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  1. Genomic Deletions in Mammalian Cell Lines

    Type
    Collection
    ...Ensure there are 2 x 10 6 cells per CRISPR pair. Resuspend 2 x 10 6 cells in 100 μl of electroporation solution...Dilute oligos 1:10 in ddH 2 O ( e.g., 1.0 μl annealed oligos + 9.0 μl ddH 2 O to yield a concentration...), 50-100 ng gDNA, and H 2 O up to 20 μl. Use the primers designed in step 2 above. Conduct PCR for “non-deletion...supplemented with 2% penicillin/ streptomycin and 1% L-glutamine, which is used for MEL cells. However, transient...expression construct. Electroporate cells with 250 volts for 5 msec in a 2 mm cuvette using an electroporation...designed based on testing the bulk sorted cells. Run samples on 2% agarose gel at 10 V/cm using 1x Tris-acetate-EDTA...frequency of indels formed on non-deleted alleles 2 , which are likely to cause frameshift mutations leading...
  2. Allen Institute for Cell Science Plasmid Collection

    Type
    Collection
    ...Transcription factor SOX-2 Transcription Factor 124607 ACTN2-mEGFP AICSDP-63 mEGFP Alpha-actinin-2 Sarcomeric z-disks...101781 CETN2-mTagRFP-T AICSDP-22 mTagRFP-T Centrin-2 Centrioles 101782 LAMP1-mEGFP AICSDP-19 mEGFP LAMP... AICSDP-83 mEGFP EZH2 Polycomb repressive complex 2 164500 POLR2A-mEGFP AICSDP-117 mEGFP RPB1 RNA polymerase...mEGFP AICSDP-77 mEGFP Telomeric repeat-binding factor 2 (TRF2) Telomeres 168799 CTCF-mEGFP AICSDP-144 mEGFP...for Cell Science has deposited plasmids to generate fluorescently tagged proteins of key cellular structures... Protein Guide Subcellular Localization Plasmids Protocols The Allen Institute for Cell Science has produced...fluorescently tagged proteins of key cellular structures in human cell lines of their choice. For a full ...
  3. Plasmids for Stem Cell Research

    Type
    Collection
    ... reprogramming of mouse somatic cells. Cell Stem Cell. 2008 Feb 7. 2(2):151-9. Jaenisch Lentivirus Mouse...during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell. 2008 Mar 6. 2(3):230-40. Hochedlinger... a synthetic self-replicative RNA. Cell Stem Cell. 2013 Aug 1;13(2):246-54. Dowdy Adenovirus Mouse Non-integrating...Dynamic Nature of Induced Pluripotency. Cell. 2015 Jul 16;162(2):412-24. Mikkelsen Lentivirus Human Expression...Lentiviral Human Small molecules enable neurogenin 2 to efficiently convert human fibroblasts into cholinergic...Conversion of Fibroblasts. Neuron. 2014 Oct 22;84(2):311-23. Yoo Fibroblasts Neurons Lentiviral Human ...
  4. COVID-19 Resources

    Type
    Collection
    ...proximal origin of SARS-CoV-2 . TMPRSS2 - Hoffmann M, et al, 2020, Cell SARS-CoV-2 Cell Entry Depends on ACE2...Converting Enzyme 2) is the host cell receptor mediating the entry of SARS-CoV and SARS-CoV-2 viruses. ( 1 ...that primes the SARS-CoV-2 S protein and is involved in virus entry into cells. ( 2 ) FURIN - an enzyme that...origin of SARS-CoV-2 . BSG - Wang, K et al, 2020, BioRxiv SARS-CoV-2 invades host cells via a novel route...page: SARS-CoV-2 Antibodies : Recombinant monoclonal antibodies that target SARS-CoV-2 nucleocapsid protein...protein. SARS-CoV-2 Plasmids : Plasmids that are available or coming soon containing SARS-CoV-2 sequences. SARS-CoV... targeting the SARS-CoV-2 nucleocapsid protein (Brian Geiss). Anti-SARS-CoV-2 Nucleocapsid Protein [mBG86...
  5. Immunology Research Plasmids and Resources

    Type
    Collection
    ...immunoglobulin heavy diversity 2-15 D2, IGHD215 IGHD2-2 immunoglobulin heavy diversity 2-2 IGHD22 IGHD2-21 immunoglobulin...heat shock 70kDa protein 2 HSP70-2, HSP70-3 HSPA4 heat shock 70kDa protein 4 APG-2, HS24/P52, MGC131852, ...variable 2-33 (non-functional) IGLV233, V1-9 IGLV2-8 immunoglobulin lambda variable 2-8 IGLV28, V1-2 IGLV3...beta 4 DEFB-2, DEFB102, DEFB2, HBD-2, SAP1 EDN1 endothelin 1 ET1, HDLCQ7 EDN2 endothelin 2 ET2, PPET2 ...receptor subfamily 2, group C, member 1 TR2 NR2C2 nuclear receptor subfamily 2, group C, member 2 TAK1, TR2R1...suppression of tumorigenicity 2 - STC1 stanniocalcin 1 STC STC2 stanniocalcin 2 STC-2, STCRP TAC1 tachykinin,... (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40) CLMF, CLMF2...
  6. New England Biolabs Cell-Imaging Plasmid Collection

