLRP3 inflammasome…

NUP98 and RAE1 are enriched in progenitors and constitute a distinct complex Between the progenitor-state versus the differentiation state keratinocytes, we identified that 4 out of 5 nuclear-basket NUPs are significantly downregulated in differentiation (Fig. 1a), leveraging the RNA-seq data that we recently generated20. To determine how the enrichment of these…

Cell lines and culture conditions All media and supplements were purchased from Gibco unless otherwise stated. OC cell line SKOV3, OVCA429, CH1 and NSCLC cell line H1299 and A549 were maintained using Dulbecco’s Modified Eagle Medium (DMEM) media supplemented with 10% (v/v) foetal bovine serum (FBS). OC cell lines HeyA8,…

Sequencing-grade modified trypsin (Cat No. V5111) and chymotrypsin (Cat No. V1061) were purchased from Promega (Madison, WI). The SARS-CoV-2 spike proteins were purchased from R&D systems (St. Paul, MN) (Cat. No’s 10561-CV-100, 10796-CV-100, 10786-CV-100, 10795-CV-100, 10878-CV-100, and 11060-CV-100). Dithiothreitol (DTT), iodoacetamide (IAA) and α-lytic protease (Cat No. A6362) were purchased…

Hi everyone, I am trying to analyse some RNA-Seq data in DESeq2, but am struggling a little conceptually in understanding how exactly to investigate what genotype specific changes I have. My data consists of 2 genotypes, 3 timepoints and 2 treatments (treated/untreated) – 48 samples in total (4 replicates per)….

Materials The lipid cetyl palmitate was a kind gift from Gattefossé (Gattefossé SAS, Saint-Priest, France). DSPE-PEG2000-NH2 (1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethylene glycol)-2000] (ammonium salt)) was purchased from Avanti Polar Lipids Inc. (Alabaster, Alabama, USA). D-Phenylalanine, D-Proline, D-Tyrosine, triethylamine (TEA), dicyclohexylcarbodiimide (DCC), N-hydroxysuccinimide (NHS), sodium hydroxide (NaOH), sodium chloride, moxifloxacin hydrochloride (MOX), farnesol 95%, Tween®80,…

CFT7455: A novel IKZF1/3 degrader, demonstrates potent anti-tumor activity in peripheral and CNS models of non-Hodgkin’s lymphoma as a single agent or in combination with clinically approved agents Samantha Perino, R. Jason Kirby, Roman V. Agafonov, Prasoon Chaturvedi, Scott J. Eron, Andrew Good, June A. Hart, Minsheng…

The LAMMPS forum is not Science Talk This forum is dedicated to discussing LAMMPS, and the volunteers here focus on helping with LAMMPS, not general scientific queries. Here are some typical queries that are out of scope for this forum, with explanations: “How do I turn mercury into gold with…

Cellchat error: data.signaling matrix error when using mouse database (Error in identifyOverExpressedGenes) 0 Hi, I’m having an error similar to this cellchat user (github.com/sqjin/CellChat/issues/264). If I run CellChatDB.mouse, and I subset my cellchat object (subsetData), I get this error: Error in identifyOverExpressedGenes(cellchat_DMSO) : Please check `object@data.signaling` and ensure that you…

Construction of proteomic content networks from an ultra-deep metaproteomic approach We define the proteomic content network (PCN) of a microbiome sample as a bipartite graph connecting each microbial taxon to all expressed functions from the taxon’s proteome. In order to gain the deepest possible understanding of sample-specific PCN of the…

Cell lines and culture A549-hACE2 [a gift from Dr. Ben tenOever3], 293 T, HEK293, A549, and 3T3-L1 pre-adipocyte cell lines (refer to Supplementary Table 1) were cultured in DMEM and 10% FBS. U937, Calu-3, and HCT116 cells were cultured in RPMI, EMEM, and McCoy’s 5 A media, respectively, with 10% FBS. Caco-2 cells…

Cell culture Cell lines (MDA-MB-231, 4T1 and RPE-1) were purchased from the American Type Culture Collection (ATCC). TP53-knockout MCF10A, TP53-knockout RPE-1 and Trex1 knockout 4T1 cells were gifts from the Maciejowski laboratory at the Memorial Sloan Kettering Cancer Center (MSKCC). OVCAR-3 cells were a gift from J. D. Gonzales. All…

