...genomic variation. These joint efforts will produce a catalog of the impact of genomic variants on genome...Consortium investigators to examine how genomic variation affects genome function to influence phenotypes...Collections IGVF Consortium Impact of Genomic Variation on Function (IGVF) Consortium Collection Read ... opens in a new window) The Impact of Genomic Variation on Function (IGVF) Consortium (Link opens in a... a new window) aims to understand how genomic variation affects genome function, which in turn impacts...perturbs the genome to assess the impact of genomic variation on genome function and phenotype and shares their...

... selecting, testing, and optimizing three key variables of an AAV vector: serotype, promoter, and titer...steps in testing are effected by multiple AAV variables.    Serotypes Serotype refers to the different...

...work, there are other options. Commonly used Cpf1 variants, with a  5’ TTTV PAM, improve targeting in AT-...respectively. Researchers also engineered SpCas9 variants with alternative PAMs like NGAG and NGCG and SaCas9... in the pool. According to this logic, ω-dCas9 variants recognizing multiple PAMs should have a fitness...promoting survival of only the broadest-targeting variants. For the final round of evolution, they used a... a no-G PAM library to enrich for Cas9 variants with activity on non-NGG PAMs, generating xCas9 3.0-3.13...confirming the flexibility of xCas9 3.7. Base editor variants with xCas9 are similarly flexible. Like the xCas9...References Hu, Johnny H., et al. "Evolved Cas9 variants with broad PAM compatibility and high DNA specificity...

...no one option is perfect, with all this variance in your variant options, you’re likely to find an application...It is a well known fact if a multicopy variant of a gene exists, there must be assays that researchers...quantify said copies. They do so using copy number variation (CNV) assays. There are several varieties of these...small as reasonably possible and set using the variance seen within multiple runs of the standard curve...identify trends in cases where the copy number variation is two or less (Muhamad, 2011). Ambiguous Taqman...Usher CL, McCarroll SA. Analyzing Copy Number Variation with Droplet Digital PCR. Methods Mol Biol. 2018...Chung WK. Quantitative analysis of copy number variants based on real-time LightCycler PCR. Curr Protoc...

...are delivered by feeding them to planarians. Depending on which planarian species one is working with, the...accessible or too challenging for amateur scientists. Planarians, wormy creatures commonly found in freshwater...provide a good potential solution to this problem. Planarians are easy to buy, cultivate, and have interesting...advanced developmental biology experiments in planarians with their recent plasmid deposit. These plasmids...in four inexpensive and commercially available planarians: Girardia sp., Dugesia dorotocephala, Phagocata...into plasmids to investigate for each of these planarian species. These plasmids all have a PR-T4 vector...technique. The expression patterns of 11 different planarian genes (all of which are available through the ...

...single polypeptides that contain the variable light chain (VL) and variable heavy chain (VH) of an antibody...technology. But what about single chain fragment variables (scFvs)? scFvs weren’t developed for another decade... 2013). The linker keeps the C-terminus of one variable domain and the N-terminus of the other domain ...oligomerization of the scFv. While you might assume that the variable domains of an scFv would mirror that of an antibody...screen for new antibodies. To do this, antibody variable domain sequences are expressed as scFvs and screened...for strong binders. Then the sequences for the variable domains of the selected scFvs are inserted into...2013) In Vivo Applications of Single Chain Fv (Variable Domain) (scFv) Fragments. Antibodies 2:193–208...

...-type. However, variants such as the P.1 (Gamma variant) and the B.1.351 (Beta variant) were much less...vaccine could neutralize many variants, including the B.1.1.7 (Alpha variant), B1.1.298, and B.1.429 (Epsilon...on the variant. The lowest levels of cross-neutralization occurs in the P.1 and B.1.351 variants tested...circulating variants. This allowed us to create pseudoviruses that represent lineages and variants that are...luminescence.     B.1.351 variant neutralization escape The lab saw that the B.1.351 variant was very resistant... distinct from SARS-CoV-2 and its variants. Yet, the B.1.351 variant, which has only 9 different mutations...we’ve seen the emergence of several SARS-CoV-2 variants coincide with increased vaccination efforts. So...

