Screening - Science topic
Screening, in medicine, is a strategy used in a population to detect a disease in individuals without signs or symptoms of that disease. Unlike what generally happens in medicine, screening tests are performed on persons without any clinical sign of disease.
Questions related to Screening
A research team is conducting a study to evaluate emotions that have been automatically generated by using GANS, through a small survey. The survey presents 20 works of art in four different versions, each aimed at evoking one of the following emotions: amusement, delight, dread, and melancholy.
Your opinion is highly valued. Kindly access the form provided via the link and indicate the emotion you perceive each one of the 20 works of art to evoke. We suggest increasing the screen brightness to have a better view of the images.
Thank you for participating in this research. Your responses will be greatly appreciated. Feel free to share with your contacts.
How to use SISSO (Sure Independence Screening and Sparsifying Operator) by PYTHON?Are there any related tutorials or materials?
When aligning the objective aperture on a F30 in diffraction mode, does the electron beam need to be in the center of the screen? For example look at the picture I have shared. The beam is off centered wen in diffraction mode. Do I need to put the beam in the middle or is it okay if it's not?
I have a highly conserved pocket in my enzyme that currently has no known function. I'm interested to see whether it binds a particular molecule. I'm wondering if anyone knows of an AI or software that can screen the pocket and identify molecules that are likely to bind there.
I am a student at the SOMT, university of Physical Therapy(The Netherlands) and I am studying for a master degree in Geriatric Physical therapy.
Currently I am working on a school assignment where I want to look further in differentiating sarcopenia (screening) in a nursing home. In a lot of literature I found that the Ishii screening tool is highly
recommended to use. Unfortunately I can't find this tool? This is maybe a bold question but can you maybe help me by telling me where I can find this exact tool?
It would really help me with my assignment :)
Thank you- anyway and also thank you for all your research and very interesting studies.
Is it more acceptable or tolerable of false positive or false negative in suicide screening for a suicide screening tool?
I want to develop an understanding for conducting Meta-Analysis studies in Psychology. how many studies to select, how to screen them, any tools which are used for the purpose. kindly explain with references how to conduct a meta-analysis
I need a set of images of emotional faces (angry or sad; neutral; happy) of infants. I would like to frontally present these faces on a screen in a computer experiment. If infant images were matched in size, luminance, position, etc, with other images of adults, it would be great! Yhank you
My lab has the NEB Gibson Assembly kit (unfortunately not the Hifi kit) and I have been struggling for months to assemble various different constructs. I'm wondering if anyone has used this kit specifically and if there are any specific things/tricks you do or use?
I have tried to insert 3 fragments (ranging between 500 bp - 2 kb) into a vector backbone, as well as overlap PCRs to insert 1 fragment into the vector. All fragments have between 30-40 bp homology regions. I PCR amplify all of my pieces (including backbone) and gel extract them because we don't have DpnI. I can get the overlap PCR working well, so I thought the primers/homology regions were designed ok. Yet, I can't get a simple 1 insert into 1 vector reaction working - I consistently get zero colonies (occasionally I've gotten an absurdly low number like 2 or 4, but screening them they're false positives).
I've used NEB's positive control to make sure the Gibson mix is working and got many colonies, but unfortunately they don't provide much information on the contents other than it's 2 DNA fragments so I'm not sure how they designed the two fragments to be ligated.
I have typically been adding 50 ng vector and tried both equimolar amounts of insert and 2-3 fold molar excess of insert. Is there a concern that there is too much salt contamination carried over from the gel extraction? I was curious about the positive control NEB provides and nanodrop read quite comparable A260:A230 ratio between that and my fragment mix. I've also tried adding 5% DMSO into the reaction in case secondary structures were preventing efficient assembly, as well as transforming 50 uL of NEB10b with 2uL vs. 10uL of the Gibson reaction. And nothing seems to stick.
Sidenote I tried IVA once and didn't work for me, but if you have any specific recommendations with that I'd also be willing to try troubleshoot that method if I continue to have issues with Gibson.
According to an article entitled "Blood Transfusion Safety, current status and challenges in Nigeria" (2017), achieving blood transfusion safety in Nigeria (and likely the rest of Sub-Saharan Africa) remains a difficult task due to a number of factors, including a lack of blood, inadequate implementation of blood transfusion guidelines, insufficient infrastructure, and a high prevalence of transfusion-transmissible infections (TTIs), particularly hepatitis and human immunization. Even though there has been a slight improvement, particularly in the area of screening donor blood for common TTIs, significant efforts are still required in the form of effective public education campaigns (on blood donation) and ongoing system improvement to move the nation's current transfusion practices in the direction of safety and self-sustenance.
