Tag: HeLa

Cell lines, culture conditions, heat shock treatment and transfections HeLa, HEK293 and 2D12 (a NOA36-knockout HEK293-cell line generated in this work) cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 100 U/mL penicillin and 100 µg/mL streptomycin at 37 °C in a CO2 incubator. For heat…

Additional Information This liquid Growth Medium is a complete medium optimized to culture select BPS Bioscience cell lines. Optimized for Use With: CRISPRa (SAM) HeLa Cell Line (BPS Bioscience, #78193), CRISPRa (SAM) HepG2 Cell Line (BPS Bioscience, #78194) Article No BPS-78221 Country Availability SE, FI, DK, NO, IS, EE, LV,…

Author Contributions Conceptualization, L.W., W.B. and V.G.; methodology, Y.H., J.S. (John Sienkiewicz), J.S. (Jinying Sun), H.Z., H.H., S.X., R.B. and L.H.; software, Y.H., J.S. (John Sienkiewicz) and J.S. (Jinying Sun); validation, H.Z. and J.S. (John Sienkiewicz); formal analysis, V.G.; investigation, V.G. and L.W.; resources, L.W.; data curation, Y.H., J.S. (John…

Cite As: Krohannon A, Srivastava M, Rauch S, Srivastava R, Dickinson BC, Janga SC. CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion. BMC Genomics. 2022;23(1):172. Published 2022 Mar 2. doi:10.1186/s12864-022-08366-2 Abstract: Background: Recent discovery of the gene editing system – CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins (Cas),…

Overview of the isoform-specific determination of dUTPase gene expression Our aim was to determine the mRNA expression level of the dUTPase isoforms specifically. First, we investigated the Ensemble, the UniProt, and the NCBI Reference Sequences (RefSeq) databases and also took into account the Consensus CDS (CCDS) project. In the Ensemble…

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…

The Ribosome: historical monolith – evolutionary chameleon The ribosome is generally considered a highly conserved ribonucleoprotein complex translating messenger RNA (mRNA) into proteins, a function that makes it essential across all species and domains of life. Composed of ribosomal RNAs (rRNAs) and proteins (r-proteins), and assembled from a small and…

SARS-CoV-2 infection induces mtDNA release and recognition by cGAS Recent studies revealed that SARS-CoV-2 stimulation could cause the accumulation of intracellular and intercellular DNA due to cell fusion, cell death and even tissue damage.17,19,27 To detect SARS-CoV-2-triggered release of DNA during infection, we first detected the cytosolic dsDNA pattern by…

Acquiring amino acid substitutions via language model consensus We select amino acid substitutions recommended by a consensus of language models. We take as input a single wild-type sequence x = (x1,…,xN)∈ \(\mathcal{X}\)N, where \(\mathcal{X}\) is the set of amino acids, and N is the sequence length. We also require a set of…

Ethics Human blood was obtained from healthy donors, approved by the Regional Ethics Committee and Imperial College Healthcare NHS Trust Tissue Bank (Regional Ethics Committee approval no. 17/WA/0161, Imperial College Healthcare Tissue Bank Human Tissue Authority license no. 12275, and Imperial College Research Ethics Committee no. 19IC5166). All samples were…

April 19, 2023 | Judicial Watch (Washington, DC) – Judicial Watch announced today it received 552 pages of records from the U.S. Department of Health and Human Services (HHS) which include the initial grant application and annual reports to the National Institutes of Health (NIH) from EcoHealth Alliance, describing the…

Small interfering RNAs (siRNAs) are novel therapeutics that can be used to treat a wide range of diseases. This has led to a growing demand for selective, efficient, and safe ways of delivering siRNA in cells.  Now, in a cooperation between the universities of Amsterdam and Leiden in the Netherlands,…

Crabtree GR, Kant JA (1982) Organization of the rat γ-fibrinogen gene: alternative mRNA splice patterns produce the γα and γβ (γ′) chains of fibrinogen. Cell 31:159–166 Article  PubMed  Google Scholar  Durnam DM, Palmiter RD (1981) Transcriptional regulation of the mouse metallothionein-I gene by heavy metals. Proc Natl Acad Sci USA…

Cell culture and reagents HEK293 and HeLa cells (American Type Culture Collection) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum, 2 mM GlutaMAX‐1, 100 μg/mL streptomycin and 100 U/mL penicillin (complete growth medium) at 37 °C under 5% CO2. HeLa cells stably expressing GFP-TIFA were previously described8. Cells…