...effects of sequence variants on abundance simultaneously called VAMP-seq, for Variant Abundance by Massively...the abundance of a protein variant library is monitored by fusing the variants to eGFP followed by an internal...Quantifying the abundance of thousands of protein variants simultaneously  With increasing sequencing power...individual’s genome. But when they find genetic variants, what does that mean? Previous research shows ...approximately 75% of all protein-coding pathogenic human variants are decreased in protein abundance, possibly due... due to misfolding. But measuring variants one at a time is time consuming and unscalable.  Melissa Chiasson...Washington sought to address the effects of genetic variants in a high throughput manner. She helped develop...

...Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh...

...devised (8). References 1. Casadaban M.J., Martinez-Arias A., Shapira S.K., Chou J. Beta-galactosidase gene...lacZ reporter gene (3, 4), there are now many variations, including many that use auxotrophic rescue genes...

..., F., Lach, R. S., Baxter, N. J., Kosik, K. S., Arias, C., Acosta-Alvear, D., & Wilson, M. Z. (2020). ...also a good way to diagnose single nucleotide variations. Also, FnCas9 cleaves in a range of temperatures...

...things she loves about working at Addgene! Maria Soriano Maria Soriano, from Addgene's UK office, discusses...

...multichannel pipet to minimize pipetting error and variability Mix samples very well by pipetting back and forth...fluorescence fluctuations and to minimize well-to-well variability that result from a variety of causes, such as...

... dissolved in water is going to have a greater variance in concentration readings than a DNA sample dissolved...

...experiment would need to be repeated to account for variability....

...new batch of 1 mg/mL PEI prepared. There may be variation between batches of PEI depending on the user, ...

... cm dish. Pro-Tip There can be batch to batch variation when making the PEI working stock, therefore the...

...Polymerase (5 units/μL) 36.8 μL Sterile dH 2 O (variable) Note: If you are doing multiple PCRs, save time...

...increases reproducibility, as it eliminates the variation associated with repeated transient transfection...

...member 1 GCNF, GCNF1, NR61, RTR NRG1 neuregulin 1 ARIA, GGF, GGF2, HGL, HRG, HRG1, HRGA, NDF, SMDF NRG2...alpha variable 27 TCRAV10S1, TCRAV27S1 TRAV29DV5 T cell receptor alpha variable 29/delta variable 5 (gene... immunoglobulin heavy variable group IGHV IGHV1-18 immunoglobulin heavy variable 1-18 IGHV118 IGHV1-2 ... immunoglobulin heavy variable 1-2 IGHV12 IGHV1-24 immunoglobulin heavy variable 1-24 IGHV124, VH IGHV1... immunoglobulin heavy variable 1-3 IGHV13 IGHV1-45 immunoglobulin heavy variable 1-45 IGHV145, VH IGHV1...immunoglobulin heavy variable 1-46 IGHV146 IGHV1-58 immunoglobulin heavy variable 1-58 IGHV158, VH IGHV1...immunoglobulin heavy variable 1-69 IGHV1-E, IGHV169, IGHV1E IGHV1-8 immunoglobulin heavy variable 1-8 IGHV18 IGHV1...

...binding) SpCas9 VRER variant 3' NGCG SpCas9 EQR variant 3' NGAG SpCas9 VQR variant 3' NGAN or NGNG xCas9...LbCpf1) 5' TTTV AsCpf1 RR variant 5' TYCV LbCpf1 RR variant 5' TYCV AsCpf1 RVR variant 5' TATV Campylobacter...Species/Variant of Cas9 PAM Sequence* Streptococcus pyogenes (SP); SpCas9 3' NGG SpCas9 D1135E variant 3' ...use, and there are several to choose from. Many variations of Cas9 exist, along with other Cas enzymes like... PAM-flexible or PAMless Cas9s. SpCas9-derived variants with non-NGG PAM sequences include: xCas9 - NG...plant genome engineering. Read more about Cas9 variants . Anti-CRISPR Prolonged Cas9 activity can increase...systems create a wide spectrum of single-nucleotide variants (somatic hypermutation) in a larger editing window...

