Molecular Minutes

Featuring Instagram Science Communicator, Jen, 'A Bookish Scientist'!

Posted by Applied Biological Materials (abm) on January 14, 2020

We recognize science can seem difficult to young scientists, and we hope to raise awareness about people who make it fun and accessible to broader audiences through social media, #SciComm!

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Meet Jen, also known as "A Bookish Scientist" on Instagram. She is a first year Cancer Biology PhD student and bookworm, who recommends good books and gives PhD tips to her follower base of almost 10K on Instagram!  


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Topics: #SciComm

What is Multiplicity of Infection (MOI)?

Posted by Applied Biological Materials (abm) on January 1, 2020

So you’ve packaged your DNA into a virus and you’re ready to infect your cells! But, how many viral particles are required for 100% infection? In this blog post and video, we’ll explain the concept of Multiplicity of Infection or MOI and take you through how to determine the best MOI for your experiment.

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Topics: Viral Vectors, Multiplicity of Infection

A New Year, A New Website

Posted by Applied Biological Materials (abm) on December 18, 2019

abm is excited to announce that we will be launching our new website in early 2020!

When abm was first founded in 2004, our goal has always been to make research more accessible. Today, our catalog has grown to over a million products and calls for a new website that can better connect scientists like you with the tools you need for your research.

Take a sneak peek at how we improved our product navigation, customer portal experience, mobile optimization and most importantly, our new rewards program.


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Topics: Announcement

Featuring Instagram Science Communicator, Sophie Arthur!

Posted by Applied Biological Materials (abm) on December 12, 2019

We recognize science can seem difficult to young scientists, and we hope to raise awareness about people who make it fun and accessible to broader audiences through social media, #SciComm!

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Meet Sophie Arthur, an award-winning science & education blogger. She currently works for the MRC London Institute of Medical Sciences as their scicomm officer.

Her job is to share the world leading medical research her colleagues do! She does this through social media by creating content for their website, filming videos, hosting events for schools and the general public and so much more!

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Topics: #SciComm

Featuring Instagram Science Communicator, Sarah Miller!

Posted by Applied Biological Materials (abm) on December 2, 2019

We recognize science can seem difficult to young scientists, and we hope to raise awareness about people who make it fun and accessible to broader audiences through social media, #SciComm!

Meet Sarah Miller, a research assistant & science communicator:

 

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Topics: #SciComm

Q&A: NGS Data Analysis 101

Posted by Applied Biological Materials (abm) on November 27, 2019

Here is the full list of answers to questions we've received during the

"NGS Data Analysis 101: RNA-Seq, WGS, and more" webinar:


  1. What file format will I get from sequencing on a MiSeq, FastQ or BCL? Do you provide the BCL files for sequencing?

  2. Do Q30 scores vary on different sequencers?

  3. I don’t have a reference genome but there is a related species that does have a reference genome. Can I use that for alignment/analysis?

  4. For analysis do you use GATK or VarScan2? ​Can I pick which one you use for my analysis?

  5. Do I have to use JBrowse? ​Does anyone still use Gbrowse?

  6. What happens if I don’t normalize my RNA-Seq data using FPKM?

  7. What should I do if I do not have appropriate “control” samples for RNA-Seq? 

  8. Can StringTie be used to identify fusions, or do I need to use another program for this?

  9. If I want to identify alternative-splicing transcripts from RNA-Seq data, do I have to do anything differently for sequencing?

  10. If I did single-end RNA-Seq, do I still normalize the data the same way?

  11. Can you do custom analysis? I want standard and custom analysis for a project.

  12. For RNA-Seq data alignment, can I use BWA-MEM as the aligner or can I use something else, like STAR (Spliced Transcripts Alignment to a Reference) software?

  13. Do I need to use replicates for my RNA-Seq experiment?

  14. Do I have to normalize my data before using DESeq2 for looking at differential gene expression? Or can I input FastQ data and the software can process it anyway?

1. What file format will I get from sequencing on a MiSeq, FastQ or BCL? Do you provide the BCL files for sequencing?

Our standard deliverable for all sequencing are FastQ files for all projects. If you would prefer to receive BCL files, please let our team know before order placement to discuss further! In most cases, we can provide these, depending on your project, and the sequencing platform.

 

2. Do Q30 scores vary on different sequencers?

Yes, the Q30 scores generally differ. For instance, NovaSeq > HiSeq > NextSeq > MiSeq, although the choice of sequencer will affect Q30 scores less than other factors such as read length, sample quality, or even the actual sequence for the sample.


