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 3,556 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 9,908 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 5,924 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 5,699 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 5,446 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 2,657 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 7,902 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 9,514 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 919 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 9,131 0 View

Is there a problem with my RNA pellet?

Hello, I am currently having problems with RNA extraction. I am using mouse liver (C57BL6J), and I have extracted RNA from mouse liver before. Before this experiment, my final RNA pellets were...

11 August 2024 7,082 3 View

Strugglling with m6A dot blot any suugesstion ?

I have been doing the m6A dot blot for a while with no improvement, I am extracting the RNA, and I can see the dots although the three biological replicas give a different reading on the memberan...

10 August 2024 8,539 5 View

RNA Extraction Using Hot Borate Method No Longer Working?

I've been performing RNA extraction on cotton petiole tissue for a few months now using the method described in the following paper, a derivative of the typical hot borate method...

08 August 2024 9,882 2 View

Does Anyone have expertise in in vitro transcription and RNA pull down assay?

I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.

07 August 2024 6,622 1 View

E.coli contamination in human RNA seq data ?

Recently, we observed that 99% of the sequences in our RNA-seq data corresponded to the E. coli genome. Despite multiple DNAse treatments after RNA extraction and ribosomal depletion, we were...

06 August 2024 807 3 View

RNA later for the preservation of RNA in fecal samples at room temperature for one day (37°C)?

I am planning to collect human fecal samples for metatranscriptomic analysis using MGI. These samples are from indigenous people living in a region with high temperatures. I will have access to a...

06 August 2024 1,367 3 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

Why my colony PCR results of my recombinant bacterial not showing any results?

I am performing ligation of the plasmid and a target gene. The steps I have taken are: 1. Double digestion of the plasmid and target gene 2. Ligation of the plasmid with the target gene 3....

05 August 2024 2,570 3 View

Do you have good tips for seaweed tissue preservation in the field for post RNA extraction?

I will be with my students collecting seaweed samples in a marine farm and later we will process this tissue for RNA isolation and further sequencing. Does anyone have tips on how to collect the...

04 August 2024 501 2 View

What is the acceptable p-value cutoff for GO enrichment analysis ?

I have an RNA-seq data that I have analysed using Limma-voom and have extracted the gene IDs, log2FC and the p-values. At p value < 0.05, I have over 10,000 DEGs, however, when I run the GO...

31 July 2024 225 2 View