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    Collection
    ...transient mammalian expression 101126 pACP-tag (m)- 2 Vector ACP/MCP-tag Empty backbone for stable and transient... sub-cellular localization (membrane, nucleus, etc.) are also available Non-toxic to living cells To learn...repair protein, and is suitable for both cell-permeant and non-cell-permeant proteins. CLIP-tag CLIP-tag ...Control for cell surface localization 101131 pACP-GPI Control Plasmid ACP/MCP-tag Control for cell surface...visualization of proteins inside cells. Depositor... Depositor Collections New England Biolabs Cell-Imaging Plasmid Collection...Collection New England Biolabs Cell-Imaging Plasmid Collection Technology Plasmids Supplemental Information ...
  7. SARS-CoV-2 Pseudotyped Virus

    Type
    Collection
    ...to infect permissive cells that express ACE2, the cellular receptor for SARS-CoV-2, in a single round of...pseudotyping with SARS-CoV-2 spike protein. Collections... Collections COVID-19 - Viral Pseudotyping SARS-CoV-2 Pseudotyped Virus...Virus Mechanisms of SARS-CoV-2 infection remain poorly understood but are critical for developing therapeutic...spread. As a Biosafety Level 3 (BSL-3) agent, SARS-CoV-2 requires specialized facilities for the study of the...replication-defective virus particles with the SARS-CoV-2 spike (S) glycoprotein on the envelope surface. Pseudotyped...particles have been pseudotyped with the SARS-CoV-2 Spike protein and you will find examples of each in...
  8. Fluorescent Protein Guide: Biosensors

    Type
    Collection
    ...of basal H 2 O 2 levels with peroxiredoxin-based probes Real-time monitoring of basal H 2 O 2 levels with...Belousov Hydrogen Peroxide (H 2 O 2 ) Cytosolic or mitochondrial sensor for H 2 O 2 oxidation (roGFP2-Orp1) ...peroxiredoxin-2-based probe. Nat Commun. 2018 Aug 7;9(1):3145. Hadley Sikes Hydrogen Peroxide (H 2 O 2 ) Monitoring...Hydrogen Peroxide (H 2 O 2 ) HyPer biosensor to measure changes in intracellular hydrogen peroxide concentration...Hydrogen Peroxide (H 2 O 2 ) Expresses hydrogen peroxide biosensor HyPer2 in plant cells Photosynthesis-dependent...encoded Ca(2+) indicator with enhanced two-photon absorption. Neurophotonics. 2024 Apr;11(2):024207. doi...Calcium Red fluorescent calcium sensors (fRCaMP1/2, GECO1/2) The kinetic mechanisms of fast-decay red-fluorescent...
  9. p53 Pathway

    Type
    Collection
    ...CCNB1 CCNB2 CCNB3 Cyclin B1, 2, or 3 Cyclin D CCND1 CCND2 CCND3 Cyclin D1, 2, or 3 Cyclin E CCNE1 CCNE2 ...kinase 1 CHK2 Checkpoint kinase 2 Cop-1 Ring finger and WD repeat domain 2 (RFWD2); E3 ubiquitin protein...SESN3 Sestrins 1, 2, or 3 Siah Siah E3 ubiquitin protein ligase 1 TSC2 Tuberous sclerosis 2 TSP1 Thrombospondin... Spring Harbor Perspectives in Biology. 2010 Feb;2(2):a001107. PMC PMID: 20182618 . Do you have suggestions...threonine kinase ATR ATR serine/threonine kinase B99 G-2 and S-phase expressed 1; also known as GTSE1 BAI-1...inhibitor 1A p48 Damage-specific DNA binding protein 2, 48kDa p53 Tumor protein p53 p53AIP1 Tumor protein... domain protein 1 PIGs Etoposide induced 2.4 PIRH-2 Ring finger and CHY zinc finger domain containing ...
  10. Lighting Up Cell Signaling with Photoswitchable Kinases

    Type
    Blog Post
    ...status of MEK1/2 was tracked at 5 minute intervals via Western blot. Phosphorylation of MEK1/2 peaks at just...PubMed PMID: 28232577. Figures 2-4 were modified from this reference. 2. Regot, Sergi, Jacob J. Hughey...Treatment of the cells with a PP1/PP2A inhibitor leads to maintenance of phosphorylated MEK1/2 levels, suggesting...precisely control the timing of kinase activity. 2. Studying negative feedback loops of signaling pathways... studied the negative feedback on endogenous MEK1/2 phosphorylation by creating a short pulse of psRaf1...activity. They did this by exposing psRaf1 to a short 2 minute pulse of 500 nm light (turn on psRaf1) followed...suggesting PP1/PP2A is responsible for this MEK1/2 negative feedback. 3. Studying signaling pathways in...
  11. Fluorescent Protein Guide: Subcellular Localization

    Type
    Collection
    ... on cell cycle) Centrin-2 EGFP Erich Nigg 41151 pEGFP Cep170 C-term Centrioles (dependent on cell cycle...sequence YFP Thorben Dammeyer 54520 mCherry-Peroxisomes-2 Peroxisome Peroximal Targeting Signal 1 (PTS1) mCherry...give the cell its shape, organize cellular organelles, and are necessary for movement and cell division...between animal cells. They are important for holding cell structures together and reducing cell stress. There... General Structures The cell contains a variety of organelles and subcellular structures each with their...example, houses the cell’s genetic material. The mitochondria produces the energy cells required for chemical...kappa-myc-dL5-2xG4S-TMst Cell surface (mammalian) PDGFR-derived dL5 FAP; mCerulean3 Marcel Bruchez 45944 pTDpelB-C_sfYFPTwinStrep...
  12. Ras Pathway