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Topics: Next Generation Sequencing, NGS, Data Analysis

Q&A: Getting Started With Whole Genome Sequencing

Posted by Applied Biological Materials (abm) on November 7, 2019

Here is the full list of answers to questions we've received during the "Getting Started with Whole Genome Sequencing" webinar: 

    1. How many cells should I use for DNA Isolation for whole genome sequencing?
    2. There is not a reference genome for the species I study, but there is a sequenced genome for a related species... Can I use that?
    3. How much coverage do I need? How do I figure this out? Help!!
    4. For Plasmid Verification, do I have to provide a reference sequence or can you do de novo assembly?
    5. For mtDNA-Seq, do you have to start with isolated mtDNA? Can I just submit purified gDNA?
    6. How many samples should I submit for WGS?
    7. If my sample has RNA contamination, can you do anything to remove it?

 

1. How many cells should I use for DNA Isolation for whole genome sequencing?

For most projects, we start with ~1 million cells. This ensures we can extract enough DNA to perform full QC, library preparation, and have enough material left over in case any step needs to be repeated.

 

2. There is not a reference genome for the species I study, but there is a sequenced genome for a related species... Can I use that?

Even for very closely related species, there can be many differences between genomes. A related species can possibly be used as a guideline for assembly, but it cannot be used as a reference. 

An analogy that may better help you to understand this is a jigsaw puzzle. Think of two different puzzles, where both depict similar, but different castles. For one puzzle, you know what the completed image should look like, but for the other, you do not. If you use the reference puzzle as a guideline, you may be able to approximate the puzzle where you do not know what the completed image looks like, but you don't know how accurate this may be.  


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Topics: Next Generation Sequencing, NGS, Whole Genome Sequencing, WGS

Featuring Instagram Science Communicator, Lauren Callender!

Posted by Applied Biological Materials (abm) on November 6, 2019

We recognize science can seem difficult to young scientists, and we hope to raise awareness about people who make it fun and accessible to broader audiences through social media, #SciComm!

A great example is Lauren Callender, @lozcallender_ 

Let's find out more about Lauren through this short interview...

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Topics: #SciComm

Q&A: Using NGS for CRISPR Validation, Antibody Screening, & Metagenomics

Posted by Applied Biological Materials (abm) on October 25, 2019

Here is the full list of answers to questions we've received during "Using NGS for CRISPR Validation, Antibody Screening, & Metagenomics" Amplicon-Seq webinar:

    1. If I have already done sequencing, but need help with the analysis, can you help me?
    2. What is the largest size of amplicon that I can have sequenced?
    3. What is the typical turnaround time for Amplicon-Seq, and can you offer an expedited service if I am in a rush?
    4. Can I do Amplicon-Seq to look for off-target effects as part of CRISPR validation?
    5. If I’m interested in metagenomics sequencing, can I do Amplicon-Seq for targets other than 16S, like fungi or other eukaryotes?
    6. Do you guarantee a minimum number of reads for projects or samples?
    7. When discussing coverage, does 50X mean 50 reads?
    8. I'm interested in CRISPR validation and metabolomics. Can I use Amplicon-Seq to look at metabolites?
    9. Is Krona the software used for identify species for metagenomic sequencing? If not, how do we determine the specific microorganisms present in our samples?
    10. Can you help design gRNA's for my CRISPR experiment?
    11. What are some considerations for using the HiSeq 4000 platform?
    12. When discussing read length, what does 2x300 bp PE mean?
    13. If I have already done sequencing, but need help with the analysis, can you help me?

 

 

1. If I have already done sequencing, but need help with the analysis, can you help me?

Our in-house bioinformatics team can assist with nearly any type of analysis (in as little as 1 week!) based on your project needs. In the near future, we will be launching a dedicated Bioinformatics Service for researchers, but if you have a project where you need help with analysis, you can contact our NGS team at ngs@abmgood.com. One of our team members can then help you with analysis you are interested in completing!


 

2. What is the largest size of amplicon that I can have sequenced?

For most projects, we can sequence amplicons that are <600bp. If you have an amplicon that is larger than this, please let us know, and we may be able to work with you on a customized solution for your project.


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Topics: CRISPR, Next Generation Sequencing, NGS, Amplicon-Seq, Metagenomics

#ScientistSpotlight - Yanquan Zhang and Huitao Liu

Posted by Applied Biological Materials (abm) on October 21, 2019

Meet Yanquan Zhang and Huitao Liu - our Spotlight Scientists. Enter our abmXchange program to be featured and get free lab materials! 

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Topics: Cell Culture, Adenovirus, abmXchange, Plasmid, Cell line

Molecular Minutes

Educational resources for life scientists and interviews with scientists/science communicators in the field.

For more in-depth articles, check out our knowledge base, which covers topics such as CRISPR, Next Generation Sequencing, PCR, Cell Culture, and more.

Blog managed by Applied Biological Materials (abm). 

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