...like ReFigure which aims to consolidate published and unpublished experiments on similar subjects in a single...the abbreviated methods section found within a published manuscript. Luckily, many organizations have been...thereby enabling you to do modified analyses on published data if you need to. Similarly, FigShare also ...averse to producing papers that repeat previously published results. This over-reliance on the perfect story...problem is that only these positive results will be published. The publication record will then show that the...success story) even though the majority of the unpublished evidence shows otherwise. Others will go on to...very active with many scientists sharing their unpublished data. There are blogs - both hosted by individuals...

...validation assays. If you’re using previously published antibodies, check the manuscript and supplementary...mitochondria or nucleus, will likely require a harsher lysis buffer than proteins easily available in ...in the cytoplasm or whole-cell lysate. A harsher, SDS-containing lysis buffer, like RIPA, should be considered.... BME smells like rotting eggs but has a longer shelf life when stored properly. Because BME is not as... 1–2 hours Easy and cheap to handcast Short shelf-life; can alter proteins due to high pH Bis-...for proteins <40 kDa 180 V, 30 minutes Good shelf life; runs at neutral pH (reduced protein alteration...for proteins > 30 kDA 200 V, 30 minutes Good shelf life; runs at neutral pH (reduced protein alteration...

...the transfection in: 15 cm dishes OR CF5 stacks Select how many dishes or stacks you plan to transfect...for the type of tissue culture dish and number of dishes used. Here’s to making AAV packaging a little easier...1 to 10 Fill in experimental details on the spreadsheet: Name your viral prep Enter the specific names... plasmids Enter plasmid concentration The spreadsheet will calculate the following μg of each plasmid...with its corresponding column in the calculator spreadsheet: We hope that this calculator will make it easier...

...Originally published May 3, 2017 and last updated Sep 24, 2020 This post was contributed by guest blogger...Gene knockout with CRISPR technology is usually accomplished by Cas9-mediated dsDNA breaks: following a cut...mRNA cap, provides the most accurate mapping (Radzisheuskaya et al., 2016). In this case, location and sequence...nevertheless still lead to activity has been established, and can be used to identify sites that are likely...Zhivich V, Najgebauer H, Allen F, Gonçalves E, Shepherd R, Doench JG, Yusa K, Vazquez F, Parts L, Boehm...Boehm JS, Golub TR, Hahn WC, Root DE, Garnett MJ, Tsherniak A, Iorio F (2019) Agreement between two large .... https://doi.org/10.1038/s41587-020-0490-7 Radzisheuskaya A, Shlyueva D, Müller I, Helin K (2016) Optimizing...

...Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (Thermo Fisher A-21131) or Goat anti-Rabbit IgG (H+L) Cross-Adsorbed...Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 (Thermo Fisher A-11012), and counterstained with DAPI. New...the payload sequence into the genome. The team established that they could reprogram the genomic target ...combine for dynamic protein labeling By Alyssa Shepard To fully understand how genes are regulated, it's...promising solution. Recently, the labs of Gord Fishell and colleagues characterized a series of new enhancer-AAV...Leyva Garcia, B., Tran, T., … Dimidschstein, J., Fishell, G., Wang, Y. (2024). An enhancer-AAV toolbox to...

...pre-clinical life science work, economics) that published research is difficult to replicate.  Why is replicating...appreciate how few details are provided in most published papers. The precise timing, order, or every combination...to a preregistration, but usually with a fully fleshed out introduction section) to one of 222 participating...scientific research. These include policies for publishers and funders in the Transparency and Openness ...citizen science and behavioral ecology of cichlid fishes. Find David online at https://orcid.org/0000-0002...

...Originally published Sep 30, 2014 and last updated Dec 10, 2020 by Benoit Giquel.   Adenoviral vectors...oncogenicity or genotoxicity seen with other vectors (Lukashev et al., 2016). The protein capsid encapsulating...Manuel Gonçalves' lab found in a second paper published in Nature Methods the same year that delivering...1051–1057 . https://doi.org/10.1038/nmeth.3075 Lukashev AN, Zamyatnin AA Jr (2016) Viral vectors for gene...doi.org/10.1038/srep05105 Stephens CJ, Lauron EJ, Kashentseva E, Lu ZH, Yokoyama WM, Curiel DT (2019) Long-...