    Type
    Collection
    ...erythroid 2 like 2 NFKB1 Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 PAK PAK1...E2F transcription factor ECT2 Epithelial cell transforming 2 EGFR Epidermal growth factor receptor EIF4EBP... Scribbled planar cell polarity protein SHC SHC1 SHC2 SHC3 SHC4 SHC (Src homology 2 domain containing)...ARHGEF2 Rho/Rac guanine nucleotide exchange factor 2 CCND CCND1 CCND2 CCND3 Cyclin D CDK CDK4 CDK6 Cyclin-dependent...enhancer of kinase suppressor of Ras CYTH2 Cytohesin 2 DUSP DUSP1 DUSP2 DUSP3 DUSP4 DUSP5 DUSP6 Dual specificity...binding protein ERBB2 Erb-b2 receptor tyrosine kinase 2 ERK MAPK1 MAPK3 Also known as MAPK; Mitogen-activated...homolog GRB2 Growth factor receptor bound protein 2 ICMT Isoprenylcysteine carboxyl methyltransferase ...
  13. Chemogenetics AAV Preps

    Type
    Collection
    ...fusion none 2, 5 Richie 121539 pAAV SYN1 HA-hM3D(Gq) hM3D(Gq) - Activation HA fusion none 2, 5 Richie 50467...none 2, 8 Roth 50476 pAAV-CaMKIIa-hM3D(Gq)-mCherry hM3D(Gq) - Activation mCherry fusion none 1, 2, 5, ...(Gq) - Activation mCherry fusion Cre-dependent 1, 2, 5, 8, 9, rg*, PHPeB Roth 44362 pAAV-hSyn-DIO-hM4D...(Gi) - Inhibition mCherry fusion Cre-dependent 1, 2, 5, 8, 9, rg*, PHPeB Roth 65417 pAAV-hSyn-dF-HA-KORD-IRES-mCitrine...mCherry hM3D(Gq) - Activation mCherry fusion none 1, 2, 5, 8, 9, rg* Roth 50475 pAAV-hSyn-hM4D(Gi)-mCherry...mCherry hM4D(Gi) - Inhibition mCherry fusion none 1, 2, 5, 8, 9, rg* Roth 52536 rAAV-CAG::FLEX-rev:: hM4D-...mCherry hM4D(Gi) - Inhibition mCherry fusion none 1, 2, 5, 8, 9 Roth 75033 pAAV CD68-hM4D(Gi)-mCherry hM4D...
  14. Rinehart Lab Phosphoprotein Reagents

    Type
    Collection
    ...111707 Mode #2 Library (NEDD4 WW2 domain) Pooled Library 111708 Mode #2 Library (NEDD4-2 WW2 domain) References...Pooled Library 111705 Mode #2 Library (14-3-3β) Pooled Library 111706 Mode #2 Library (14-3-3σ) Pooled Library...discovered by fluorescence-activated cell sorting (FACS). The mode #2 phosphosite library with four different...phosphorylation-dependent protein-peptide interactions (“mode #2” expression, Barber et al, Nat. Biotech. 2018). The... WW2 domain of NEDD4, and the WW2 domain of NEDD4-2; 111705-8 ) is available from Addgene. Screening kinases...iSPI_pSer_Subpool#1 Pooled Library 188527 iSPI_pSer_Subpool#2 Pooled Library 188528 iSPI_pSer_Subpool#3 Pooled Library...pos ctrl Plasmid 111883 pNAS1b split mCherry NEDD4-2 WW2 Plasmid 111882 pNAS1b split mCherry NEDD4 WW2 ...
  15. CRISPR Pooled gRNA Libraries

    Type
    Collection
    ...3rd 1, 2, or 4 49,766 arrays Broad GPP kinome Brunello 75314, 75315 (1 plasmid) 75312, 75313 (2 plasmid...GPP genome-wide Brunello 73179 (1 plasmid) 73178 (2 plasmid) Knockout Human Doench and Root 3rd 4 76,441...Broad GPP genome-wide Brie 73632 (1 plasmid) 73633 (2 plasmid) Knockout Mouse Doench and Root 3rd 4 78,637...172651 (Set D) Knockout Human Doench and Root 2nd 2 40,710 Inzolia Human CRISPR/Cas12a Multiplex Knockout...3,052 Broad GPP kinome Brie 75317 (1 plasmid) 75316 (2 plasmid) Knockout Mouse Doench and Root 3rd 4 2,852...MinLibCas9 Library 164896 Knockout Human Garnett 3rd 2 37,722 Green monkey (Chlorocebus sabaeus) sgRNA library...Library (Gattinara) 136986 Knockout Human Doench 3rd 2 40,964 Ingolia lab S cerevisiae CRISPRi v1 – barcodes...
  16. When is a Monomer not a Monomer? The Top Three Ways Your Favorite Fluorescent Protein Oligomerizes in Cells

    Type
    Blog Post
    ...difficult to ignore [1, 2]. 2. Fusion to an obligate dimer or oligomer Several cell proteins normally self-associate.... J Cell Biol, 2003. 163(2): p. 257-69. PubMed PMID: 14581454. PubMed Central PMCID: PMC2173526. 2. Zacharias...Kd is unlikely to form dimers in a cell. The Kd of EGFP is 0.11 mM [2]. Following the simple logic outlined... nature are prone to dimerization (i.e. EGFP) [1, 2] or even form obligate tetramers (i.e. DsRed) [3]....organized smooth endoplasmic reticulum (OSER) whorls. 2)A dimerizing protein of interest fused to a dimerizing... designed to detect resulting in false positives [2, 4]. Solutions to the polymer problem There are some...Citrine) can be monomerized with an A206K mutation [2]. Addgene has many of these constructs and they are...
  17. Giving gRNAs a Facelift - Synthetic and Beyond