IgG plasmids Antibody sequences and Fc-tagged ACE2 were cloned into the CMV/R plasmid backbone for expression under a CMV promoter. The antibodies with variable HC/LC were cloned between the CMV promoter and the bGH poly(A) signal sequence of the CMV/R plasmid to facilitate improved protein expression. The variable region was…

Cells Human cervix epitheloid carcinoma HeLa cells (ECACC 93021013; RRID:CVCL_0030) were cultured at 37 °C in Dulbecco′s Modified Eagle′s Medium (DMEM) with 3 mM glutamine, 10% (v/v) fetal calf serum (FCS), 10 mM HEPES, 100 IU/ml penicillin, 100 μg/ml streptomycin, and 5 mM glucose in humidified air with 5% CO2. Human osteosarcoma 143B cells were purchased…

KEGG ORTHOLOGY: K25971     ORTHOLOGY: K25971 Help Entry K25971                      KO                                      Symbol A25 Name Orthopoxvirus A-type inclusion protein A25 Pathway Brite KEGG Orthology (KO) [BR:ko00001] 09120 Genetic Information Processing  09125 Information processing in viruses   03268 Virion – Orthopoxvirus    K25971  A25; Orthopoxvirus A-type inclusion protein A25 09180 Brite Hierarchies  09185 Viral protein families   03200 Viral proteins    K25971  A25; Orthopoxvirus A-type inclusion protein A25Viral…

To meet the challenge of sample depletion during preparation, there have been a number of recent advances in what is now a rapidly moving field of study of SCP, with important contributions from several investigators. Earlier work combined capillary electrophoresis (CE) with high-resolution mass spectrometry (HRMS) to analyze proteomes of…

FG spectrum in pediatric AML patients A combinatorial approach, including conventional and next-generation sequencing (NGS)-based assays, was employed to profile the FG landscape (see Methods). FG analysis was feasible for 138 patients (94% of the entire cohort, Supplementary Data 1) from whom suitable testing materials were available. The most common FGs…

The 5′ stem-loop of the U4 snRNA and the box C/D motif of the box C/D snoRNAs can both be folded into a similar stem-internal loop-stem structure that binds the 15.5K protein. The homologous proteins NOP56 and NOP58 and 61K (hPrp31) associate with the box C/D snoRNPs and the U4/U6…

The effect of hygrothermal conditions on the linear as well as nonlinear free flexural vibration of anisotropic shear deformable laminated rounded backside can be looked at. The rounded layer is made from fiber-reinforced composites (FRCs) with all the support staying allocated both evenly (UD) or perhaps functionally scored (FG) of…

NIPBL KD affects cohesin-STAG1 and cohesin-STAG2 in opposite ways. a Asynchronously growing HeLa cells mock transfected (control) or transfected with siRNA against NIPBL (NIPBL KD) were analyzed by flow cytometry 72 h later. Contour plots of the indicated proteins in control (gray plots) and NIPBL KD cells (colored plots) were overlapped…

Multiple proteins are required to maintain the fidelity of transcription in yeast Using genetically engineered yeast strains21,36,37 and massively parallel sequencing technology34,35, we and others previously demonstrated that the non-essential subunits Rpb9 and TFIIS enhance the fidelity of transcription of RNAPII in living cells16,21,26,34,35,36,37,38,39. In addition, we showed that the…

Received: 9 February 2023 / Revised: 4 March 2023 / Accepted: 6 March 2023 / Published: 9 March 2023 Round 1 Reviewer 1 Report In this paper, they reviewed the role of a long non-coding RNA, H19, in liver cancer. H19 is a lncRNA, which has been extensively studied. Multiple…

Keywords SARS-CoV-2, COVID-19, cyclic guanosine monophosphate-adenosine monophosphate synthase-stimulator of interferon genes pathway, lung damage, interferon, cytokines Introduction Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) pandemic with origin in Wuhan, China [1]. With confirmed 522 million infections and death of 6.27 million until May…

Overview Product name Description Rabbit polyclonal to Smad4 Host species Rabbit Tested applications Species reactivity Reacts with: HumanPredicted to work with: Mouse, Rat, Sheep, Horse, Cow, Dog, Pig, Chimpanzee,…