Source: Aneke JC, Okocha CE. Blood transfusion safety; current status and challenges in Nigeria. Asian J Transfus Sci. 2017 Jan-Jun;11(1):1-5. doi: 10.4103/0973-6247.200781. PMID: 28316432; PMCID: PMC5345273
Given the disproportionately high risk provided by blood-borne pathogens, regular monitoring of blood transfusions is required to avoid disease transmission. ELISA and Rapid diagnostic immunochromatographic technique are the two most extensively used methods for detecting HBV, HCV, and HIV infection in blood donors. Although ELISA are considered more accurate worldwide. With this, what are the drawbacks of using the rapid immunochromatographic kits for screening blood donors compared to ELISA?
Source: Al-Matary, A. M., & Al Gashaa, F. A. S. (2022, November). Comparison of different rapid screening tests and Elisa for HBV, HCV, and HIV among healthy blood donors and recipients at Jibla University Hospital yemen. Journal of medicine and life. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9762378/#:~:text=This%20study%20showed%20a%20significant,infectious%20markers%20for%20blood%20donors.
In responding to a request for a text I've always clicked on "View Request" and then get a screen where I can choose to respond or not. I don't get that anymore -- it's just an abstract of the paper they've requested. I can find no way to send the text. Please advise. Thanks.
I have try to establish a CRISPR screen in primary T cells，sgRNA transduce with
lentivirus and Cas9 protein delivered by electroporation (SLICE). But in the pilot experiment, we found that the efficiency of knocking out CD45 through this system is very low. The same experiment on Jurkat also failed.
Then I tried to change the experimental conditions, for example, increasing the amount of Cas9 protein or using Cas9 mRNA, or change CD45 sgRNAs.
None of these attempts have improved CD45 knockout efficiency.
I would appreciate it if you could give me some good advice!
Oral cancer has a high morbidity and mortality rate and clinical examination has resulted in late diagnosis. What reason has led to a delay in the implementation of a complementary screening test to the conventional clinical test?
covidence a screening software, and for full text screening if i want to keep article for my supporting document but not include in study how should i flag it?
Some papers refer to calculate FRAP value as
FRAP value = = [(A1 − A0)/(Ac − A0)] × 2, where Ac is the absorbance of the positive control, A1 is the absorbance of the sample, and A0 is the absorbance of the blank.
Some other papers refer to calculate FRAP value as
FRAP value will be Trolox equivalent using Y=mx+c equation.
Please let me know the original process for the FRAP value calculation.
I am looking for a dataset where people recorded the simplest possible reaction time task. Something like pressing a button as soon as the screen turns red. Or maybe any variations that are not too far from such an experiment.
I know research on reaction time has been going on for the past ~40 years. But somehow I can not find a dataset for it. Wonder if any of you have seen it?
Thank you in advance!
I am trying to do a impact analysis through workbench explicit dynamics.
I establish the model in Explicit Dynamics and mesh it at first, and then, I go back to the project schematic page and drag the Autodyn component into there. Then, I connect Autodyn and Explicit Dynamics two parts together. I click the " setup" icon in Autodyn part and update it. Later, I go into the screen of Autodyn and find nothing in there. I attach all of my processes in this poster. Is there any body could tell me how to import the model in Explicit Dynamics in Autodyn?
I need to screen the toxicity of several compounds that will be applied locally to an open wound of bone and muscle injury, which human cell lines (good for several passages) would be most appropriate for this experiment beside hMSC?
I want to screen for antimicrobial activities of spices extract against fungal isolates from food. what method /methods is best for it?
For example QTL (x) is identified for disease screening in the mapping population where the parents are A and B. Can this QTL (x) be used as marker to screen the another population where its parents are C and D for the disease resistance?
E coli strain JM109(DE3) has its genotype listed as endA1 glnV44 thi-1 relA1 gyrA96 recA1 mcrB+ Δ(lac-proAB) e14- [F' traD36 proAB+ lacIq lacZΔM15] hsdR17(rK-mK+) (λDE3).
It seems like it should be suitable for blue-white screening because of the lacZΔM15 deletion and but Promega states it isn't suitable. Another supplier, IntactGenomics says it is good for blue-white screening.
Anyone have an explanation? Is it just that it's an expression strain and not a cloning strain?