    Type
    Blog Post
    ...same site, is 2’-fluoro (2’-F), which substitutes a fluorine for the hydroxyl group at the 2’ position. ...most common of these is 2’-O-methylation, where a methyl group is added to the 2’ hydroxyl group of the...them together, for example phosphorothioates with 2’-O-methyl modifications, proved more stability than...generated by introduction of a single photocleavable 2-nitrobenzyl linker in the 20-bp targeting region of...photocleavable gRNAs. Molecular Cell 81, 7, 1553-1565 (2021). https://doi.org/10.1016/j.molcel.2021.02.007 Moroz-Omori...evolved ways to prevent degradation of important cellular RNA molecules with post translational modifications...slightly more efficient and less toxic to mammalian cells (Allen, et al., Frontiers in Genome Editing).  Some...
  18. Brain Armamentarium

    Type
    Collection
    ...expressing mCherry-tagged channelrhodopsin-2 driven by PV+ basket cell-targeting enhancer Gordon Fishell Viviana...expressing mCherry-tagged channelrhodopsin-2 driven by chandelier cell-targeting enhancer Gordon Fishell Viviana...construct expressing mCherry-tagged channelrhodopsin-2 driven by SST interneuron-targeting enhancer Gordon...construct expressing mCherry-tagged channelrhodopsin-2 driven by Lamp5 interneuron-targeting enhancer Gordon...construct expressing mCherry-tagged channelrhodopsin-2 driven by VIP interneuron-targeting enhancer Gordon...construct expressing mCherry-tagged channelrhodopsin-2 driven by cholinergic neuron-targeting enhancer Gordon...
  19. Trimmer Lab NeuroMab Collection

    Type
    Collection
    ...FHF2 Human Mouse IgG2a 114527 Anti-JIP-2/IB-2 [N135/37.2R] JIP-2/IB-2 Mouse Mouse IgG2a 114529 Anti-Pan-SAPAP...Anti-CDY1/2/L1/L2 [N143/36R] CDY1/2/L1/L2 Human Mouse IgG2a 206535 Anti-CDY1/2 [N143/38R] CDY1/2 Human Mouse...206763 Neuroligin-2 scFv [L107/90] L107/90 scFv Neuroligin-2 Mouse Mouse 206764 Neuroligin-2 scFv [L107/95...receptor Rat Mouse IgG2a 114484 Anti-Stonin-2 [N346/9R] Stonin-2 Human Mouse IgG2a 114485 Anti-NSD3 [N348...Pan-FHF-A Human Mouse IgG2a 114510 Anti-REEP1/2 [N326D/29R] REEP1/2 Mouse Mouse IgG2a 114511 Anti-Kv3.1b K+ ...Mouse Mouse IgG2a 114547 Anti-Mitofusin-2 [N171/17.4R] Mitofusin-2 Mouse Mouse IgG2a 114548 Anti-Mortalin...Mouse IgG2a 140065 Anti-SCG10/Stathmin-2 [L5/1R] SCG10/Stathmin-2 Rat Mouse IgG2a 140066 Anti-Co-Rest/RCOR1...
  20. Genetic Code Expansion

    Type
    Collection
    ...48696 pANAP AnapRS E. coli 3-(6-acetylnaphthalen-2-ylamino)-2-amino-propanoic acid (Anap) Mammalian TAG Peter...Mammalian TAG Huiwang Ai 73544 pEvol-pAcFRS.2.t1 pAcFRS.2.t1 E. coli p-acetyl-l-phenylalanine (pAcF) Bacterial...Bacterial TAG Farren Isaacs 73546 pEvol-pAzFRS.2.t1 pAzFRS.2.t1 E. coli p-azido-l-phenylalanine (pAzF) Bacterial..._AnapRS AnapRS E. coli 3-(6-acetylnaphthalen-2-ylamino)-2-amino-propanoic acid (Anap) Mammalian TAG Simon...Jesse Rinehart 71403 pCMV-DnpK PylRS M. barkeri N6‐(2‐(2,4‐dinitrophenyl)acetyl)lysine (DnpK) Bacterial,...pDule-IBBN (G2) IBBN (G2) synthetase M. jannaschii 4-(2′-bromoisobutyramido)-phenylalanine (IBBN) and structurally...pDule2-IBBN (G2) IBBN (G2) synthetase M. jannaschii 4-(2′-bromoisobutyramido)-phenylalanine (IBBN) and structurally...
  21. Starter guide to induced pluripotent stem cells (iPSCs) part 1:  A renaissance in regenerative medicine

    Type
    Blog Post
    ... Regenerative Medicine. Acta Naturae, 2010. 2(2): p. 18-28. PubMed PMID: 22649638. PubMed Central PMCID...specialized cell types [2]. We general speak of 4 levels of stem cell potency: Totipotency: When a cell has ...embryonic stem cells (ESCs), which I discuss in detail below [2]. Multipotency: When a cell can differentiate...mammalian development, cells found in the zygote through to the morula stage are totipotent [2-4]. Pluripotency...PubMed Central PMCID: PMC4686367. 2. Jaenisch, R. and R. Young, Stem cells, the molecular circuitry of pluripotency...Pharmacological Sciences, a Cell Press reviews journal. Stem cells are special types of cells that can develop ...pluripotent cells can be thought of as descendants of totipotent cells. An example of pluripotent cells is embryonic...
  22. 3 Tips to Improve HDR Efficiency for CRISPR Editing in Human Cells