...eukaryotic cells as an intermediate of heme metabolism (Shemetov et al, 2017). Modern state-of-the-art NIR FPs ...Shcherbakova et al., 2018) and iGECI calcium indicator (Shemetov et al., 2021). In addition to FRET, intensiometric...daria_gift_shch.     References and resources References Shemetov, A.A., Oliinyk, O.S. & Verkhusha, V.V. How to ...scales. Nat Commun 11, 239 (2020). Oliinyk, O.S., Shemetov, A.A., Pletnev, S., Shcherbakova, D.M. & Verkhusha...near-infrared FRET. Nat Chem Biol 14, 591-600 (2018). Shemetov, A.A. et al. A near-infrared genetically encoded...

... substantial overlap in the activation curves (Marshel et al., 2019) for each tool, and you may have to...the right information When using a previously published system in your own work, you’ll need to know (... Tye, K. M., Ferenczi, E. A., Ramakrishnan, C., O’Shea, D. J., Prakash, R., Gunaydin, L. A., Hyun, M.,...13(3), 387–392. https://doi.org/10.1038/nn.2495 Marshel, J. H., Kim, Y. S., Machado, T. A., Quirin, S.,...

... to replicate at a higher frequency (Summers & Sherratt, 1984; Summers et al., 1993). These larger plasmids...the monomeric version of the plasmid (Summers & Sherratt, 1984; Summers et al., 1993; Summers, 1998). Multimeric...of plasmid multimers (Bedbrook & Ausubel, 1976; Fishel et al., 1981). E. coli strains such as DH5α, HB101...10.1128/microbiolspec.PLAS-0025-2014. PMID: 26104344. Fishel RA, James AA, Kolodner R. recA-independent general...2958.1993.tb01648.x. PMID: 8361350. Summers DK, Sherratt DJ. Multimerization of high copy number plasmids...

...with your blocking, first check your antibody spec sheet. Some antibodies work better with specific blockers...include recommended blocking conditions on the spec sheet. If you’re still seeing high background after following...longer incubations at both temperatures if needed. Washes Check your antibody manufacturer for wash recommendations...consider adding a detergent like Tween-20 to your washes — although this can be harsh and inhibit some detection... Inefficient blocking Check antibody spec sheet for buffer recommendations Use a chemical blocking...signaling after each round of stripping* Use a harsher stripping buffer Too little signal Large ...

...yearly planning meetings revolve around two simple worksheets, each of which is filled out separately by the...the trainee and PI before the meeting. These worksheets, summarized briefly below (and available of in...facilitate honest conversation. Goals and Planning Worksheet: Lists accomplishments, research/professional...often give ourselves credit for what we have accomplished. Starting with a recap of accomplishments, from...

...CRISPR-based phenotypic screen datasets. Original published CRISPR screen data is curated and deposited in...in BioGRID ORCS to allow facile queries of published data by biomedical researchers and ready access to... approach serves to maintain consistency with published screen interpretations and allows users to query...curators at [email protected] to submit their published data for rapid curation review and upload. In ...

...wanted to do when I grew up until I was all but finished my undergraduate degree (and I hope I’m not alone...towards a career in science communication, an established field of inquiry with which I was not yet familiar... a scientific background and bring with them established interests and areas of expertise. Perhaps the...strongest aspect of science communication, then, is its sheer versatility in the face of disparate spheres of ...

...2013 there have been 33 CRISPR software tools published and documented by OMICtools. It must be confusing...The first of only three such databases, EENdb (published 1 Jan 2013, no longer available), is a simple ...sgRNA designs. The second database, CrisprGE (published 27 Jun 2015), is noteworthy for its broad scope... content, and ease of access. The third, WGE (published 15 Sep 2015), is more similar to EENdb than CrisprGE...in detail, but that is already covered in the published articles. Instead, I have broken down the tools...

...available. With new fluorescent proteins being published every month, deciding on the best protein for ... to choose fluorescent proteins that can be distinguished from one another and that can be imaged with...common use (particularly not the most recently published ones), they can be a good starting point. In many...abundant proteins or marking compartments. I hope this sheds some light on multicolor imaging with fluorescent...

...Central PMCID: PMC3785459. 2. Krashes MJ, Koda S, Ye C, Rogan SC, Adams AC, Cusher DS, Maratos-Flier E, Roth...induce neuronal silencing in vitro and in vivo (Krashes et al., 2011). The various serotypes available ...by the small molecule clozapine N-oxide (CNO) (Krashes et al., 2011). Viruses expressing pAAV-hSyn-DIO-hM4D...

...scientific communication needs. Going to present some unpublished results at a conference? Post your working manuscript...scientific community. Most preprints are eventually published in journals after formal peer review, with the... as the source or were deposited when the now-published article was a preprint. Depositing plasmids that...bioRxiv. https://doi.org/10.1101/833400  Stern BM, O’Shea EK (2019) A proposal for the future of scientific...