Antibiotic resistance , enzyme production are types of screening method . Both have advantages and disadvantages so , in these two which method is more preferred to insert in vector and provides maximum results . Are there any considerations of these methods while performing gene cloning?
I am conducting a systematic review and after screening have come up with 9 included studies 6 of which are systematic reviews. Am I able to use these in my report and discussion? As the articles the reviews utilise / mention are outside of our date range?
In the REDIAL project funded by Kidney research UK We are looking for a dynamic and talented early career researcher in the field of Computational Materials Science with a focus on Separation and Biomedical applications, who can effectively exploit Artificial Intelligence tools for the design of functional Materials and Sustainable Processes in the SusProM Group. https://www.suspromgroup.eng.ed.ac.uk/
- To work in a highly interdisciplinary Research Team with Chemical Engineers, Bioengineers an Experts in Artificial Intelligence and undertake research on the computational simulation and screening of materials for the miniaturisation and circularisation of the hemodialysis process.
- To exploit the research results to improve the life of kidney patients, in collaboration with Kidney Research UK and frequent contacts with patients, nephrologists and biologists during National events.
- To deal mostly with computational work, but willing to carry out experimental validation in the lab if needed.
Your skills and attributes for success:
- Computational material science skills (Molecular Simulations, Macroscopic models and Machine Learning)
- Strong fundamental knowledge of materials for separation theory
- Ability to apply fundamental skills to problem solving
- Coding skills (Python preferred, Pytorch/tensorflow desirable)
- Basic experience in the lab.
I need to use the AutoDock program, but I tried both versions 1.5.6 and 1.5.7. I had no problem loading, my only problem is that when I open the program, the loading remains around 9% in the window that opens. Then the window closes with the command page that opens. It will be more understandable when I add screen shots. I am using Win11 operating system, I have an HP brand laptop, I really can't figure out where the problem is. In the screenshot I attached, it stays as it is. The program closes directly.
Metabolomics has emerged as an invaluable tool for prognostic and diagnostic purposes, last in the cascade of others OMICS -genomics, transcriptomics, and proteomics. Omics training usually covers experiment design, data generation, and collection, data preparation, data analysis, and the last but not the least - data interpretation.
At the end of this meticulous energy, time, and financial-consuming path, it might be totally none sense to fail to put your results into the broader biological context.
For those like me that have never been trained to interpret metabolomics data, how can we make sure to not miss important points? Is Basic knowledge in Biochemistry, Physiology, or physiopathology of the disease of your interest, enough to harness the full potential of metabolomics technologies for biomarker screening u.a?
I would like to discuss with experts out there, the most important assets for a right and successful data interpretation of metabolomics data.
Thank you for sharing your experience in the Metabolomics journey as well.
I just established a cell line after long-term term culturing and would like to screen for contamination. I only have Hoechst 33342, and I would like to know whether it can be used for mycoplasma screening.
For example, if a biparental mapping population is screened for abiotic stress tolerance (drought/salt) with physiological parameters.
I have done simulation of 100 ns by using gromacs.. and the following is hbond plot but its different i dont understand that every thing is fine but the data formate in .xvg file is different, its look like mixed up .. here i am attaching two screen shots but if you want to check the .xvg file then i will send you
Please someone help me i dont know the solution
I'm looking to implement a fast method to screen anti-inflammatory products. Avoiding protein denaturation is linked to anti-inflammatory properties.
There is a nice number of papers describes a rapid and low cost screening method based on an incubation of the tests compound and a BSA solution (about 1 to 5% w:w) at higher temperature (usually 72°C) for a given time (between 5-20 min) buffered to ph6.4-6.6. Reading is done by spectrophotometry (usually 660nm). The method seems simple but when I try to implement, my reading is zero. I noticed that each laboratory introduces a slight change on the most cited protocol. I have introduced the major changes reported without any reading. Papers reporting the raw data indicates that after incubation the negative control (no test product of anti-inflammatory drug) DO is about 0.3-0.4.
Notice that all weightings, control and technicians have been investigated to try to find the root cause, unsuccessfully. Do anyone have any experience on this that can give me any advice?
I wish to perform a genotype-phenotype correlation study in a family with a known mutation in RPGR-ORF15.
However, the RPGR-ORF15 region is very tricky because it contains GC repeats and thus its not possible to amplify with standard PCR conditions.
Special protocols are needed for both PCR amplification as well as during Sanger sequencing.
Therefore, I would greatly appreciate if anyone could suggest me a commercial facility where I can send my samples for screening the specific mutation located in the RPGR-ORF15 region?