MAGECK MLE design matrix 0 @ea5b2e2a Last seen 7 hours ago Finland Hi, which one of the following design matrices would be correct for a CRISPR screen with DMSO as control and 4 drugs carried out for 18 days? OR Thanks! -Monika mageck MAGeCKFlute • 19 views Login before adding…

Cell lines Human melanoma cell lines (A375 and A875) were kindly donated by the Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 100 μg/ml penicillin and 100 μg/ml streptomycin at 37 °C in a…

How to make the profile line of `deepTools::plotHeatmap` more smooth? 1 Why the profile line has so many wiggles?How to make the profile line more smooth?I assume there are some peaks in the .bed file that are highly repeated, how can I delete those peaks?Thanks a lot computeMatrix reference-point –referencePoint…

Introduction Interleukin (IL)-2 was the first Food and Drug Administration approved immunotherapy for use in patients with metastatic melanoma and renal cell carcinoma.1 2 However, the use of recombinant IL-2 (Proleukin/aldesleukin) has been problematic due to low response rates, off-target effects, and severe dose-dependent toxicities. Due to its potent T-cell…

Positive beta-scores of essential genes in drug-treated cells 0 @ea5b2e2a Last seen 14 hours ago Finland Hi, I ran both MAGECK RRA and MAGECK MLE on my CRISPRi screen data set where I have samples: DMSO control day 0 DMSO control day 18 (end of experiment) drug 1 day 18…

A) Raji cells transduced with lentivirus shControl (shCtrl) or shPLOD1 (pool a) were assayed by Western blot for PLOD1, EBNA1, EBNA2, LMP1, or Actin at 7 days post-transduction. Each lane is a biological replicate. B) Raji (left) or LCL (right) treated with DMSO or 2,’2-dipyridil (2-DP, 200 μM) were assayed…

KRAS mutations are among the most frequent gain-of-function alterations found in patients with cancer and their therapeutic targeting has long been a key objective in precision oncology8,9,10,11,12. The KRAS GTPase cycles between an active (GTP-bound) and an inactive (GDP-bound) state. GTP hydrolysis is enhanced by GTPase-activating proteins13, whereas GDP to…

Statement on ethical considerations All animal work was approved and permitted by the Local Ethical Committee on Animal Experiments and conducted according to the Guidelines for Animal Experimentation recommendations (ARRIVE guidelines). In particular, mouse work related to C57BL/6NCrl mice was approved and permitted by the Institute of Molecular Genetics of…

Freezing CHO CellsChristina McGee 4-5-2012 Grow 10 cm dish to 50-90% confluency in T-75 cuvette Tolerate cells with 3 ml Trypsin/EDTA, wait for cells to detach. Add 7 ml media, transfer to 15 ml sterile tube. Centrifuge 250 G/5 min. Remove resilient. Easy resuspend cell pellet in 2 ml thawing…

This protocol describes the fabrication and characterization of a photoresponsive prodrug-dye nanoassembly. The methodology for drug release from the nanoparticles by light-triggered disassembly, including the light irradiation setup, is explicitly described. The drugs released from the nanoparticles following light irradiation exhibited excellent anti-proliferation effects on human colorectal tumor cells. This…

This protocol is significant because it enables researchers to mature commercial or in-house-made hiPSC-CMs to an adult-like phenotype that significantly improves the predictive value of hiPSC-CMs in cardiotoxicity screening. The main advantage of this protocol is that it delivers mature hiPSC-CMs in a high throughput format for optical mapping of…

Leukemia cell culture The human acute promyelocytic leukemia cell line (NB4) and the human acute lymphocytic leukemia cell line (MOLT-4) were purchased from Cell Lines Service (Eppelheim, Germany). Leukemia cells were cultured in RPMI-1640 medium supplemented with 10% (v/v) FBS and 1% (v/v) penicillin–streptomycin (Gibco Life Technologies, Waltham, MA, USA)….

