Adding social media links to your email signature

It has been a long time since I posted. I was busy searching for jobs and I realized the importance and power of social media. This holds true whether you are applying for academic or corporate jobs. When I was applying for postdoc position, one PI told me during my interview – ” You are hard to find on social media”. As a matter of fact, I used Twitter a lot for science communication and networking activities, but I used a pseudo name. That’s when I decided to include my social media links in my email signature.

I would like to share a tip with you which would/might make your job search more productive.  The less amount of work you make the recruiter/hiring manger do, the better. It’s better to have your social media (LinkedIn (LI) profile/Twitter) link in your email as it makes it easier for the person who you are sending an email to find you.

Without wasting more time, let me tell you the quick steps to include your social media links in your email signature:

  • Go to iconfinder.com
  • Search for the desired social media. In this case, we will use LI.
  • You will see a lot of icons. Select one that suits you.Screen Shot 2018-03-14 at 5.53.30 PM
  • Once you click, it will show two options for saving – select download as PNG. You can also select the size. I prefer 20 x 20 or 24 x 24 as it is not too big for the signature.Screen Shot 2018-03-14 at 5.59.20 PM
  • Next, go to imgbox.com.Screen Shot 2018-03-14 at 6.01.35 PM
  • Upload the downloaded file here.
  • Once the file is uploaded, it will create a link. There will be two options – Thumbnails or full size. Click on full size and copy the link.Screen Shot 2018-03-14 at 6.17.53 PM
  • Go to Gmail settings – Scroll down to signature – you will find an option to upload an image.
  • Paste the URL that you copied from imgbox.Screen Shot 2018-03-14 at 6.17.39 PM
  • Once uploaded, you can click on the image and adjust the size.Screen Shot 2018-03-14 at 6.09.40 PM
  • Last step, click on the chain icon and link your LinkedIn page with your name.
  • You are all set to go.
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PLoS blog

Recently, I started writing blogs for PLoS too. My first post is about brain clearing methods and the title of the post is “Seeing through the brain”. The link to the article is below and is also present on the publication tab.

http://bit.ly/2gCMnY2

NormFinder for analyzing stable reference genes

NormFinder is another tool (an Excel add-in) to validate candidate reference genes. It best works with MS Office 2003 and up. Like GeNorm, the user has to convert the raw Cq values to relative quantities by using the ∆ct equation as shown in the last post on GeNorm. I have used NormFinder with MS Office 2003 on Windows 10 system. NormFinder can also be used with R, but I haven’t tried it yet.

Once the data is prepared i.e. raw Cq values have been converted to relative quantities, follow the steps mentioned below:

  1. Once you have calculated the relative amounts, arrange your data like this. The reference genes should be in columns, and the samples (including the control(s)) should be in rows. Here 1,2,3…. are the sample names while A, B, C…. are the gene names. Don’t forget to add “group” at the end. Grouping enables to show stable reference genes in groups. Here I have two different time points i.e. 1-5 samples are from the 1st time point, and 6-10 are from the 2nd time point. We will come to it in the next steps.1
  2. Now you are ready to start NormFinder. Once you double-click the add-in file (downloaded from the site), it should show in the menu bar.

2

3. A short disclaimer message will show up. Just click Ok.

Screen Shot 2016-08-26 at 11.02.04

4. Select the input data just by dragging all the cells including the group.

Screen Shot 2016-08-26 at 11.02.34

5. Check all the boxes – Sample name, gene name and group identifiers. If you don’t include the group identifiers, then uncheck it. But as I suggested earlier, it would be useful to have the group identifiers.
Screen Shot 2016-08-26 at 11.02.25

6. Click on Go and within a few milliseconds it will create a new tab and would show            the results like this:
Screen Shot 2016-08-26 at 11.02.48

7. If you uncheck simple output only, then it will show a detailed result page which includes stable genes, Intra- and inter- group variations. But if you check simple output only it will show only the ranking of stable genes and the most stable genes. The advantage of using group identifier is that it gives a combination of two best genes which can be used. For example, in the above case, we can use only gene A or we can use both gene A and J as the most stable gene combination.

Screen Shot 2016-08-26 at 11.03.10

References:
1. Normalization of Real-Time Quantitative Reverse Transcription-PCR Data. A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets. 2004, Andersen CL et al.
2. NormFinder Documentation.
3. NormFinder plugin: http://moma.dk/normfinder-software. – Check the download section on the right-hand side.