Number of samples to be screened = 05
For example, when searching over the PubMed database, we get 125,000. But PubMed has some limitation that just allow us to screen until 1000 results. Do anyone come across this situation, and what you do to solve this issue, or anyway to report the results?
Hi everyone, I wanted to know if there is a method that allows us to screen bioactive molecules with protective power against UV rays. For example, exposing a support containing the molecules to UV rays, and then we observe directly (visually) a character that allows us to select the protective molecules. Thank you in advance
Field screening of rice genotypes against brown plant hopper was done on the basis of hopper population/hill/week. The genotypes are to be categorized under different levels of resistance but there is slight confusion in choosing the standard scale for BPH evaluation under field conditions. Please help verify the two scales attached in JPG format or share any article or web link regarding my query.
I am working on the degradation capacity of naphthol by 6 bacteria isolated from wastewater which are : Pseudomonas aeruginosa , Pseudomonas Putida , pseudomonas fluorescens , Bacillus thuringiensis , Citrobacter freundii and Escherichia coli but I want to know which is the best composition of the minimum medium for the screening of these bacteria .
Thank you in advance.
I wonder whether there is a way to find the original natural product from the modified structure? It is very common to use natural product derivatives in HTS/HCS/in silicon screening to find more potent structures and/or SAR. Once, we have a candidate structure, is there any database where we can do search (based on structure similarity/substructure) and find the originated structure and the source (which plant, microorganism etc.)? Thanks
I am currently trying to screen the behavioral effects of the 6-OHDA unilateral injection in the striatum of Wistar male rats to confirm a Parkinson's animal model by apomorphine-induced turning behavior test (or rotameter test).
Although the dose of apomorphine is prepared according to the articles and is injected intraperitoneally to the rats, but instead of turning against the injection site of the neurotoxin, the rats become extremely relaxed and even fall asleep, and it is not possible for me to check the behavior.
I have request from dear students, professors and scientists that help me to find out what the main problem is and share the tips of rotameter test with me.
Please feel free to have contact with me.
Thank you for reading and helping!
I have National Cancer Institute screening results of my compounds. Upon submission, I am asked by the reviewers to provide standard deviations, what kind of statistical analysis was performed, and its significance. I have scourged the NCI methodology section and many publications throughout the years and couldn't find anyone who met these criteria.
I used 0.5% Aq. AcOH solution to dissolve chitosan and derivative to evaluate their antimicrobial activity and performed anti-bacterial activity and antifungal activity using the broth dilution technique in 96-well micro-trays (NCCLS, 1993) and the antifungal screening method (NCCLS M27-A2 protocol, respectively. The cytotoxicity tests of prepared chitosan derivatives were assessed by MTT assay.
Now reviewer have following comment.
kindly help me in replying the comments of reviewers
comment of reviewer: if the derivates are still not soluble in water how are they be used in the kind of treatment proposed? What it's the implication of using acidic media in antimicrobial or cytotoxic treatment ?
I have a bit of a semantic question in relation to a paper I am writing.
Recently, I had a discussion with my supervisor on Type-II errors. In my recent statistic course, the type-II errror was defined as falsely not rejecting H0. A lack of power is often described as a cause of a type II error. As such, I was under the assumption that a type-II error is mostly used in the context of statistical tests.
However, my supervisor explained that "type-II error" could just as well be used describe any false negative result, also when it relates to methodological problems e.g. using the wrong measurement instrument for your aims and falsely not finding any effect.
I cannot find anything on pubmed on this matter. I screened some papers mentioning the Type-II error but all used it in a statistical context, not more general.
As such, my question is whether 'type-II error' only relates to a statistical problem or also to a broader definition of false negative outomes?
I have read various articles in which plastic degraders are screened using PEG-containing MSM media. But which PEG is used is not mentioned. So, I used PEG-6000 as the sole Carbon source to isolate the plastic degraders.
I want to get suggestions about the best solid medium for plastic degraders.
I need to screen my plant extract for all the compounds present in it. So i want to know which technique (without using standards) will give me the results
I submitted a paper in the field of neutron/ gamma pulse shape discrimination and received a reviewer's comment requesting the following: "A scatter diagram and FoM diagram of screening factors shall be supplemented appropriately."
Hoping anyone can tell me what the reviewer means by screening factors. Thanks.
I would like to create peptidomemetics based on a certain known peptide in silico.
For this I am asking if there can be any good references on this topic. (in silico specifically)
What I Want to do is; to create a small library of these peptidomemetics, then to screen their ability to dock a certain active site, then to run a molecular dynamics simulation to check the stability of the complex and the affinity to each of them.