    Type
    Blog Post
    ...into account that HDR is rare, usually 2-5% of the edited cells in our hands, these combined pitfalls ...hundred clones to find the right one Step 2 – Edit the cells a second time using a repair template that...improving editing accuracy by preventing re-editing and (2) optimizing “cut-to-mutation distance”. Furthermore...Additional CRISPR Resources on Addgene's CRISPR Guide Page 2. Optimizing "cut-to-mutation distance"  Even though... wisely (and let them cut close).   Figure 2: Relationship between cut site to mutation distance...PMID: 23287718. PubMed Central PMCID: PMC3795411. 2. Mali, Prashant, et al. "RNA-guided human genome engineering...sequence change the cell must undergo homology-directed repair (HDR), a distinct cellular DNA repair pathway...
  23. Fluorescent Proteins 101: Visualizing Subcellular Structures & Organelles

    Type
    Blog Post
    ...ImageJ plugins JACoP and Coloc 2, BioImageXD, and customized CellProfiler pipelines. Image analysis software...optimized for diverse cellular environments. Since colocalization relies upon the detection of 2 independent fluorescent...Markers of Subcellular Localization Poster here! References 1. Allen Institute Plasmid Pages 2. Cooper ... to the lysosome where they are finally degraded (2, 3). Once you've created your fusion protein, it's...colocalization analysis example is given in Figure 2 (adapted from 4) - Dunn et al. 2011 provides an in-depth...organs, cells comprise compartments and structures, called organelles. Take a sneak peak inside a cell with...vesicles via the secretory pathway to their subcellular or extracellular destination. At the end of their life...
  24. DNA Service - Cloning Grade DNA

    Type
    Collection
    ... Direct transfection into cells is not recommended. Can I order more than 2 µg of cloning grade DNA? At...plasmids in bacterial stabs. DNA Service Details Amount 2 µg Volume 20 µl Concentration 100 ng/µl (± 5 ng/µl... At this time, to order more than 2 µg of a single plasmid, multiple orders would need to be placed through...Can I directly transfect cloning grade DNA into cells? Cloning grade DNA is designed for use in cloning...
  25. Synthetic promoter AAVs for cell-type specific expression in retinal cells

    Type
    Blog Post
    ...the start codon of retinal cell-type specific genes from mice. Strategy #2 (ProB): Create promoters using...horizontal cells transduced by both AAVs would express Cre-mCherry and GFP.   Figure 2: Synthetic...doi.org/10.1038/s41593-019-0431-2  Neff, E.P. An AAV library for retinal cell expression in mouse, macaque... horizontal cells, and Cre-dependent-GFP expresses in horizontal cells and ganglion cells, only the horizontal... in retinal cells. To do this, the group developed a new strategy for finding retinal cell-type specific...and high cell-type specificity.  Strategy #3 (ProC): Create promoters by repeating mouse cell type specific... to test for cell type-specific expression of GFP. Half (113) expressed in retinal cells four weeks post-injection...
  26. Cellosaurus: A Cell Line Information Database

    Type
    Blog Post
    ...can browse entries by cell line groups, such as their vaccine production, SARS-CoV-2 research, or adenovirus...Knowledge Resource. J Biomol Tech. 2018; 29(2): 25-38....in which the cell line was described. Using Cellosaurus Cellosaurus is searchable by cell line name (recommended...resource called Cellosaurus, a growing cell line information database describing nearly 145,000 cell lines. Cellosaurus... Cellosaurus Cellosaurus seeks to identify and describe all cell lines used in research, using four methods... related cell lines when annotating a cell line Community submissions via email: cellosaurus@sib.swiss...with cell line catalogs and collections. Importantly, Cellosaurus also identifies problematic cell lines...
  27. Zhang Lab CRISPR Page

    Type
    Collection
    ...Feng G, Sharp PA, Zhang F. Cell . 2014 Oct 9;159(2):440-55. doi: 10.1016/j.cell.2014.09.014. Epub 2014 Sep... Aug 29. Erratum in: Cell. 2013 Oct 10;155(2):479-80. PubMed . Genome engineering using the CRISPR-Cas9...SpCas9n with 2a-Puro and 2a-EGFP are also available. 2. SpCas9 (or SpCas9n, D10A nickase) + CRISPR RNA array... system - lentiCRISPR - sgRNA and SpCas9 together 2 vector system - lentiCas9-Blast and lentiGuide-Puro...two MS2 RNA aptamers at the tetraloop and stemloop 2 The MS2-P65-HSF1 activation helper protein Full references...backbone with MS2 loops at tetraloop and stemloop 2 and EF1a-zeo resistance marker. Contains BsmBI sites...inverted terminal repeats (ITR) from AAV serotype 2. SaCas9 only: This plasmid ( PX600, #61592 ) contains...
  28. AAV Packaged on Request

    Type
    Collection
    ...yields are generally lower, with a minimum titer of 2 × 10 12 GC/mL and a typical titer of 7 × 10 12 GC/... 10 weeks. This breaks down as follows: Request 1–2 days Look for the banner on an eligible plasmid page... your request. We will send you an email within 1-2 days with a response. Most requests will be approved...make sure it is ready for your experiments. Shipping 2–7 days We will email you with tracking information... tools that effectively transduce many mammalian cell types. AAV is used in a wide range of experiments...
  29. CRISPR 101: Making a Knock-In Cell Line

