What are the "units" in RNA seq data processed by RSEM?

Hello! I've been using gene expression data from the TCGA, where the RNAseq is processed using RSEM. I did a few graphs such as boxplots showing the expression of different genes in normal vs...

14 October 2020 2,721 2 View

Which is best way to purify my His-tagged protein after eluting from a Ni NTA column in denaturing conditions (urea 8M)?

I have cloned two versions of my protein of interest to produce antibodies in mice. It is not soluble in native conditions, so I am trying to purify it in denaturing conditions with urea 8M. Now,...

18 February 2020 7,305 3 View

Multi-layer wells "robbed" of pumping rates?

By the way, I send attached the workflow I've performed. It is strange that in the Link to parameters window, in the Topology processing, instead of "no topology processing", now what I get is "no...

17 February 2020 8,662 3 View

How to reject authorship of some papers?

You added in my published paper list some article that don't belong to me. The author has the same family name as me, but is being active in a total different area of research. Thank you in advance

24 January 2019 5,795 3 View

Is there an easy way to count the diatoms in a rock sample in a short amount of time?

Hello! I have a bit of a struggle with my diatomites samples. I have tried all the methods to break the diatoms from the rock but I got a negative results (they are highly silicified) and I want...

04 September 2018 6,353 3 View

Any recommended (free) software to rectify and post-process coastal oblique images?

We have a fixed time-lapse camera (RGB) located on a hill oriented towards a sandy coastal area. Images are taken every 30 min. By using a set of ground control points (GPS) we aim to rectify and...

24 October 2017 4,632 5 View

Does Pfu Taq polymerase generate 5'P end?

Does the PCR product amplified using pfu polymerase have 5' phosphate groups to use for blunt cloning?

22 June 2016 1,058 3 View

How can I break the exopolysaccharide capsule of the mucous colonies to extract the RNA and DNA?

Hello to everyone! I'm working with strains of Acinetobacter baumannii resuspended in NaCl 0.45% (8 McF in 2 mL). Colonies of Acinetobacter baumannii are mucous so that they can not be separated...

15 June 2016 6,500 1 View

Why do I have a smear in gel for my bacterial RNA sample?

I have a question.....i have made a agarose gel of bacterial RNA and i have obtained a smear....what's happened? the RNA is 588mer. Moreover, i have done a Real Time PCR of these RNA without...

25 October 2015 7,189 4 View

Large-scale reaction with TnT T7 quick coupled transcription translation system (Promega)?

I wonder if the TnT T7 quick coupled transcription translation system (Promega) works in a large-scale reaction. They suggest a final volume of 50 ul and I would need a final volume reaction of...

17 August 2015 8,270 1 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

How optimize the Size Exclusion Chromatography?

Hello! I'll do a size exclusion chromatography, but I only have an open column, and I'll perform the peptide extraction from yeast, using buffer lysis (sodium phosphate 50 mM/NaCl 30 mM/DNAse and...

01 March 2021 2,215 2 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

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

RNA degraded after good nanodrop readings?

23 February 2021 8,850 2 View