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...This post was contributed by guest bloggers Samantha Zyontz and Neil Thompson from the MIT Sloan School... Under such circumstances, we would observe this same correlation, but it wouldn’t be causal. To control...Addgene deposits as if they were published in the same journals as those that did make deposits to Addgene...3 times as many citations as other papers in the same journals! So, is all this remaining difference caused...along the way. Many thanks to our guest bloggers, Samantha Zyontz and Neil Thompson. Special thanks to Addgenies...for helping compile the data used in this work. Samantha Zyontz is a Ph.D. candidate at the MIT Sloan School...

...mutation.  Once the samples arrive, each group of plates will have select samples prepared and screened...and performs DNA minipreps for small batches of samples. As soon as that process is complete, QC scientists...day. Nothing like waking up to fresh data! These same plasmids are then added into our normal full plasmid...screened by NGS to spot check the samples, the rest will be put into a status we call “Archived.” This status...for all several thousand plasmids at once. Any samples that are requested by scientists, will immediately...

... not robust. Sampling noise There is, of course, simple noise in the process of sampling and inference-making...methods, QRPs, and small samples, then when replications do not come out the same as an original research...data and a new, preregistered experiment. Reduce sampling noise with registered reports, the gold standard... special emphasis on positive controls and good sample sizes, concerns that are too easy to overlook when...

... PCR Digital PCR (dPCR) involves splitting up a sample into thousands of physically isolated partitions...of target DNA molecules present in the original sample with a great deal of precision. This means digital...theoretically detect a single target molecule in a sample. Digital PCR assays for mutation screening Now...amount of both mutated and wild type target in each sample can be quickly calculated (details in [2]) and ...mutation in a bulk or single cell-derived genomic DNA sample as part of a precision genome editing workflow....easily able to distinguish single-cell derived samples with mono-allelic mutations versus those with the...

...sequentially adding different ligands to the same sample to label sub-populations of your protein of interest...probably find lots of different plasmids containing the same protein of interest tagged with different fusion...affinity purification tags, another version with that same red fluorescent protein somebody made because they...ligands (Gautier et al., 2008). Although based on the same original enzyme, SNAP-tag and CLIP-tag show good... structures or low levels of expression with the same imaging workflows you already use. Or you can really...purified proteins in vitro, you can even use the same tag for multiple proteins but label each separately...

...complexes before applying them to samples, such as when performing IHC in a sample where your secondary antibody... fragments that are the same species as your secondary antibody to your sample prior to adding your primary...antibodies. Their smaller size allows them to get into samples more efficiently and can also improve localization...a better chance of getting the complex into the sample. Alternatively, Fab fragments can be used as a ...

...different synthetic promoter driving expression of the same transgene: an optogenetic reporter, channelrhodopsin...in mice is not a good predictor for targeting the same cell class in NHPs (R=0.38) and humans (R=0.32),...), but the odds of that promoter targeting the same cell class in all three species are still greater ...in monkeys was a good predictor for targeting the same cell class in humans (R=0.67).  A database of the...promoters can be paired for targeted expression. This same pairing of synthetic promoters were also used to... al., 2019).  While tested in retinal cells, the same design principles could be used to create synthetic...

... on plasmid preps, not all plasmid preps are the same. Your downstream application will dictate how much...plasmid DNA itself, which can happen if you leave the sample in a lysis buffer for too long or if you get a ...you mix specially coated magnetic beads into your sample and use magnets to isolate the beads for the wash...situation as you can simply add more beads to your sample. But, you’ll need to ensure you have an appropriate...extracting DNA from tissues, blood, virus, or other samples, for PCR and gel cleanup, and for extracting RNA...option for you, some manufacturers offer trial or sample sizes of their kits, which you can use to test ..., transfection-grade While we’ve included a sample of some commonly used kits, please note that Table...

...simultaneously express two or more separate proteins from the same mRNA. We've discussed promoters before so in this...expressing your gene as they are both derived from the same transcript. Of course multicistronic vectors do ...anytime you want to express multiple genes in the same cell. Although it is possible to drive co-expression...expression cassettes, having the genes expressed from the same cassette is sometimes advantageous, particularly...produce equimolar levels of mulitple genes from the same mRNA. The term "self-cleaving" is not entirely accurate...successfully utilized 2A and IRES elements within the same multicistronic vector, effectively making a construct...