    Type
    Blog Post
    ...Disable the other repair mechanisms Mammalian cells have 2 primary repair mechanisms besides HR - Non-homologous... However, if you have a larger knock-in (200 bp – 2 kb), a dsDNA donor will need to be used due to synthesis...accidentally change your protein of interest.   Fig. 2: Stop re-cutting with PAM and guide RNA disrupting.... Com., 8(2024), (2017). 10.1038/s41467-017-01836-2 Charpentier, M., Khedher, A. H. Y., Menerot, S., Brion...varying across cell types. Variance can be caused by cell cycle rates; rapidly diving cells will have higher... of your cells. Enrich S-phase cells HR operates predominantly in S and G2 phase of the cell cycle, when...HDR events, ensure cells are actively cycling through the cell cycle stages. If cells are overly confluent...
  30. mTOR Pathway

    Type
    Collection
    ...Laplante M, Sabatini DM. Cell. 2012 Apr 13;149(2):274-93. doi: 10.1016/j.cell.2012.03.017. PubMed PMID...known as RPS6KB1; Ribosomal protein S6 kinase B1 TSC1/2 TSC1 TSC2 Tuberous sclerosis VHL Von Hippel-Lindau...Rictor RPTOR independent companion of MTOR, complex 2 SGK Serum/glucocorticoid regulated kinase 1 Return... (mTOR) is a key metabolic regulator controlling cell growth and proliferation. mTOR, a serine/threonine...signals to determine the nutritional state of the cell and regulates the switch from anabolic to catabolic...growth factors, including insulin. mTORC2 influences cell survival and cytoskeletal organization. Cancer Impact... promotes the conditions needed for uncontrolled cell growth and proliferation, including an abundant ...
  31. AAV Production in HEK293 Cells

    Type
    Protocol
    ...3319, 3180 cm 2 Cellstack 2, Corning 3269, 1272 cm 2 Heat-inactivated FBS (HI-FBS) Pro-Tip Different brands... 4 °C. Cell Lysis Buffer : 50 mM Tris HCl, 150 mM NaCl, 2 mM MgCl 2 Add the following to the 2 L sterile... solution can be stored at 4 °C for up to 2 months. After 2 months, discard the tube and thaw a new working... mL of PBS. Aspirate PBS and add 2 mL of 0.05% Trypsin/EDTA. Wait ~2 min. Neutralize trypsin by adding...Seed cells in CS2 Day 2: Seed cells in CS5 Day 3 (am): Transfect cells Day 7 (am): Harvest cells Equipment...times to obtain a single cell suspension (no clumps of cells). Pool cells from 2 x T-175 flasks. Adjust ...touching the cells when replacing media. T-175 flask, Corning 430825, 175 cm 2 Cellstack 5, Corning 3319...
  32. Opto-Nanobodies: Using Light to Manipulate Cell Signaling and Protein Purification

    Type
    Blog Post
    ...non-specific proteins, and then elute YFP.  Option #2: Opto-Nanobodies (OptoNBs) purification You skip adding...blue lights. Which option do you choose?  Option #2 may sound like fiction, but light-controlled protein...experiments.  AsLOV2 Inertion Site mCherry #1 mCherry #2 GFP Loop 1 dark-induced dark-induced dark-induced...OptoNBs to control cell signaling The second application for OptoNBs takes us into cells: light-based control... regulation of endogenous signaling activity in cells.  Let’s shed some light on the key components of...their use for protein purification and controlling cell signaling. Key components of OptoNBs OptoNBs have...can bind, it co-localizes with its target at the cell membrane and when the OptoNB can’t bind, it localizes...
  33. Rett Syndrome

    Type
    Collection
    ... mutations in the gene methyl-CpG binding protein 2 ( MECP2 ). MECP2 Rett syndrome is an X-linked disorder...X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet . 23, 185–188. (Link opens in a new window... Cuddapah et al. 2014. Methyl-CpG-binding protein 2 (MECP2) mutation type is associated with disease severity... Specific mutations in methyl-CpG-binding protein 2 confer different severity in Rett syndrome. Neurology...males with mutations in Methyl-CpG binding protein 2. Am J Med Genet B Neuropsychiatr Genet . 180, 55–67...Unpublished Joost Gribnau Human Cell Line Models Induced pluripotent stem cells (iPSCs) are a powerful system...opens in a new window) LUHMES cell line , an immortalized pre-neuronal cell line that can be differentiated...
  34. Photosensitizer Induced Cell Ablation with FAP-TAP MG-2I-dL5**

    Type
    Blog Post
    ... post treatment (see figure 2). Induced cell death was confirmed by TUNEL staining.  The video below shows...fluorogen activating protein - dL5** in this case), and 2) a fluorogen (the TAP - targeted and activated photosensitizer...PMID: 26808669. PubMed Central PMCID: PMC4916159. 2. Jacobson, K., Rajfur, Z., Vitriol, E., & Hahn, K....HEK293 cell culture and in live zebrafish. For cell culture experiments, only dL5**-expressing cells treated...inactivate target proteins or cells while having little effect on neighboring cells. The photosensitizer used...Here Light-induced cell ablation with MG-2I-dL5** He et al tested out light-induced cell ablation with MG...effective killing of dL5** cells without death of neighboring bystander wild-type cells.   Zebrafish experiments...
  35. MAPK Plasmids

    Type
    Collection
    ...46, JNK1, JNK1A2, JNK21B1/2, PRKM8, SAPK1, SAPK1c MAPK9 JNK-55, JNK2, JNK2A, JNK2ALPHA... PRKM11, SAPK2, SAPK2B, p38-2, p38Beta MAPK12 ERK3, ERK6, P38GAMMA, PRKM12, SAPK...Mitogen-activated protein kinases (MAPKs), also known as extracellular signal-regulated kinases (ERKs), are serine/...threonine-specific protein kinases. They regulate diverse cellular programs by acting as an integration point for...
  36. Lentiviral Prep Service