...Single-chain fragment variables (scFvs) contain only the variable heavy chain and variable light chain regions... way to produce antibodies, with the highest variability in antibodies produced. Cells - Antibodies can...large amounts of a single antibody with little variation. Recombinant plasmids - Antibodies can be produced...the plasmid. This produces the least amount of variation between antibodies, allows for the antibody’s ...easily confirmed via sequencing, and enables the variable region and constant regions of the antibody to.... The tips of the Fab fragments contain highly variable regions, shown in light blue and light orange,...covered in the following Isotypes section. The variable region of the antibody is the antigen binding ...

...protein variant (CyPet) optimized for FRET measurements with a yellow fluorescent protein variant (YPet)...protein variant (YPet) optimized for FRET measurements with a cyan fluorescent protein variant (CyPet)... periplasm. Series contains vectors with a YFP variant that functions in the periplasm and can be co-localized... pCri System Various Plasmids T7/lacO and lacO variants that can be expressed in B. subtilis Various combinations...

...that many of the articles linked below include variants with different binding affinities or negative-... Calcium Yellow protein calcium sensor jYCaMP1 variants (Constitutive or Cre-dependent) jYCaMP: an optimized...Int Ed Engl. 2018 Jun 27. Tetsuya Kitaguchi ATP Variants of ATP sensor iATPSnFR1.0 and iATPSnFR1.1 (cytoplasmic...Loren Looger Glutamine FLIPQTV3.0 glutamine sensor variants Visualization of glutamine transporter activities...Glutamate Ultrafast glutamate sensors (iGluSnFR variants) Ultrafast glutamate sensors resolve high-frequency...1720648115. Katalin Torok Glutamate Membrane displayed variants of fluorescent glutatmate sensors (iGluSnFR1) ...pH Superfolder pHluorin pH sensor A superfolder variant of pH-sensitive pHluorin for in vivo pH measurements...

...information. Plasmids Expressing Spike and Spike Variants Full-length wildtype SARS-CoV-2 spike protein ...D614G change which is present in many circulating variants. The table below lists expression plasmids that...protein (MERS, CoV-1, CoV-2), modification, or variant. ID Plasmid Description Mutations Industry PI Due...Pseudoviruses Expressing SARS-CoV-2 Spike Protein Variants Addgene COVID-19 Resources and Collections COVID...

...J. D., Pelkey, K. A., Chittajallu, R., Guo, B., Arias-Garcia, M. A., Allaway, K., Sakopoulos, S., Schneider...unique tropisms are now available. These include variants with broad CNS or PNS transduction, cell type ...Tabebordbar et al., 2021) method, selecting for variants that were effective in C57BL/6J mice, BALB/cJ ... by transferring the 7-mer peptide region from variable region VIII of AAV9-X1.1 to that of AAV1. AAV1...BALB/cJ and C57BL/6 mice and rats. In mice, no variation in transduction efficiency was seen between different...lower than those seen with AAV9, they were highly variable and were not lower than those of AAV-PHP.eB (Goertsen...resources on the Addgene blog Viral Vectors 101: AAV Variables That Matter Viral Vectors 101: An Introduction...

...expression systems and variables for using CRISPR in mammalian cells. Some of the variables include: Species...modify prior to designing your gRNA, as sequence variation between your gRNA targeting sequence and target...to consider alternative Cas enzymes ( see Cas9 variants and PAM sequences ). Once possible PAM sequences...

