Geetha Nagaraj
Working as Associate Professor at Central Research Laboratory, KIMS, Bengaluru. PhD graduate with 17yrs of research experience in Genomics, Molecular biology, microbiology, proteomics and immunology.
Location India
Activity
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Carrier RNA is added to facilitate total RNA extraction. We are performing amplicon based sequencing for SARS-Cov2 wherein specific regions located on viral genome are amplified. I think, carrier RNA should not pose any problem during downstream analysis.
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RNAlater/RNAshield is basically used for transportation and storage of tissue samples. For example, you will collecting the biopsy tissue from surgery room and your laboratory is quite far away. Then you will put the tissue in RNAlater/RNAshield solution and transport to lab, subsequently the samples are shifted to -80C storage
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Qubit and PicoGreen assay is used for dsDNA quantification, while use of nanodrop (where no reagents are required other than DNA), gives quality of DNA. Bioanalyzer gives the overall quality, area, peak size and quantity of DNA/RNA library before and also can be used for final pooled libraries prior to Miseq sequencing
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Yes. Negative controls are very important
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Hi Beathe. I agree with Charlotte Williams. SNV calling accuracy if high for Illumina reads as compared to ONT reads. For SARS-CoV2 sequencing, reads from ONT is sufficient for variant calling. For bacteria, if we perform hybrid assemble using Illumina and ONT reads, we could get complete genome without gaps.
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Hi James, at CRL, KIMS, Bangalore, we used both Illumina and Nanopore sequencing during pandemic. I personally prefer ONT platform for pandemic ie COVID19 genome sequencing. We used ONT in the hospital where minimal facilities were available. We can multiplex upto 96 samples on ONT using rapid barcoding kit. Procedure for rapid barcoding is very simple as...
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Geetha Nagaraj replied to José Antonio Pastor Martínez
Hi Jose Antonio Pastor Martinez
Please take look at the below link
https://www.cogconsortium.uk/what-do-virologists-mean-by-mutation-variant-and-strain/
This would give you an understanding on the topic. -
Agree
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Gloves, mask, hair cover, goggles, lab shoes, lab coat
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It is likely safe to store the amplified cDNA for up to two weeks. The risk of storing it longer is that there will be a lower number of genes detected per cell if the cDNA is degraded. The safest thing to do is to process the amplified cDNA within 1 week of storage.
Purified RNA should be stored at –80oC in RNase-free water. Qiagen claims that, when... -
Libraries are prepared by following step wise protocol of either Illumina kit or ONT rapid barcoding/native barcoding kit. These library preparation steps are explained in detail in week 2.
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Yes. ONT has come up with new version of flow cell R10.4.1 generates data at a modal accuracy above 99%.
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Hi Dario,
Our experience of nanopore sequencer is with Minion Mk1C platform. This platform does not require internet for running. Internet is required for transferring the data to the server after the completion of run and basecalling. After base calling, the data will be stored in the designated folder in the system. -
Geetha Nagaraj made a comment
Hi, I am a post doc research scholar perfomring wet lab of NGS. Joined this coure to learn how to perform Bioinformatics analysis of the data obtained
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Geetha Nagaraj made a comment
I have used command line during my degree days where we had MS-DOS classes
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Within the genome, all of the potential drug targets and all of the potential vaccine targets. And by using, firstly, genomics and then comparative genomics, we can identify what are good targets for drugs, for developing novel drugs, or for re-targeting known drugs, or what are the targets of vaccines. And by looking at comparative genomics, we can understand...
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Geetha Nagaraj made a comment
I am interested in Lindsay Pike's research area, antibiotic resistance genes and its spread
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Geetha Nagaraj made a comment
Thanks you
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Geetha Nagaraj made a comment
Hi, I am a PhD scholar from India. Interested in learning about Bacterial genomes and AMR