    Type
    Collection
    ... Morris CellTag Barcode Library Version 2 Ready-to-use lentiviral particles carrying version 2 of the ...the CellTag barcoding library. Version 2 of the Celltag library contains 4934 barcodes to combinatorially...carrying version 1 of the CellTag barcoding library. Version 1 of the Celltag library contains 19973 barcodes...barcodes to combinatorially index cells for single-cell analysis of clonal dynamics. This library expresses...combinatorially index cells for single-cell analysis of clonal dynamics. This library expresses EGFP for easy visualization...carrying version 3 of the CellTag barcoding library. Version 3 of the Celltag library contains 5737 barcodes...
  37. Starter Guide to induced Pluripotent Stem Cells (iPSCs) Part 2:  Reprogramming and Transdifferentiation

    Type
    Blog Post
    ...Induction of Human Germ Cell Fate from Pluripotent Stem Cells. Cell Stem Cell, 2015. 17(2): p. 178-94. PubMed... of human induced pluripotent stem cells. Stem Cell Rev, 2015. 11(2): p. 242-53. PubMed PMID: 25578634...differentiated somatic cell to revert back to a pluripotent stage (iPSC formation) [2, 3]. The iPSCs then...somatic cells via various methods. Some of the more common delivery methods include retrovirus [2], lentivirus...PubMed PMID: 16810240. 2. Takahashi, K., et al., Induction of pluripotent stem cells from adult human fibroblasts...three routes to regeneration. Nat Rev Mol Cell Biol, 2011. 12(2): p. 79-89. PubMed PMID: 21252997. 37. Merrell...differentiation of human ES cells and iPS cells into mature pancreatic insulin-producing cells. Cell Res, 2009. 19(...
  38. Neurodegeneration Research Collection

    Type
    Collection
    ...different inherited genes: Presenilin 1, Presenilin 2, and APP gene.The majority (>90%) of individuals develop...study aggregation. Saha et al. Nat Commun. 2023 Feb 2. Study the C terminal domain of TDP-43 to better understand... rodent species. Boender et al. Sci Adv. 2023 Jun 2. Use Cas9 in astrocytes. Endo et al Science. 2022 ...with the iPSC toolbox . Lam et al. bioRxiv. 2022 Dec 2. Use PiggyBac plasmids with tet-inducible expression...protein-protein interactions and nerve cell function within the cell. Parkinson's Disease Parkinson’s disease...inducible vector . Harley et al. Cell Rep. 2023 Dec 26. Induce CNS cells with concomitant expression of ...with the disease and implicate a wide range of cellular processes. The vast majority of cases (90-95%)...
  39. Allen Institute for Brain Science AAV Enhancer Collection

    Type
    Collection
    ...Layer 2-3_IT Isocortex 230803 pAAV-AiE2638m-minBG-iCre(R297T)-BGHpA AiP20142 AiE2638m Cre Layer 2-3_IT ...Layer 2-3_IT Isocortex 220727 pAAV-AiE2543m-minBG-iCre(R297T)-BGHpA AiP2048 AiE2543m Cre Layer 2-3_IT ...Layer 2-3_IT Isocortex 230402 pAAV-AiE0680m-minBG-iCre(R297T)-BGHpA AiP15072 AiE0680m Cre Layer 2-3_IT ...to target a variety of cell populations in different brain regions. Labeled cell populations were tested...to primate neocortex. Cell Rep. 2021 Mar 30;34(13):108754. doi: 10.1016/j.celrep.2021.108754. PMID: 33789096...regulatory sequences — termed enhancers — to drive cell type-specific expression. The Allen Institute for...differential chromatin accessibility across different cell types and cloned into an AAV backbone. Most enhancers...
  40. Adeno Associated Virus (AAV) for Cell and Gene Therapy

    Type
    Blog Post
    ...postmitotic, long-lived cell types. AAVs in the clinic Thus far, AAV vectors AAV1, AAV-2, AAV1-AAV2 hybrids...neutralizing antibodies against some AAV types, AAV1, 2, 3 and 5 are thought to be as high as 70% among the... 10.24 (2003): 1999-2004. PubMed PMID: 14566358.  2. Hirsch, M. L., et al. "Self-complementary AAV mediates... do so, their T-cells were grown in vitro, their mutations corrected, and the T-cells were transferred...functioning T cell repertoire (1). In this example, it was possible to transduce the T-cells outside the...a wide range of cell types including but not limited to muscle, liver, and brain cells. There are a multitude...chain (c) and is characterized by a lack of immune cell development and function. To date, gene therapy ...
  41. Cloning Mammalian Cells with the Agarose Method

    Type
    Blog Post
    ...splitting transfected cells into 3 plates at different densities for selection). A 2% agarose solution is...transition from a 48-well cell plate to a 96-well assay plate. We generally freeze at least 2 ampules each of 4...of agarose, which is then overlaid with the firmer 2% agarose gel solution discussed above for picking.... a wide variety of cell lines, from HEK to CHO cells to neural and endocrine cells such as AtT-20, PC12...then handled. Additionally, many cell lines, especially the endocrine cell lines we most commonly work with...specific cell line, and its transfection efficiency. We often trypsinize the transfected cells on the day...increased). For some cells, add a drop of serum to aid in outgrowth. Depending on the cell type, we sometimes...
  42. CRISPR Plasmids - Double-Strand Break (Cut)

