How can I compare two (or more) networks?

Suppose you have built a network based on gene expression or protein interaction. How can I compare the current network with that from KEGG? Is there any statistics or software? Best regards,

31 December 2014 115 3 View

How can I methylate or demethylate certain loci in human cell lines?

31 December 2014 2,586 3 View

Is there any recommended pipeline or procedure for Illumina Methylation 450K microarray analysis?

Is there any recommended pipeline or procedure for Illumina methylation 450K array analysis. and What we can do as a analyst when we obtain some methylation 450K array for some paired case and...

31 December 2014 4,793 9 View

Can anyone help to make a pathway analysis with Ingenuity Pathway Analysis?

31 December 2014 5,605 3 View

How can I get the secondary structure of pre-microRNA?

31 December 2014 3,834 4 View

Do you know of any R packages for analysis of case-control studies in genetic epidemiology?

As we know, case-control based genetic epidemiological studies has played important role in susceptibility factor identification. Now, would you mind suggesting some helpful R packages to do SNP...

31 December 2014 701 3 View

How can I do sample size estimation for GWAS study?

Usually, when we conducted candidate gene based association study, we need to estimate the sample size and the power. Is it necessary to do it when we conduct GWAS study? If yes, is there any...

31 December 2014 7,577 2 View

Powerful pipeline for miRNA-seq analysis?

Which pipeline is a suitable one for miRNA-seq analysis? CAP-miRSeq, miRNAkey or others?

31 December 2014 114 4 View

How can I get the KEGG Pathway Network in mathematical form?

We can get the elements (genes) of each pathway of KEGG from KEGG website of UCSC database. However, how can we get the network relationship in the form of network for KEGG pathway as the...

31 December 2014 2,665 3 View

Can we perform Extension of Methylation of the 450K microarray?

As we know that Methylation 27K and 450K has been widely used in genome-wide DNA methylation detection. However, they are still very small compared with whole genome CpG sites. Is there any larger...

31 December 2014 6,243 0 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Does anyone have a recommendation for yeast reporter gene plasmid/protocol?

Hi, could anyone recommend a plasmid and/or protocol for reporter gene assay in S. cerevisiae? I want to assess the effect of growth conditions on a transcription factor, so I want to clone it`s...

01 March 2021 210 1 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 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

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

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View