...sensitivity of the assay, targeted DNA or RNA from a sample is first amplified using RPA (recombinase polymerase...adding Csm6 and a Csm6 specific reporter (in the same fluorescent channel as the Cas13 reporter), they...presence of your DNA or RNA of interest within a given sample is simply determined by the number of bands present...and a closely-related virus, Dengue from multiple sample sources. SHERLOCK could also detect low-frequency...test is started using RNA purified from patient samples and can be read using a dipstick in under one hour... high selectivity and sensitivity from patient samples. Find the DETECTR plasmids here! Applications of...

...lab often tests samples of new bacteria from anywhere they can find, whether the samples are from a rain...was safe to say the sample had their attention! They isolated DNA from the sample, amplified the CRISPR...range of mammalian cell lines. However, in those same comparisons, the AbuGoot lab reported no detectable...thousands of different mutations, all found in the same gene. If we only have small, directed editing abilities...

...restriction and ligation steps together in the same tube at the same time, however, it can prove itself to be...agreed on universally using the same four-base overhangs for the same type of parts to ensure that these...rest of the genes? And do you want it to be in the same (forward) or in the opposite (reverse) orientation...than a solution of a shorter DNA fragment with the same concentration. What really matters is the molar ...

... with the same titer and serotype previously used in a different brain region that the same result will...sites will be flanked by two lox sites now in the same orientation. Next, the loxp site is excised since...since it is between two lox2272 sites in the same orientation preventing the transgene from reverting. Figure...scrambled one pair of lox sites and either used the same sequence to flank a transgene (homologous pairs)...the DIO/FLEx vector. This step is essentially the same as what was used to optimize the serotype, except...

...not powerful enough for large brain samples. For large brain samples, we recommend pretreatment with ScaleCUBIC1...time points, sacrifice the animals and fix the samples. When you use AAVs, it typically takes a few weeks...excessive amount of XFPs expressed. Then, clear the samples and visualize. For more details on this procedure..."Optical clearing and index matching of tissue samples for High-resolution fluorescence imaging using ...

...IHC, not all IHC experiments are the same. Differences in sample processing, fixation, antigen-retrieval...make sure you’re not trying to choose between the same antibody sold under different names.  If all else...staining patterns of multiple antibodies against the same target; tagged protein strategies that express a...antibodies may perform differently in different samples and experimental conditions. Be prepared to troubleshoot...

...produce the same signal, so only one HRP-conjugated RANbody can be used at a time. Samples can be sequentially... lower background and better penetration of the sample due to the smaller size of RANbodies compared to...sequentially stained with two HRP RANbodies if the sample is stripped. HRP-RANbodies are, however, compatible...it is approximately as sensitive as detecting the same antigen with a standard primary/labeled secondary...

...reason you can’t then ask that same question in your next interview. The same goes for answers interviewers...interview questions. Story telling shares many of the same elements as a STAR answer: a setting, a conflict...pay attention. Your interviewers will not have the same experiences as you, so set them up for success by...and your interviewers. You’re probably all in the same boat, but there are a few things you can do to make...

...affinity binding, such as immunoprecipitations. Your sample species should also be considered when choosing...immunoglobulins naturally present in the tissue sample. There are species-on-species staining protocols...secondary antibodies that are all derived from the same host species and have been cross-adsorbed. The cross-adsorption...using mouse IgG2a and rat IgG1 antibodies in the same application, using a Goat anti-mouse IgG2a cross-adsorbed... species, and secondary antibodies raised in the same species that have been cross-adsorbed to reduce ...

...high and above what would be expected in patient samples (e.g.: blood, urine). Adapting toehold switches...pathogen’s genome as unique barcodes to identify samples containing the virus. Of the 48 sensors, targeting... diagnostic results.  Our approach now detects samples at clinically relevant concentrations (1-3 fM; ... look at viral load in patient blood and urine samples; we showed that we can detect the virus directly...Interview with Previous Collin's Lab Member and Sample 6 Cofounder Michael Koeris Learn How Minigenomes...

...removing excess dye from the sample, which is particularly important for samples where washing is difficult...reason is something called “the photon budget”: each sample has a limited number of fluorophores and each fluorophore...of information one can extract from a biological sample is wholly dependent on the photon budget and pushing... desperate to extract a few more photons from a sample. Chemical fluorophores can be substantially brighter...