Potential inquiries are;
Which software to use for building?
Which software for docking?
Which software to get parameters for these peptidomemetic to run the Mds? Or is there a preferred forcefield for these compounds?
Should I deal with them in the same way as small molecules (this can be an answer that reliefs me at the end)
Is there any maximum number for studies that can be included in scoping review?
This is Homa Arshadi, Ph.D. Candidate of medical library and information sciences. I need some help with the following question. Could you please kindly advise me.
I'm doing a scoping review on text mining topic. The number of records identified after searching databases are about 10,000. After screening of 60 percent of these records, about 500 of papers are eligible, which must be read by full text. Is it reasonable to perform such review? What is the maximum number of studies to be included in a scoping review?
Many thanks in advance!
I am looking for advice regarding my research project. I collect number of patients with diagnosis and number of patinet with those diagnosis who were screened for sertain conditions each year 2019/2020/2021 (for instance blood glucose among diabetes patients). Therefore, those two numbers provide a rate for specific year. My idea is to compare those rates between years. However, I am not sure what kind of test to use? Fluctuation between years in denominator were not so big beyond natural flow. But, I also think that someone who skipp a screening one year has to intention to skipp it again.
Any other idea and solutions are welcome
Thnaks for your replays.
Hi, I need to check microbial growth on wastes rich in proteins that tends to ferment pretty quickly. To get an idea of what and how much it's growing, I thought about using Plate Count agar, YS or YM for screening for yeasts, maybe Violet Red Bile for gram negative. What can I use to check protease activity? Since it's a mixed colture, I cannot use super selective media.
Could this course of action work for a totally uknown mixed colture? The goal is to identify the microrganisms responsible of spoilage and fermentation.
Thanks in advance for the help.
In some papers I find out they are using both the cell lines (STF and STF3A cells) for screening of Wnt inhibitors.
Is it okay to use only STF3A cells for screening of Wnt inhibitors?
I am used to pre-incubate the test compounds with enzyme for durations ranging from 15 min to 45 min before adding the substrate and initiating the reactions. However, in process of designing a high-throughput method, that seems to be a lagging factor.
Hence the question.
On screening If MNS blood grouping is incompatible, can the blood go forward for blood transfusion?
Most experts agree that adults should limit screen time to less than two hours per day outside of work-related activities. Excessive screen time not only produces its own negative effects like eye strain and headaches, but it also steals time from more healthful pursuits like forging real-world connections and exercise.
I usually spend 3-4 hours on screen besides work related activities and I am trying to reduce it.
Solid phase extraction (SPE) commonly forms part of LCMS, GCMS analytical chemistry or in vitro bioassay testing workflows to screen for organic environmental chemicals. Once samples have been passed through columns (E.g. HLB, C18, C8 etc.), the organic compounds are eluted using a solvent, dried and re-constituted in the solvent of choice.
The drying step is typically performed using nitrogen gas. I have seen protocols describing the drying of SPE extracts under a stream of air (such as in an extraction hood) instead of nitrogen.
Is there a particular reason why N2 is used for drying? Such as chemicals becoming oxidized? Could simple drying using air compromise the integrity of a sample?
50+ genotypes, 2 Treatments, 26 parameters are recorded during screening data. so what is your recommendation about graph making software and graphs name. Your answers will be highly acknowledge.
this is regarding nitrate determination by 4500-NO3 B. Ultraviolet Spectrophotometric Screening Method. when the organic matter content is high, can we use an Allum solution to precipitate the organic matter (we have a wastewater sample which contaminated with tannin. this is from coir industry) once we add allum, colour and turbidity can be removed. so can we use the above method to determine the nitrate content?
We performed a TMS-related meta-analysis, and most of the TMS studies were within-subject designs. The reviewer said that "the conventional method for estimating effect size is not applicable to the within-subject design. However, it seems that the authors simply ignored this methodological issue and did not utilize other measures to calibrate the values they derived." We have no idea why within-subject effect sizes were un-applicable for meta-analysis, because numerous previous studies did so. And we are unaware of "other measures" to calibrate the within-subject effect sizes. To note, these studies screened for meta-analysis were finely designed, not the ones taking pre-and post-tests without a control condition for observing the intervention effects.
I am going to test the antimicrobial activity of extracts against different bacteria. I need to test a few thousand compounds so I am going to do this in a 384-well plate. Does anyone have a protocol for the screening in a 96-well or 384-well plate? Thank you
I am having a problem with my PCR products, made from genomic DNA extracted from samples of Euphausia superba, basically Krill from Antarctica.