Overview Product name Description Rabbit monoclonal [EPR4389(2)] to XRCC1 Host species Rabbit Tested applications Suitable for: WB, IHC-P, ICC/IFmore detailsUnsuitable for: Flow Cyt or IP Species reactivity Reacts with: …

Almost no peak output after peakcalling of mtDNA with MACS2 0 I am new to the CHIP-seq analysis. I am basically trying to call peaks using MACS 2 with the proccessed data of mitochondrial DNA only in bedgraph format given in the accession number GSE48176 under the link www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48176. I…

Here, we describe a novel, simple, and low-cost device to successfully perform in vitro photodynamic therapy (PDT) assays using two-dimensional HeLa cell culture and verteporfin as a photosensitizer. Photodynamic therapy, PDT, offers several advantage to cancer treatment, and its efficacy depends on a light source to activate a photosensitizer. Although…

Rath S, Sharma R, Gupta R, Ast T, Chan C, Durham TJ, Goodman RP, Grabarek Z, Haas ME, Hung WHW et al (2021) MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. Nucleic Acids Res 49:D1541–D1547 CrossRef  CAS  PubMed  Google Scholar  Smith AC, Robinson AJ (2016) MitoMiner…

Biosafety statement All experiments with cell lines and viral infections were carried out in a Biosafety Level 2 facility under the approval of the Biosafety Office in the Department of Environment, Health and Safety and the Institutional Biosafety Committee at the University of North Carolina at Chapel Hill. The laboratory…

Samples and Cell Lines A total of 78 pairs of tumor samples and the adjacent non-carcinoma control samples were collected by surgery from CC patients in our study. The peripheral blood was also sampled from each individual and the serum was prepared and preserved under − 80 °C till further analysis. The Medical…

Feb 01, 2023 DOI: dx.doi.org/10.17504/protocols.io.bp2l69r8klqe/v1 Protocol Citation: Francesca Tonelli 2023. Immunofluorescence-based assay to assess LRRK2 recruitment by Rab29. protocols.io dx.doi.org/10.17504/protocols.io.bp2l69r8klqe/v1 License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited…

Here we provide a tool that directly selects biallelically edited knock-ins using cell-surface displays, thereby eliminating the need for extensive clonal verification. By doing so SNEAK PEEC greatly reduces the considerable effort currently expended to obtain biallelically edited clones. The ability to generate a clonal population with multiple edits is…

CDKs support SARS-CoV-2 RdRp-mediated gene expression To identify cellular proteins that modulate the SARS-CoV-2 RNA synthesis, we first performed immunoprecipitation coupled with mass spectrometry (MS) to determine cellular proteins that associate with SARS-CoV-2 RdRp. Briefly, Flag-tagged nsp7, Flag-tagged nsp8, and Flag-tagged nsp12 plasmids were co-transfected into HEK293T cells, and the…

We designed pDOC to support multiple strategies for analyzing protein degradation in vitro, specifically cell-free systems. The device is based on a MITOMI integrated microfluidic chip, originally developed to quantify protein-ligand interactions at equilibrium24,33. The MITOMI module was modified to contain an array of 16 × 64, 32 × 32…

Ethics statement All procedures involving laboratory mice were approved by the Duke University IACUC under the protocol numbers A189-18-08 and A142-21-07. Mice were housed with up to five mice per cage and the ambient room conditions ranged from 70–74 °F and 30–70% humidity with a 12-hour dark/light cycle. Animals were assessed…

Reagents, antibodies, viruses and cells LMW-Poly(I:C), LPS, 2′3′-cGAMP and DMXAA (InvivoGen); hydroxyurea, camptothecin and mitomycin C (MCE); GM-CSF, Flt3L (peproTech); lipofectamine 2000 (Invitrogen); polybrene (Millipore); RNAiso Plus (Takara); HT-DNA (Sigma); SYBR (BIO-RAD); dual-specific luciferase assay kit (Promega); ELISA kit for murine Ifn-β (PBL); ELISA kits for murine IP-10 (Biolegend) were…

Bibliographic Details Author Ghadami, Mohammad Shagoshtasbi, Hooman Mahjoob, Mohammad Jahromi Lee, Yi-Kuen Issue Date 2013 Source The 8th Annual IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS 2013), Institute of Electrical and Electronics Engineers (IEEE), 2013, p. 895-898 Abstract This paper describes a comparative study of two feedback…

