What is exactly the application of EDGE?

I know the estimate degree of gene expression (EDGE) method is a comprehensive approach that is suitable for data with or without replicate, and for both single group and multiple group tests. But...

11 December 2015 4,702 2 View

Is it necessary to confirm the RNA-seq results by quantitative RT-PCR?

We have RNA-seq data set and we selected some genes which involve in hormone pathways for verification the RNA-seq results but some genes are not in DEGs list. Could we report these results...

11 December 2015 4,825 8 View

Why the AgriGO, panther and plant MetGenMAP give different results?

11 December 2015 7,683 2 View

How can I calculate the student's t-test by R?

We want to identify genes which have differential expression between sensitive and tolerant genotypes in RNA-seq data by R. Which package is suitable for our query?

11 December 2015 9,801 5 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

Can I run spearman's correlation on non monotonic data? Is it advisable?

Hi all, I am running a partial correlation analysis on mood data. I want to see if there is a correlation between scores on a novel hypomanic mood scale and existing measures of hypomania - the...

25 February 2021 1,619 3 View

How to handle studies which report perfect effect sizes in a meta-analysis using Pearson's r?

I'm in the process of updating a meta-analysis and in one of the new studies, effect sizes are reported as Tau-U. Two of the effect sizes are reported as Tau-U = 1.00. I am using Andy Field's...

24 February 2021 2,265 3 View

What is the best concentration of cDNA to be used for qPCR?

I have synthesised cDNA from 500ng/ul of RNA. The concentration of the cDNA Is about 5000ng/ul. Should I dilute my cDNA or just use it as it is for my qPCR? I usually use 2ul of cDNA for a 20ul...

24 February 2021 8,618 3 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 3 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Is it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View