Viral particles sequencing

Anna Marzec - Grządziel @Anna-Marzec-Grzadziel

01 January 1970 1 6K Report

What would be the best system for sequencing viral particles from environmental samples? I have two possibilities - MiSeq oraz HiSeq4000 (Illumina). I will have 3 samples of DNA and 3 samples of cDNA (rewritten from RNA).

Aleksei Korzhenkov

MiSeq is preferable because of easier run preparation. You may have up to 20M reads, it could be up to 10Gb depending on read length and library insert size. This amount of data equals 1000 viral genomes 100Kb length with 100x coverage.

Badges
Science topic

More Anna Marzec - Grządziel's questions See All

Is it Ok to decline to write a chapter for a IntechOpen to the lack of experience?

I have been asked by IntechOpen to write the chapter for a book they are going to publish, but as I don't have enough experience in the area they proposed me to write I declined their offer. Now...

24 February 2021 2,802 4 View

How to inerpret whether PCR went OK?

Dear friends! I am back to work after 3 years career break. Now performing a PCR, feeling like a newbie... Please, help to understand whether RT-PCR reaction "worked" or not. Which results should...

14 February 2021 3,129 8 View

Which fungicide are good for primary cells? Does it yeast contamination? How to get rid of them without killing the cells? How to get rid of spores?

Hello! Our lab is working with primary cells which we are isolating from the colorectal tissue. During the isolation, we are washing the tissue with pen-strep and then also add some pen-strep in...

07 February 2021 8,258 3 View

EMOJI-POLL-3 (Emoji-Association): Can you join the survey?

https://docs.google.com/forms/d/e/1FAIpQLSfaaCWZZqMIhoz5yj_5dxggvb6-cISx3GUHssYUWZWKbpx3UA/viewform Dear colleagues! We ask you to participate in a series of surveys related to the scientific...

26 January 2021 5,969 3 View

The same lC-MS for Forensic Toxicological and Chemical expertises?

Dear Colleagues! How correct and appropriate is it to carry out a forensic toxicological examination of drugs and psychotropic substances in biological objects (in blood, urine, hair) and a...

24 January 2021 4,489 2 View

GC-Headspace (HS-GC) chromatography for Forensic toxicological and Food expertises?

Dear Colleagues! How correct and appropriate is it to conduct forensic toxicological and food examination of volatile substances (ethanol, methanol, propanol, ethyl glycol, etc.) in blood and...

24 January 2021 5,645 2 View

How to choose mouse cell line to work on?

Hey, I am looking to start working on mouse cell line for some genomics experiments. I have the following requirements: 1) Normal chromosomes composition. 2) Possible to transfect. 3) Possible to...

03 January 2021 4,387 2 View

How to describe the method described below?

I do research on the relationships between universities and local governments by asking the research question (how) can universities contribute to the design (and implementation) of public...

29 December 2020 4,522 12 View

How can I change the media for THP-1 cells without dislodging them from the surface of my well plate?

I am working with THP-1 cells at the moment and am having trouble with maintaining a high confluence once I seed them on a 24-well plate. I usually try to seed around 100,000 cells per well and...

29 December 2020 1,567 3 View

What glass vials do you use for small volumes (400ul-2000ul) that fit in the centrifuge?

I am planning some NMR experiments that require glass vials (due to chloroform). I am looking to find glass vials that would take 400-2000ul volumes, fit in the centrifuge and allow me to separate...

01 December 2020 3,259 2 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Would fecal samples stored at -20C for over a year impact metagenomic analysis?

Dear All, I have access to some rodent fecal samples that have been stored at -20C instead of -80C. Anyone have experience with the impact of stowage condition on comparative metagenomic analysis...

01 March 2021 2,512 1 View

Where to find data on trees in tropical agroforestry?

Hi, I'm looking for data (mainly related to management: growth rate, canopy size, soil and climate preferences, etc.) about tropical trees used in tropical agroforestry. Have you ever heard about...

28 February 2021 7,356 8 View

Does different dilution factors affect negatively on NH3 reading ?

I have a sample of treated water sample & asked to obtain ammonia conc. in sample using a machine with 5-25 ppm detection range. However, upon testing with different dilution factors, all...

27 February 2021 8,483 3 View

How to compare 2 samples recruited with different sampling methods?

If I want to compare characteristics of 2 groups of patients, one group is recruited from a random sample of the general public while another group is from a sample with a fixed gender (male to...

26 February 2021 3,526 3 View

Can random sampling have inclusion criteria?

As random sampling means that everyone in the population have an equal chance to be chosen, can it have inclusion criteria? My research participants have been chosen based on the inclusion...

26 February 2021 6,905 10 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Can I use FLEXBAR to detect and remove barcodes out of my short reads without demultiplexing ?

Hello, I have demultiplexed my short reads and I have removed the Illumina adapter left in the sequences and now I need to remove the barcodes used by the sequencing centre from my reads. I have...

22 February 2021 9,873 3 View

Where can I find raw quantitative datasets on ecosystem services?

I'm an Undergraduate student on the search for a research topic which has to involve any ecosystem service(s) and a response to environmental change. I'm looking for raw quantitative data sets (I...

19 February 2021 5,911 2 View

Resume Book UEP2013 Asian Edition, dis somebodey has it?

I am looking for a copy of the resume book of UEP2013 Asian Edition (Urban Environmental Pollution 2013 Asian Edition) held in Beijing. If somebody has it, please I would like to obtain an...

11 February 2021 2,247 2 View