... short ~100 nt guide RNA ( gRNA ) that uses 20 variable nts at its 5’ end to base pair with a target genomic... and LbCpf1) for use in mammalian cells SpCas9 variants with no detectable off-target effects Modified...specifity of Staphylococcus aureus Cas9 (SaCas9 KKH variant) Engineered CRISPR-Cas9 nucleases with altered ...

...gRNA sequence exactly match your genomic target? Variation between a given gRNA sequence and your genomic... increases off-target effect. Which species or variant of Cas9 ( S. pyogenes , S. aureus etc.) was this...compatible with a single species or PAM binding variant of Cas9. For instance, wild-type SpCas9 must be...

... base editors are available with multiple Cas9 variants including high fidelity Cas9’s. Further advancements...fusions, modifying the linker region between Cas variant and deaminase to adjust the editing window, or ...systems create a wide spectrum of single-nucleotide variants (somatic hypermutation) in a wider editing window...

... by tRNA variant that suppress the TAG nonsense codon, and tyrU gene replaced by tRNA variant inactivated...knocked out, tyrTV and tyrU genes replaced by tRNA variant that suppress the TAG nonsense codon). Expresses...knocked out, tyrTV and tyrU genes replaced by tRNA variant inactivated by the truncation of the anticodon ...

...gRNA sequence exactly match your genomic target? Variation between a given gRNA sequence and your genomic...gRNA activity. Know your target. Which species or variant of Cas9 ( S. pyogenes, S. aureus etc.) was this...compatible with a single species or PAM binding variant of Cas9 (e.g. Wild-type SpCas9 must be used with...elegans TCCGCTACCATAGGCACCA 71479 cut VQR Cas9 variant 26680661 Fire dpy‐10 C. elegans GCTACCATAGGCACCACGAG...

... See article for more cre-lox shRNA expression variants. Jacks 19319 pLJM1-EGFP 3rd CMV-driven EGFP fusion... drug selection markers. See article for more variations. Campeau 39481 pLenti-puro 3rd CMV driven expression...fusion. See plasmids 36083 and 36086 for other FP variants. Tsoulfas 41393 pCW57.1 3rd Inducible lentiviral...

...ChETA, C1V1 (t/t) Inhibitory Arch and variants eNpHR and variants Jaws stGtACR iC++ OPN3 PdCO PPO Bidirectional...AAVrg PHPeB Clear Filters ID Name Promoter Opsin Variant Tag Activity Serotype PI 20071 pACAGW-ChR2-Venus-AAV...

...suits your particular experiment. Some important variables include: Type of genetic modification - CRISPR...library 155199 Knockout Human Moffat Blencowe 3rd variable 92,746 CHyMErA Exon-deletion hgRNA pooled library...library 155200 Knockout Human Moffat Blencowe 3rd variable 91,948 Toronto KnockOut - Version 1 1000000069...

...to generate and characterize single nucleotide variant lines in an isogenic cellular background. All cell...create cell lines with endogenously-tagged gene variants or to differentiate human iPSCs into other cell...

...for AAV production or direct transfection, slow variant Kaspar Podgorski 135421-AAV1 pAAV-syn-FLEX-axon-jYCaMP1s...for AAV production or direct transfection, slow variant Kaspar Podgorski 135424-AAV1 pAAV-syn-jYCaMP1s ...for AAV production or direct transfection, slow variant Kaspar Podgorski 135630-AAV1 pAAV-S5E2-dTom-nlsdTom...

...publications, focused on somatic variants found in lung adenocarcinoma as well as variants found across cancer types...

... with EF1alpha addition of an mCherry reporter variant nuclear reporters via an H2B fusion shuttle plasmid...fusion for gene activation CRISPR/Cas9 Plasmid Variants Figure 1: Schematic of the CRISPR Collection. ...

...immortalized cells (see Weinberg Lab page for resistance variants) Weinberg 1773 pBABE-hygro-hTERT MoMLV Expression...expression; also expresses GFP. Also see pMIG-w , a variant that has WRE, a post-transcriptional regulatory...

