Iddo Magen

11 Questions 11 Answers 0 Followers

Questions related from Iddo Magen

Validating NGS data with regular Taqman or advanced Taqman miRNA assay?

Hi, I wish to validate NGS data of miRNA sequencing from human plasma samples. The obvious way to do it is of course Taqman, but there are two different assays: the 'traditional' one in which...

01 January 2019 7,014 0 View

How to find reference genes for qPCR from RNA-seq data?

Hi everyone, I did RNA-seq for small RNA, and now I want to confirm the results with qPCR. What is the best way to find reference miRNA genes from the NGS data, for the normalization of the...

01 January 2019 779 4 View

Discrepancy between DESeq2 data and raw data?

Hi, i performed NGS for small RNA and ran DESeq on the data. there is one miRNA that is upregulated by 2-fold in the patients compared to healthy controls. However, when i look at the raw...

07 July 2018 3,455 3 View

Protocol for plasma preparation?

Hi, I need to isolate plasma from blood for RNA extraction afterwards. Does it have to be in a cold centrifuge? Do you need in general to isolate plasma in a refirigerated centrifuge or is it...

05 May 2018 6,049 5 View

Doing more PCR cycles to get higher concentrations of libraries?

Hi, I am preparing small RNA libraries for NGS, using the QIAseq kit of Qiagen Usually I get Canadian concentrations of around 1-10 ng/ul, but in the last batch all of the libraries were

05 May 2018 2,065 5 View

Is "camel hump" in tape station a sign for adapter dimer?

Hi, I got these results in tape station (attached). The small RNA library size should be around 173bp, so I think that libraries 28, 31, 34, 36, 37 also have an adapter dimer. I am going to...

10 October 2017 2,501 1 View

Perfusion or post-fixation?

Hi, I have brains that express GFP under a promoter of an endogenous protein so they actually express a fusion protein. I want to visualize GFP and thus know where the endogenous protein expresses...

05 May 2017 3,676 6 View

PCR plates or PCR strips for library prep?

Hello, If I use a PCR plate for library prep and I need the products after each step in the protocol (in my case it's polyadenylation, RT and PCR), is it safe to open the plastic foil that covers...

04 April 2017 9,163 3 View

Working with PCR plates for large-scale preparation of cDNA libraries for sequencing?

Hi, Does anyone have experience with preparing cDNA libraries from small RNA, for next-generation sequencing? If so, has anyone tried doing it in PCR plates instead of strip tubes? I have a large...

01 January 1970 9,597 3 View

Does anyone know of a method to measure enoxacin in plasma?

Hi, Does anyone have an experience with measuring levels of enoxacin which is a fluoroquinolone antibiotics, in the plasma? Thanks Iddo

01 January 1970 8,737 3 View

Any recommendation for a bioinformatic pipeline for small RNA sequencing?

Hi, I am looking for a pipeline to analyze bioinformatically Fastq files from small RNA sequencing. Can anyone recommend something that is straightforward? Do I need to store the file on a...

01 January 1970 4,092 4 View