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Tag: K562
[PDF] A Scalable, Off-the-Shelf, and Cost-Effective NK Cell Manufacturing Platform for Developing NK Cell-Based Immunotherapy
Natural killer (NK) cells are innate lymphocytes that play a key role in the control of infection and malignancy. NK cells are potent killers of target cells and act in an MHC-independent manner, enabling their application as allogenic therapy for cancer. Human iPSCs are pluripotent with the ability to self-renew,…
New lipidic peptide IK14004 shows promise in treating cancer and reducing autoimmune complications
A recent study published in Nature’s Scientific Reports described a lipidic peptide, named IK14004, which fosters the growth of immunosuppressive T regulatory (Treg) cells and separates interleukin-2 production from interferon-gamma, while also activating CD8+ T cells. Study: An immunomodulating peptide with potential to suppress tumour growth and autoimmunity. Image Credit: crystal light/Shutterstock.com…
ABCB1 and immune genes in breast cancer
Introduction Chemoresistance is a major challenge for breast cancer treatment.1 The mechanisms of chemoresistance are complex because of crosstalk between receptor tyrosine kinases and downstream pathways, deregulation of cell-cycle and apoptosis regulators, and modulation of tumor-infiltrating immune cells.2 The ATP-binding cassette (ABC) superfamily is one of the largest families of…
CRISPR screening in hematology research: from bulk to single-cell level | Journal of Hematology & Oncology
Transcriptomics CROP-seq [46] Jurkat Poly-A CRISPRko Cas9 119 – 5798 (+ 1320 cells with NT gRNA) Lentiviral DROP-seq RNA Perturb-seq [43, 44] K562 Barcode CRISPRi dCas9-KRAB UPR epistasis screen: 9 triplet combinations UPR Perturb-seq experiment: 91 Up to 3 gRNAs in a single vector UPR epistasis screen: 15006 UPR Perturb-seq experiment:…
Ingenio Kit-Amaxa 100 rxn, 0.2 cm Cuvette/Droppers
Description High Efficiency Electroporation– Deliver to hard to transfect cell lines and primary cells Compatible with Most Conventional Electroporation Devices – Use your existing system including the Ingenio® EZporator®, Lonza-Amaxa®, Bio-Rad® or Harvard BTX® Save Money and Reduce Research Costs Without Sacrificing Performance – Ingenio® Electroporation Solution is available as a stand-alone solution or…
NadPrep rRNA Blocking Reagent (Human) – Library Preparation
Feature Simple and Convenient Mix the rRNA Blocking Reagent directly with the reaction system in a single pipetting step Fast and Efficient Efficiently block rRNA in just 8 min Effectively enrich low-abundance RNA Enhance informative content and reduce sequencing costs Flexible Compatibility Compatible with samples of different RNA quality Support…
Cost-effective DNA methylation profiling by FML-seq
The FML-seq method The protocol for FML-seq comprises only three steps (Fig 1A). First, genomic DNA (gDNA) is digested by a methylation-dependent restriction endonuclease that cuts at a certain distance from the 5-methylcytosine or 5-hydroxymethylcytosine in its motif and leaves a short overhang (10). Second, a master mix is added…
capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements
Cell culture All cell lines were grown in 6 cm dishes at 37 °C in a 5% CO2 incubator. The K562, MDA-MB-231 and HCT 116 cell lines were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotics (pen-strep). NCM460 cells were cultured in RPMI 1640 medium supplemented…
Efficient delivery of a large-size Cas9-EGFP vector in porcine fetal fibroblasts using a Lonza 4D-Nucleofector system | BMC Biotechnology
Isolation of PFFs PFFs were isolated from the 30-day-old fetuses of a Large White pig purchased from Fujian Yongcheng Agricultrual & Animal Husbandry Science and Technology Group Co., Ltd (Jiangxi Province, China). Briefly, the sow was euthanized by intravenous injection of potassium chloride solution (100 mg/kg) under anesthesia by an intramuscular…
Using metagenomics to identify viruses in plasma samples
Overview of the study design. We conducted RT-qPCR on 670 plasma samples, followed by metagenomic sequencing of 593 of the samples, received from (i) individuals suspected to have Lassa Fever (LF; caused by Lassa virus, LASV), collected from teaching hospitals with clinical expertise in viral hemorrhagic fevers; (ii) suspected infectious…
Encode eCLIP-seq bed.gz header name
Encode eCLIP-seq bed.gz header name 0 I am trying to understand ENCODE eCLIP-seq bed.gz data. I can assume chromosome, start, end, RBP_cellline, but then I do not understand the rest of the column’s meaning. I tried to search everywhere, but I couldn’t find it. Any idea of the rest of…
SF3B1 hotspot mutations confer sensitivity to PARP inhibition by eliciting a defective replication stress response
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)….