doi: 10.1007/978-1-0716-2477-7_26. Memberships Expand Connections 1 Department about Chemical and Systems Biology, Stanford University, Stand-ford, CANCER, USA. [email protected] 2 Department of Chemical and Systems Nature, Stanford University, Stanford, CA, USA. [email protected] Freely PMC article Item in Clipboard Magdalena P Crossley et aluminium. Methods Mol Bil. 2022. Free PMC books Show details…

hiPSC cell culture and differentiation hiPSCs were maintained on 1:40 matrigel (Corning, #354277) coated dishes in supplemented mTeSR-1 medium (StemCell Technologies, #85850) with 500 U ml−1 penicillin and 500 mg ml−1 streptomycin (Gibco, #15140122). For the differentiation of cortical neurons the protocol described previously21 was followed with slight modifications. Briefly, hiPSC colonies were seeded…

Study design The overall goal of this study was to explore the molecular mechanisms of remdesivir-related cardiotoxicity in anti-COVID-19 therapy. We first performed the GPCR screening using major anti-COVID-19 drugs as ligands (n = 3 per GPCR). We validated the results of GPCR screening by concentration-response analysis and determined the EC50 and…

Ethics statement All experiments with hamsters were performed in accordance with the Science Council of Japan’s Guidelines for the Proper Conduct of Animal Experiments. The protocols were approved by the Institutional Animal Care and Use Committee of National University Corporation Hokkaido University (approval ID: 20-0123 and 20-0060). All protocols involving…

Phylogenetic tree construction Tree diagram showing relationships between CDK proteins was constructed from a multi-sequence alignment (MSA) using Geneious95. The “Geneious Aligner”, was used to generate the MSA, and the neighbor joining method was used to construct the tree. All default parameters were used except where otherwise indicated. Combinatorial CRISPR…

Sample selection We identified parent–child trios from the 1KG in which the child cell line banked within the NHGRI Sample Repository for Human Genetic Research at the Coriell Institute for Medical Research was listed as having zero expansions and two or fewer passages, and rank-ordered representative individuals as follows. Loci…

In this section, we derive a simplified expression for the proportionality constant \(\alpha\) that enables quantitative ChIP-seq and we introduce some consequences for track building. This new expression is more intuitive to understand, easier to evaluate, and more accurate to sequencing outcomes than the previous expression. While values derived from…

Introduction Hypertension is one of the main risk factors of cardiovascular disease. According to the Chinese hypertension survey, the prevalence rate of adult hypertension in China is 27.9%, showing an increasing trend and the awareness rate, treatment rate and control rate are respectively 51.6%, 45.8% and 16.8% (Citation1). Compared with…

Plasmid design The information on each plasmid for combinatorial libraries is indicated in Supplementary Table S1. Plasmids used in this study to generate combinatorial libraries for SpCas9, enAsCas12a, CHyMErA, enAsCas12a (dual-gRNA), CHyMErA.v2, multiSPAS were deposited to Addgene (IDs: 189632, 189633, 189634, 189635, 189636, 189637, respectively). 3Cs oligonucleotide design The protocol…

Ethics statement All experiments in this study comply with guidelines of the U.S. Public Health Service and were approved by the Institutional Biosafety Committee at the University of Pittsburgh. All animal husbandry and experimental procedures were conducted in accordance with U.S. Public Health Service policy and approved by the Institutional…

We present a method for culturing and gene editing primary rhesus macaque B cells using CRISPR/Cas9 and recombinant adeno-associated virus serotype 6 for the study of B cell therapies. The method is relatively simple and allows efficient gene editing of rhesus macaque B cells. The method allows the testing of…

Introduction Nontuberculous mycobacteria (NTM), a mycobacterium other than the Mycobacterium tuberculosis complex (MTC) and M. leprae, are conditional pathogens widely found in the environment.1 Studies have shown that the probability of NTM transmission is extremely low, and exposure comes primarily from the environment, soil, water, etc.1 In recent years, lung…

Ribozyme search of the Sequence Read Archive Observing that ribozymes are sufficiently short to be captured on a short sequence read (less than 100 nt), we reasoned it will be possible to screen large volumes of sequencing data to identify libraries potentially containing ribozyme agents. To this end we adapted…

Approval of Breyanzi based on the pivotal Phase 3 TRANSFORM trial, in which Breyanzi significantly improved event-free survival compared to standard of care with a manageable and well-established safety profile PRINCETON, N.J.–(BUSINESS WIRE)– Bristol Myers Squibb (NYSE: BMY) today announced that the European Commission (EC) has granted approval for…