Methods to find RNA binding proteins?

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Fisher's LSD vs Tukey's HSD test?

I am looking at the effect of stress on a number of stress genes via a qRT PCR. I have put them into graphpad where my groups are +/- the chemical inducing stress and each row is one gene - all...

30 December 2023 194 0 View

2-way ANOVA using an interaction term versus not: getting different p value significance?

Using GraphPad Prism, when I carry out a 2-way ANOVA with an interaction term, data between two groups is not significant. The post-hoc tests shows non significant interaction between my column...

24 December 2023 7,172 3 View

How important is it to add BafA while studying autophagy?

I am working with iPSC-derived macrophages and looking at autophagy in these cells. Rapamycin induces expression of LC3II while bafilomycin prevents its turn over. From my data (and previous data...

10 January 2023 2,327 1 View

When do I add bafilomycin A1 following rapamycin treatment to my cells for a LC3 read out assay?

I am using iPSC-derived macrophages and am looking for LC3 levels as an indication of autophagy. I'm using rapamycin as an inducer of autophagy and was wondering when (or if?) I need to add...

03 August 2022 2,648 0 View

How do I show that different cell line growth is statistically significant?

I'm comparing the growth of two different cell lines across a fixed time period - what sort of test do I do to show that they are statistically significant (or not)? Would I do a 2 way ANOVA as...

26 March 2021 1,741 3 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

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 3 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

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

Transfection in HEK293T cells?

Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...

31 July 2024 9,892 4 View

Adam B Shapiro

I don't know if you will consider it easy, but RNA affinity chromatography is a method. A protocol can be found here:

https://en.bio-protocol.org/en/bpdetail?id=808&type=0

Joachim R. Grün

It is definitely not that easy. Here is a link to what we did to extract ribosomal proteins of the small subunit of Sulfolobus acidocaldarius:

Data Fließ-Schema zur Gewinnung des Totalproteins TP30 (kleine Un...