PCR products are for a 16s sequencing of the hypervariable region V3-V4, 500 bp construct.
I run the gDNA to understand if the problem is in the extraction part (because these are samples extracted from another lab) and the run went well, then I run the normal PCR products and all the signal is in the wells.
Then, I cleaned up gDNA and PCR products with magnetic beads, and after the PCR cycle to amplify those regions of the newly cleaned gDNA I had the same problem, with both samples (cleaned up amplified gDNA and cleaned up old PCR products) stuck in the well.
THEN, I thought that maybe the problem might be caused by DNA binding protein or by some ions that "screen" the charges and there is no migration (because this creature lives in super cold regions and might have some sort of molecular mechanism that protects against freezing), so I used isopropanol + ammonium acetate to try to extract DNA from them, but even with this step, I had the same result.
Before I try with SDS to achieve the extraction ( or before I drink it to end my life), does someone have the same problem?
I uploaded one of the gels (the one with PCR products that weren't cleaned up).
The first 4 columns are the same protocol but with a different creature (you can see the pcr products near the marker, and the other ones are all PCR from krill). Those bands below are clearly primer dimers.
My source laser is a 20mW 1310nm DFB laser diode pigtailed into single-mode fiber.
The laser light then passes into an inline polarizer with single-mode fiber input/output, then into a 1x2 coupler (all inputs/outputs use PM (polarization maintaining) Panda single mode fiber, except for the fiber from the laser source into the initial polarizer). All fibers are terminated with and connected using SC/APC connectors. See the attached diagram of my setup.
The laser light source appears to have a coherence length of around 9km at 1310nm (see attached calculation worksheet) so it should be possible to observe interference fringes with my setup.
The two output channels from the 1x2 coupler are then passed into a non-polarizing beam splitter (NPBS) cube (50:50 reflection/transmission) and the combined output beam is projected onto a cardboard screen. The image of the NIR light on the screen is observed using a Contour-IR digital camera capable of seeing 1310nm light, and observed on a PC using the software supplied with the camera. In order to capture enough light to see a clear image, the settings of the software controlling the camera need to have sufficient Gain and Exposure (as well as Brightness and Contrast). This causes the frame rate of the video imaging to slow to several second per image frame.
All optical equipment is designed to operate with 1310nm light and the NPBS cube and screen are housed in a closed box with a NIR camera (capable of seeing 1310nm light) aiming at the screen with the combined output light from the NPBS cube.
I have tested (using a polarizing filter) that each of the two beams coming from the 1x2 coupler and into the NPBS cube are horizontally polarized (as is the combined output beam from the NPBS cube), yet I don't see any signs of an interference pattern (fringes) on the screen, no matter what I do.
I have tried adding a divergent lens on the output of the NPBS cube to spread out the beam in case the fringes were too small.
I have a stepper motor control on one of the fiber beam inputs to the NPBS cube such that the horizontal alignment with the other fiber beam can be adjusted in small steps, yet no matter what alignment I set there is never any sign of an interference pattern (fringes) in the observed image.
All I see is a fuzzy blob of light for the beam emerging from the NPBS cube on the screen (see attached screenshot) - not even a hint of an interference pattern...
What am I doing wrong? How critical is the alignment of the two input beams to the NPBS cube? What else could be wrong?
I prepped a cDNA library from ovarian cancer cell line RNA (all RIN scores were 9+ on TapeStation 4200) using a KAPA HyperPrep mRNA kit and UDI adapters for Illumina sequencing. When we ran the TapeStation (D1000 HS screen tapes) on the prepped libraries, we saw extra peaks around 230-250bp. On some samples it was a more pronounced peak, but others it was more of a shoulder. We are baffled on what this could be from. We did a QC sequencing run on an illumina nextseq P2 100 cycle and are wondering if our inner distance plot could look like this due to the smaller fragments we see on the tape station? I've had some people suggest the extra peak on the tapestation a bubble peak from over amplification of the library, but bubble peaks would appear larger, not smaller. Our anticipated library size was 200-300bp. For most samples the average size was 350bp, so including the adapter sequences this seems right. We just have no idea what the smaller peak would be that appear in nearly every sample. I've included images of a couple electropherograms and gel images from the tapestation and the inner distance plot. You can see these smaller extra peaks appear as bands on the gel images and how they slightly vary in size from sample to sample.