    Type
    Collection
    ...DSB and 2. a specific edit close to the gRNA PAM site. When a repair template is present, the cell may repair...Cas enzymes? CasPEDIA is an encyclopedia of Class 2 CRISPR systems with wiki entries describing enzyme...sequence. DSBs are preferentially repaired in the cell by non-homologous end joining (NHEJ), a mechanism...
  43. AAV Molecular Tools

    Type
    Collection
    ...diphtheria toxin receptor fused to GFP for studying cell ablation. 2 Jessell , Azim 45580 pAAV-flex-taCasp3-TEVp...constitutive Expression of the tet-off transactivator (tTA) 2 Gradinaru 99120 pAAV-ihSyn1-tTA Inducible Synapsin...Scanziani Tools for Cell Ablation These AAV encode tools that can be used for cell ablation. ID Name Expression...Transactivators Affinity Purification Neurophysiology Cell Ablation Tetracycline Transactivators and Inducible...expression of designer pro-taCasp3 and TEVp for studying cell ablation. 5 Shah , Wells Don’t See What You’re Looking...
  44. Production of Virus in Insect Versus Mammalian Cells

    Type
    Blog Post
    ...AAV); 8–10 kb (lenti) 38 kb Cells HEK-293T Sf9 Time to collection 2–4 days 5–10 days Purification... R.M. (2002). Insect cells as a factory to produce adeno-associated virus type 2 vectors. Human Gene Therapy...Centrifugation Titration time ~1 day (AAV); ~1 week (lenti) 2–10 days Initial titers Higher Lower Resources...that already do mammalian cell culture. HEK-293T cells are the most common cells used in viral production...versus insect cells for viral production Consideration Mammalian cells Insect cells Viruses AAV ...type of cells that will be used to make the virus. Viruses can be produced in many different cell types,...produced in bacteria cells. However, some viruses can be produced in multiple different cell types, including...
  45. Viral Production

    Type
    Collection
    ... a new vial of early passage cells. Approximately 2 weeks post-thaw, cell culture supernatant is tested...item (see maps section for images). Figure 2: AAV Pro cells were transduced with either pAAV-Ef1a-mCherry-IRES-Cre...suggests that titers obtained using ddPCR are generally 2–3 fold higher than those achieved using the standard... preparations are added to cells in culture. Three to five days later, cell cultures are inspected for...involves transducing cells with serial dilutions of the lentiviral vector, harvesting cells several days later... (55634-AAVrg) alone at 1.7E6 viral genomes (vg)/cell, pAAV-CAG-FLEX-rc [Jaws-KGC-GFP-ER2] (Addgene 84445...Production Lentiviral preparations are produced in 293T cells using the 2nd generation psPAX2 and pMD2.G packaging...
  46. CRISPR Protocol for Genomic Deletions in Mammalian Cell Lines [Video]

    Type
    Blog Post
    ...deletions in human cells using zinc finger nucleases. Genome Res. 2010 Jan;20(1):81-89. PubMed. 2. Bauer DE, ...with TALENs, in collaboration with the Porteus lab [2]. With the advent of CRISPR/Cas9, we began to explore...CRISPR plasmids into MEL cells by electroporation, sort your transfected cells via FACS, primer validation...article "Generation of Genomic Deletions in Mammalian Cell Lines via CRISPR/Cas9" from the Journal of Visualized...CRISPR/Cas9 to create genomic deletions in mammalian cell lines. Below Bauer and Canver discuss the motivations...deletions is to produce monoallelic deletion clones. Cells with just a single intact copy at a given locus ...screening by conventional PCR. Biallelically disrupted cells can be easily identified. Even in the case of clones...
  47. TALEN Guide

    Type
    Collection
    ...par with ZF arrays, if not slightly lower. Figure 2: Simplified representation of the Voytas/Bogdanove...variety of backbones in just a few steps ( Figure 2 ). The Bogdanove group also hosts web-based software...mammalian transcription. Nat Biotechnol. 2011 Feb;29(2):149-53. PMID: 21248753 . TALEs for the masses. Rusk.... Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Sander JD, Cade L, Khayter...
  48. CRISPR History and Development for Genome Engineering

    Type
    Collection
    ...RNA-guided regulation of transcription in eukaryotes. Cell . 154(2):442-51. PMID: 23849981 Ishino Y, Shinagawa ...Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell . 163(3):759-71. PMID: 26422227 Zetsche...transcribed to make the pre-CRISPR RNA (pre-crRNA). (2) The pre-crRNA is processed into individual crRNAs...2015. Class 1 (Multi-subunit effector complex) Class 2 (Single multi-domain effector) Type I (Cas3) Type ... with unprecedented speed and specificity. Figure 2: An overview of CRISPR and NHEJ/HDR. The Cas9/gRNA...genomic loci in living human cells by an optimized CRISPR/Cas system. Cell . 155(7):1479-91. PMID: 24360272... for Mapping Multiprotein Complexes in Human Cells. Cell Rep . 13(3):621-33. PMID: 26456817 Fu Y, Sander...
  49. Mammalian RNAi Tools

    Type
    Collection
    ...degrades the mRNA. RISC includes argonaute protein 2 (Ago2), which facilitates cleavage of the target. ... International Journal of Biomedical Science, 13 (2), 48–57. PubMed (Link opens in a new window) . Moore... in therapeutic settings. As a tool in mammalian cell systems, silencing is achieved through the delivery...). Origins and mechanisms of miRNAs and siRNAs . Cell, 136 (4), 642–655. PubMed (Link opens in a new window...
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