...Clover Green Mammalian Expresses Clover (a GFP variant) commonly used with mRuby2 pLSSmOrange-N1 Orange...LSSmOrange mRuby2 Red Mammalian Expresses mRuby2 (a RFP variant) commonly used with Clover pGWF1 Cyan & Yellow ...

...AAV6 Vectors: Strategies for Overcoming Donor-Variation and Implications in Genome Editing. Sci Rep . ...

...combination of gene variation and lifestyle or environmental factors. For example, variations of Apolipoprotein...

...nervous system function. While there is wide variability in symptoms even within patients with the same...algorithms for data analysis to calculate heart rate variability (Link opens in a new window) Protocols.io - protocol...

...Independent variables – factors which are not affected by other variables (cause). Dependent variables – factors...assumptions: Distribution – Normal Variables – Independent Variance – Approximately equal Data type - ...two (two-way ANOVA) independent variables on a single dependent variable. A two-way ANOVA could test the... the effect of two dependent variables on up to two independent variables. For example, a one-way MANOVA... assesses multiple independent variables on a single dependent variable. I know what you’re thinking –...and MANCOVA All variants of ANOVAs discussed so far assume that the independent variables are independent...have discrete effects on the dependent variable, and those variables are the only things that matter. However...

...create cell lines with endogenously-tagged gene variants or browse Addgene’s entire collection of Stem ...c-Myc from polycistronic cassettes KLF4 N-terminal variance modulates induced reprogramming to pluripotency...

...Calcium Sensor: GCaMP7c 105321 pGP-AAV-syn-jGCaMP7c variant 1513-WPRE Syn jGCaMP7c none Constitutive 1 Kim ...Kim 105322 pGP-AAV-syn-FLEX-jGCaMP7c variant 1513-WPRE Syn jGCaMP7c none Cre 1 Kim Calcium Sensor: GCaMP6f...

...individual variants found in tumors are exceedingly rare. As a result, how most of these “variants of unknown...cancer clinical sequencing report includes rare variants that haven’t been characterized? Some have developed...approach this challenge, using attributes of cancer variants such as evolutionary conservation, or predicted...hope researchers can use to characterize these variants in a high-throughput manner and therefore push...precision medicine a reality. Challenges for cancer variant characterization For many years, we’ve hoped that...laboratory-based functional experiments that classify which variants are likely gain-of-function, loss-of-function ...these experiments could find correlations between variants in a gene of poorly classified function and a ...

...four novel SpCas9 variants with altered PAM binding specificity: SpCas9 variant Mutations (relative...SpCas9) PAM sequence D1135E variant D1135E NGG VQR variant D1135V, R1335Q and T1337R NGAN...NGAN or NGNG EQR variant D1135E, R1335Q and T1337R NGAG VRER variant D1135V, G1218R, R1335E...the VQR and VRER variants is similar to wild-type SpCas9, indicating that the variants are likely just ...reported the development of near-PAMless Cas9 variants. These variants, named SpG and SpRY, can target NGN PAMs...limitation: 1) the use of novel S. pyogenes Cas9 variants with varying PAM sequences, 2) the use of Cas9...R1335E and T1337R NGCG The D1135E variant is far more selective for the canonical S. pyogenes PAM...

...try developing a variant with an enhanced response. Evolution of a new variant Maria and the team set ...suggest she deprioritize the project, Maria’s screens of AsLOV2 variants showed some significant gains! After...several other labs. Andrew and Maria expect that further-improved variants of MagLOV will be possible with...applications that don’t even exist yet? Andrew York, Maria Ingaramo, and their team at Calico Life Sciences...right through our tissues unimpeded. Andrew and Maria dreamed about the possibilities of a magnetoresponsive...appears to be weak — if they exist at all. Andrew and Maria were encouraged by previous reports that described...developing useful tools. A lucky start As Andrew and Maria explained, “to our surprise and delight,” the very...