What is the best online tool to find transcription factor binding elements in a DNA sequence?

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Is it possible to transfect cells with a plasmid using DharmaFECT 1?

I need to transfect cells with a plasmid (GFP). I normally would use a transfection reagent such as lipofectamine or fugene but I only have DharmaFECT 1, which I use for siRNA. Do you think I...

05 February 2023 6,407 4 View

Does it make sense to conduct a moderation analysis if X and Y are not significantly correlated?

Does it make sense to still conduct a moderation analysis if X and Y are not significantly correlated?

12 October 2022 8,380 7 View

Assessment of gut microbiota (16S rDNA) using pyrosequencing?

Has anyone ever used 16S rDNA pyrosequencing to identify gut microbiota populations? We have a PyroMark Q96 and I would like to adapt the sequencing protocol to assess gut microbiota in faecal...

18 August 2021 4,815 3 View

DNA quality and purity for pyrosequencing experiments?

Is there a 260/280 ratio cutoff for DNA that is to be used for bisulfite conversion and pyrosequencing? How pure does the DNA have to be?

30 July 2018 9,671 1 View

Can RNA later be used to preserve adipose tissue?

I would like to store adipose tissue (from Wistar rats) in RNA later but have heard that the reagent cannot be used to stabilise RNA in adipose tissue due to the high abundance of fat.

21 June 2017 4,042 5 View

Why coefficients showed by GGplot differ from those obtained by multiple regression model?

I was plotting some results when I realized that the coefficients shown by GGplot differ from the model I've tested. It shows the 2 models (m2 and m3) separately. Note that the coefficients change...

02 May 2017 7,064 2 View

What is the best way for including log scale data in a meta analysis in which most data isn't in a log scale?

Most of results are shown in a normal/normal plot. However there are some studies that are in log scale, if I transform back the results, it looks like an outlier and compromises the...

18 September 2016 3,231 3 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

How to confirm the site-directed mutagenesis result without performing NGS?

I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...

08 August 2024 4,645 2 View

I can't see the ssDNA band after performing asymmetric PCR. Is there any way to do this?

After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...

08 August 2024 1,668 3 View

Does crude extraction using NaOH and Tris work well with Fungi?

I'm trying to find a DNA extraction method for fungi that does not require equipment and heating. Is there anyone who can suggest an alternative option? Thank you

08 August 2024 4,733 2 View

Why after performing site directed mutagenesis ,I don't see any colony after transformation?

I want to introduce a point mutation (change in one nucleotide) into my gene of interest (DNA binding domain) I have designed primers as recommended on the Data sheet of the kit : -Both primers...

05 August 2024 9,059 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 know best conditions for formation of best REE deposits?

I want to know more about REE deposits.

03 August 2024 6,930 2 View

Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...

01 August 2024 2,079 0 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