...affinity: stronger binding antibodies will require harsher stripping to remove, so start with the weaker binding... membrane will remove some of your sample —and harsher stripping means more sample loss. If you are still...a recipe like the ones shared by Bio-Techne, ThermoFisher, or Millipore Sigma. We’ll share the basic composition...solutions below. Alternatively, companies including ThermoFisher, Millipore Sigma, and Azure Biosystems offer...

... easily applied to multiple dishes, remember that handling multiple dishes will take longer and may increase...scaling up by either increasing the number of 10 cm2 dishes or increasing the vessel size. Opting for a larger... opt for simply increasing the number of 10 cm2 dishes. While this option is attractive because the same...

...performance in our system and yet none of that data was published.    Fig. 1: Testing of three different ... for your system or to successfully replicate published works. Of particular importance to these efforts...build on others’ results is available not through published manuscripts, but through word of mouth or old ...asked your team members or colleagues: How much unpublished AAV data do you have sitting in computers and...

...This post was originally published on the Quilt Genomics Blog and is republished here with permission. Quilt...enhancers, check out the Appendix. Conclusion: Shedding light on dark matter Precise knowledge of which...identified 23-mer gRNA. Off-target determination was established with Bowtie2 using the parameters first described...

...factors OCT3/4, SOX2, KLF4, and c-MYC is the established model for reprogramming somatic cells. A common...Polycistronic cassettes that contained KLF4s had overall diminished KLF4 expression levels; this altered stoichiometry...as inhibitory GABA-ergic interneurons, Gordon Fishell’s lab has developed a new AAV approach using regulatory...to Choosing the B(right)est Fluorescent Protein. Shen Y, et al. PLoS ONE. 2017. PubMed PMID: 28241009 ...independent of another TTAGGG binding complex, shelterin. Swapping the DNA binding domain of another telomeric...

...centrifugation or a magnet. 4) Unbound proteins are washed away. 5) The target protein is eluted.     ...and as in the first method, unbound proteins are washed away and the target protein eluted.  Immobilization...providing a solid support while unbound proteins are washed away.  While both Protein A and Protein G have ...because they do not require centrifugation between washes which can cause loss of beads, break weak protein...

... to only do the dishes once a month, resulting in a dangerous mountain of dirty dishes or you could choose...choose to do the dishes after every meal and be reassured that your dirty dishes won’t tumble out of the...

...chamber is divided into two halves that are distinguished visually through different patterns and the ...recently studied in detail thanks to optogenetics. In Goshen et al, inhibition of the CA1 region using HR was...your own neuroscience sub-discipline that has published using the technique and ask if they would be willing... opsins." Nature methods 9.2 (2012): 159-172.5. Goshen I, et al. Dynamics of retrieval strategies for ...

...cytoskeleton and cell membrane dynamics. First, a quick refresher.  The tools below use the following optogenetic...reversible. Late last year, the Akhmanova Lab published a new optogenetic tool for localized microtubule...the membrane itself? The Baskin Lab previously published OptoPLD, an optogenetically controlled phospholipase...available for controlling cell dynamics. Need a refresher on VVDfast, iLID, LOV, CRY2-CIB, and other optogenetic...

... Additional resources ThermoFisher Scientific: Biotinylation ThermoFisher Scientific: Biotinylation...more information on ABC and IHC check out Thermo Fisher Scientific's guide. There are an array of other...which biotinylation reagent to use check out Thermo Fisher Scientific's Biotinylation Reagent Selection Tool...

...publications and funding. If any of these three pillars crashes, the lab's success and the careers of its researchers...not enough. A 2013 study showed that out of 238 published scientific articles, only 46% could be reproduced...adopting simple note-taking tools, others using excel sheets or organizing folders in complex ways, there are...everything in one place. From pictures to excel sheets, researchers today generate vast amounts of digital...

...sequencing or other readout. Cellular memory is accomplished by the use of sequence-specific enzymes (e.g...also available, N1-LOC8R.  These plasmids are unpublished Unnatural amino acid incorporation in mammalian...detection of neuronal action potentials. The Cohen lab wished to improve on the Arch indicator and their collaborators... that their sgRNA-RNA fusions were functional, Shechner et al used the constructs in their study to target...contiguous with the sgRNA core (see image above). Shechner, et al. Nat Methods. 2015. PubMed PMID: 26030444...regulation in live cells since their introduction by Sherf and Woods in the nineties. However, reliance on ...guess what? pXPG is now available at Addgene. Sherf, et al. 1994. Promega Notes Mag. Giannakis, et...