Göteborgs universitet möter samhällets utmaningar med mångsidig kunskap. 56 000 studenter och 6 600 medarbetare gör universitetet till en stor och inspirerande arbetsplats. Stark forskning och attraktiva utbildningar lockar forskare och studenter från hela världen. Med ny kunskap och nya perspektiv bidrar Göteborgs universitet till en bättre framtid. We seek…

Bibliographic Details Author Zhao, Xu Liu, Haixiang Wang, Xiaoyi Zhao, Cong Izhar Tang, Benzhong Lee, Yi-kuen Issue Date 2020 Source 15th IEEE International Conference on Nano/Micro Engineered and Molecular System, NEMS 2020 / IEEE. New York, NY, USA : IEEE, 2020, p. 230-233, Article no.: 9265581 Abstract Electroporation (EP) is…

Biogenesis, biology and characterization of circular RNAs Kristensen LS et al. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet. (2019) Summary text Biogenesis and properties of circRNAs Biogenesis of cirRNA Characteristics of circRNAs Discover and analyze circRNAs circRNA genome-wide analysis CircRNA site-specific analysis circRNA visualization Biological functions…

Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…

Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar  Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…

doi.org/10.1016/j.bioelechem.2006.05.008Get rights and content Abstract In this study, a new micro electroporation (EP) cell chip with three-dimensional (3D) electrodes was fabricated by means of MEMS technology, and tested on cervical cancer (HeLa) cells. Extensive statistical data of the threshold electric field and pulse duration were determined to construct an EP…

Badaoui B, Rutigliano T, Anselmo A, Vanhee M, Nauwynck H, Giuffra E, Botti S. RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence. PLOS ONE. 2014;9:91918. Article  Google Scholar  Bateman A, Birney E, Cerruti L, Durbin R, Etwiller…

Altman, B. J., Stine, Z. E. & Dang, C. V. From Krebs to clinic: glutamine metabolism to cancer therapy. Nat. Rev. Cancer 16, 619–634 (2016). CAS  Article  Google Scholar  Hensley, C. T., Wasti, A. T. & DeBerardinis, R. J. Glutamine and cancer: cell biology, physiology, and clinical opportunities. J. Clin….

Certain, it’s good when I’ve an image of some object, and a neural community can inform me what sort of object that’s. Extra realistically, there is perhaps a number of salient objects in that image, and it tells me what they’re, and the place they’re. The latter process (referred to…

NoClassDefFoundError: htsjdk/samtools/util/IntervalTree 0 When I run circm6A (github.com/canceromics/circm6a) example code: cd ../.. java -Xmx16g -jar circm6a.jar -ip test_data/HeLa_eluate_rep_1.chr22.bam -input test_data/HeLa_input_rep_1.chr22.bam -r test_data/gencode_chr22.gtf -g test_data/hg38_chr22.fa -o test_data/example_Hela The following error occurred: Start at 2021-12-12 16:33:26 Exception in thread “main” java.lang.NoClassDefFoundError: htsjdk/samtools/util/IntervalTree at main.Method.loadGenes(Method.java:200) at main.Method.run(Method.java:66) at main.Main.main(Main.java:9) Caused by: java.lang.ClassNotFoundException: htsjdk.samtools.util.IntervalTree…

Introduction Invaded by exogenous or endogenous pathogens, the host immune system will be activated accordingly to resist harm and maintain homeostasis, which includes innate immunity and adaptive immunity. As the first line of host immune defense, innate immunity plays a critical role in recognizing extracellular and intracellular pathogens (1, 2)….

Introduction Chronic obstructive pulmonary disease (COPD) is a chronic respiratory disorder that progresses slowly and is characterized by an obstructive ventilatory pattern, which is rarely reversible. The main risk factors are active smoking, genetic factors, and air pollution. In particular, COPD has been a major public health problem and will…

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…

The Human Genome Project, from a certain point of view, began in 1981 with the publication1 of the entire human mitochondrial DNA (mtDNA) series. The Cambridge Reference Sequence (CRS), as now controlled, remains indispensable for studies. human evolution, population genetics, and mitochondrial disease; however, it has been identified for some…

Introduction Carrión’s disease is a vector-borne biphasic illness restricted to the South American Andes, with Peru as the most affected country. 1 Gomes C Pons MJ Del Valle Mendoza J Ruiz J Carrion’s disease: an eradicable illness?. The causative agent, Bartonella bacilliformis, is transmitted to humans by sandflies (Lutzomyia spp)….