Epilepsia citation style

I was submitting a paper to Epilepsia and I use “Paper” as my citation manager (for more details, please see the “Scientific tools section”). Everyone has their own citation manager. Some use Endnote which is popular but a paid one while others prefer using Mendeley which is an open source program. Yes, you heard it right, it’s free !! And then there is Papers which is not free but is cheaper compared to Endnote.

Coming to business, while submitting to Epilepsia I found that they have a new reference style which is a modified version of “Vancouver superscript style”. The only changes are after three authors, “et al.” should follow, no need for entering the month of publication, and the use of journal abbreviation instead of the complete journal name.

I started to make the changes manually as there is no citation style that matches and the patch that Epilepsia provides are “.OS style patch” which works only with Endnote while Papers, Endnote, Zotero only accepts a “.CSL style”. Therefore, I modified the Vancouver style patch to make it compatible with Epilepsia using the visual editor. The only problem with the new “Epilepsia citation style” is that it doesn’t recognize many journal abbreviations (out of my 40 references, it recognized around 25 and changed it) so you have to do it manually. Other than that, it works perfectly. I am not a pro at Visual Editor so if anyone finds a way around to get this fixed, please let me know.

Just download and drag the file to your reference manager (works for papers) and it will install it.

You can find more citation style which is not available on your citation managers.

Hope it works for everyone else too. If you encounter any problem, let me know and I will try to fix it.

Cheers.

Download: http://bit.ly/2bbhpo0

Guidelines for qPCR

RNA extraction:
1. While extracting RNA be careful on the use of Trizol. Trizol inhibits microRNA (Trizol skews microRNA results). There are two kits which are trizol free – Zymoresearch RNA extraction kit and Qiagen miRNA isolation kit.
2. To avoid frothing of tissue, while homogenizing, I would recommend using “Reagent DX” from “Qiagen.”
3. If the kit contains in-column DNase treatment, then you should use it – saves time.
4. RNA elution could be done in either DEPC water or TE buffer and store at -80°C. If possible, RNA should be aliquot and stored so as to avoid repeated freeze-thaw.
5. RNA should be measured (if thawed again) for determining if there is any degradation. Before measuring RNA, give it a brief spin and pipette it up and down at least thrice so that the exact measurement of RNA can be determined.

cDNA synthesis:
1. cDNA should be made immediately or within a day of RNA extraction so as to avoid freeze-thaw of RNA.
2. After reverse transcription of RNA, dilute and aliquot the cDNA.
3. Store all the aliquots at -20°C and take out one at a time. You can store one aliquot at 4°C for a maximum of 1-2 months.

qPCR:
You have to be extremely careful while preparing the plate and the qPCR machine.
1. Wipe off the bench and all the pipettes that are going to be used for qPCR first with 100% ethanol and then RNAse Zap. You can purchase RNAse ZAP from Sigma-Aldrich, which is cheaper (link below) compared to life technologies.
2. First, make the master mix by adding the qPCR master mix, the primer pair, and water. After, you are done with the primer pair place it back in the fridge or keep it far away.
3. Now take out the qPCR plate from its package and pipette the master mix to the qPCR plate.
4. Take the cDNA out of the fridge and add it to the qPCR plate and immediately cover the plate with optical seal cover.
5. Give the qPCR plate a brief spin down (high speed for 2 min).
6. Place the qPCR plate in the machine and run the program.

Links to products:
I am in no way endorsing the products, be careful with your samples, and I am not responsible for the loss of your valuable samples. I would also recommend the use of DEPC water. These products work best in our research

DEPC water: https://www.carlroth.com/en/en/Chemicals/A-Z-Chemicals/W/Water/Water/p/000000010000562d00020023_en
Reagent DX: https://www.qiagen.com/de/shop/lab-basics/buffers-and-reagents/reagent-dx#orderinginformation
Zymo Research RNA extraction kit: http://www.zymoresearch.de/rna/rna-isolation/routine-rna-isolation/quick-rna-miniprep
cDNA synthesis kit: https://www.thermofisher.com/order/catalog/product/K1612?ICID=search-product
qPCR master mix: https://www.thermofisher.com/order/catalog/product/4385610?ICID=search-product
RNAse Zap: http://www.sigmaaldrich.com/catalog/product/sigma/r2020?lang=de&region=DE

 

 

Guidelines for publishing your article

Some of you reading this may have already published and some of you are writing your manuscript and some are going to submit. Here is a nice post published in Biomed central about how to make a good impression to the editor and get your manuscript for peer review.

The title of the article is How to get published: making a good first impression. It may help you and it has some nice tips on the “abstract title”, the “abstract” and the “cover letter” for the journal.