Time course gene expression analyses: RNA seq over mass spec?

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Why the need to use different minimal media to grow bacteria?

I am trying to identify bacteria on skin that can utilise lactic acid as carbon source. So i intend to swab skin and then grow bacteria on minimal media supplemented with lactic acid. My question...

11 December 2018 3,432 0 View

Cell Biology field: Relative easeness in publishing papers?

Hi, I am hoping to get opinions/input since I am undergrad and I see certain trends that I am highly curious about. I have been doing lab rotation to get an extensive research experience....

09 October 2018 9,760 0 View

What other phohpshorylated components can i look for downstream of activated FAK and P38 MAPK?

I applied some mechanical stresses on cells and discovered that FAK and p38 MAPK are activated by phosphorylation. For the purpose of publishing, i feel that it will be great if i can look for...

03 April 2018 5,791 0 View

Are they any phosphorylation-specific proteins for hypoxia effect on cells?

Im looking to expose cells to hypoxic conditions in minutes (

02 March 2018 5,548 0 View

Hypoxia induced: No HIF-1a overexpression seen at transcript level but seen a lot of hypoxia and HIF-1A -induced genes?

hi i need advise on the matter i performed RNA-seq after exposing cells to mechanical stress. I had designed a device to deliver this stress to cells. Looking at the RNA-seq data, i see some...

02 March 2018 5,300 8 View

Proliferation assay : manual cell counting?

How is proliferation assessed by manual cell counting? I will be happy if anyone can provide protocol on this. I have been told this method is much useful than indirect assays like CFSE but i...

11 December 2017 2,510 0 View

QPCR: analyses involving in-between plates?

hi i am not sure if it is alright to analyse my data this way. So i prepared 3 samples of controls, 3 samples of condition at 1hr exposure, 3 samples of condition at 6hr of exposure. i collected...

07 August 2017 7,743 5 View

Why is RNA expression analysis better than protein for looking time course gene expression analysis?

why is it that people usually look at mrna expression rather than protein expression when conducting a time course gene expression analysis?

06 July 2017 9,379 0 View

RNA expression vs protein expression patterns upon stimulation- are RNAs more dynamic?

Let say if i stimulate a cell at 1 hr and 6hr, the RNA expression upregulated at 1 hr may not be reflected at 6hr, but same protein upregulated at 1 hr will be reflected at 6hr. How do i explain...

06 July 2017 783 0 View

Phosphoproteome SILAC: can it identify if cells are definitely undergoing apoptosis?

i intend to apply mechanical pressure on cell to look at mechanotransduction pathways. i will be using a SILAC based phosphoproteomics. Can the data also indicate that the cell is undergoing...

05 June 2017 8,936 0 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

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 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

Genome-wide gene identification protocol ?

Is there any book chapter/book, webpage or research article available to understand genome-wide gene identification?

28 February 2021 8,095 1 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