Bioconductor – preciseTADhub
DOI: 10.18129/B9.bioc.preciseTADhub Pre-trained random forest models obtained using preciseTAD Bioconductor version: Release (3.17) An experimentdata package to supplement the preciseTAD package containing pre-trained models and the variable importances of each genomic annotation used to build the model parsed into list objects and available in ExperimentHub. In total, preciseTADhub provides…
Optimized minimal genome-wide human sgRNA library
sgRNA collection and enzyme cut site annotation All sgRNAs corresponding to potential NGG-containing target sites on the human (GRCh38/hg38) genome were calculated by a customized Perl script. The enzyme cut site was set at the 17 position from 5’ to 3’ of each sgRNA sequence. These sgRNAs have more than…
Single-cell quantification of ribosome occupancy in early mouse development
PDMS chip fabrication Moulds were 3D-printed by Proto Labs with WaterShed XC 11122 at high resolution (Supplementary Fig. 1). Reusable moulds were assembled by taping 3D-printed molds to glass slides (5″ × 4″; Ted Pella). Sylgard 184 PDMS monomer and curing agent (4019862, Ellsworth Adhesives) were mixed at a 10:1…
Tox4 regulates transcriptional elongation and reinitiation during murine T cell development
Pan-hematopoietic Tox4 deletion reduces number of multipotential progenitors and impairs T cell development To understand the role of TOX4 in development, we generated Tox4 conditional knockout mice by the CRISPR-Cas9 methodology, and two loxP sites in the same orientation were inserted upstream and downstream of exons 4–6, respectively (Supplementary Fig. 1a). Considering…
uridine-derived ribose as an alternative energy source
In a recent study published in Nature Metabolism, researchers attempted to identify new genes and molecular pathways that might supply energy when the availability of glucose or other nutrients is limited. Study: Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions. Image Credit: Irina Anosova/Shutterstock.com Background In…
Researchers discover a way to improve nonviral gene editing as well as a new type of DNA repair
Modification of HDRTs with interstrand crosslinks increases HR during gene editing. (a) Top panel: Cas9 RNPs introduce a double strand DNA break (DSB) at a targeted region in the genome, which can be repaired by error prone end joining (EJ) processes that rejoin the ends of the break, or homology-directed…
Targeting Poly(ADP)ribose polymerase in BCR/ABL1-positive cells
Cells and cell culture KOPN30, BV173, and K562 are BCR/ABL1-positive leukemia cell lines. All leukemia cell lines, as well as Ba/F3 cells, were maintained in RPMI-1640 medium supplemented with 15% fetal bovine serum (FBS) and penicillin–streptomycin (100 U/mL) at 37 °C in an atmosphere containing 5% CO2. KOPN30 cells were obtained…
Stable expression of large transgenes via the knock-in of an integrase-deficient lentivirus
CLIP enables high-efficiency knock-in into an essential locus To create CLIP, we leverage integrase-deficient lentiviruses (IDLV) to deliver an HDR donor template as a viral RNA genome to cells25,26. IDLV consists of lentiviral components but with a D64V mutation in the integrase, maintaining this enzyme’s ability to package and nuclear…
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…
Generation of Natural Killer Cells from Human Expanded Potential Stem Cells
The present protocol shows how to differentiate CD3−/CD45+CD56+ cells with mild cytotoxicity from human expanded potential stem cells (hEPSCs) under both 3D and 2D culture conditions. This allows for routine phenotypical validation without the destruction of the complex microenvironment. Speaking of significance, generating NK cells from an expandable source is…
Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes
Multiple H2BNTac sites occupy the same genomic regions H2BNTac sites are similarly regulated by CBP/p30018 (Supplementary Fig. 1a), yet the reported genome occupancy patterns of H2BNTac sites are dissimilar from each other22,23 (Supplementary Note 1). To resolve this conundrum, we systematically compared H3K27ac and H2BNTac genomic occupancy and regulation by…
Deep genomic characterization highlights complexities and prognostic markers of pediatric acute myeloid leukemia
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…
Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements
Abstract CRISPR-based gene activation (CRISPRa) is a promising therapeutic approach for gene therapy, upregulating gene expression by targeting promoters or enhancers in a tissue/cell-type specific manner. Here, we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific, CRISPRa-responsive cis-regulatory elements and the…
ANKLE1 cleaves mitochondrial DNA and contributes to cancer risk by promoting apoptosis resistance and metabolic dysregulation
ANKLE1 is the causal gene for breast and ovarian cancer risk in the chr19p13.1 region Expression quantitative trait loci (eQTL) data have revolutionized how geneticists identify candidate causal genes from genome-wide association study (GWAS) loci. We integrated the most recent meta-analysis of breast cancer GWAS10 and Genotype-Tissue Expression (GTEx) project…
Simplified DNA Quantification and Normalization
Sponsored Content by TecanJan 25 2023 Making Double-stranded DNA Quantification and Normalization easy and fast using Promega QuantiFluor® dyes with the Fluent® Laboratory Automation Solution from Tecan. Introduction The field of genomics demands double-stranded (ds) DNA quantification and normalization to a high standard of reliability. While absorbance techniques have been…
RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins
Abstract Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However,…
The Point of Base Editors: Correcting Point Mutations
Some genome editing systems are highly conspicuous. They introduce double-strand breaks to DNA that attract the attention of cellular mechanisms such as nonhomologous end joining and homology-directed repair. If a genome editing system is so brash as to attempt a sizable insertion of new DNA, homology-directed repair must ensure that…
Dissecting Cancer with Single-cell DNA Sequencing & Multi-omics | Learning Center
CANCER & SINGLE-CELL ANALYSIS The heterogeneity and dynamism of cancer present formidable challenges to understanding and treating the disease. As discussed in the last section, tumor evolution often leads to considerable genetic variation across clones. But the complexity of tumors does not stop at the level of DNA. Intratumoral phenotypic…