Are there special considerations in primer design of a gene within a gene cluster?

i would like to amplify arcA, a part of the arcRACB gene cluster in Halobacterium salinarum after reverse transcriptase PCR. However i am pretty much worried the product size of arcA in the...

11 December 2012 2,661 4 View

How accurate are singleplex reactions compared to multiplex reactions in real time PCR assays?

I've never done RT PCR assays before. I'm an independent researcher and am worried that multiplex assays are more expensive than singleplex. However, I'm not sure singleplex assays will give...

11 December 2012 6,686 7 View

Is it normal, for a virus and its host, to have too different codon usages?

Codon usage of a virus must coevolve with its host for the virus to use the host machinery more efficiently and therefore replicate faster. When the codon usage of a virus becomes too deviated...

11 December 2012 2,665 14 View

I'm relatively new in rt PCR analysis. How do we normalize in rt PCR using housekeeping genes?

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10 November 2012 6,056 10 View

After isolation of microorganisms, do you usually screen the 16s rna first with restriction fragments before sending them for sequencing?

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10 November 2012 438 4 View

My incubator doesn't have light for the culture of phototrophic microorganisms. Any suggestions for low cost remedies?

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10 November 2012 9,237 6 View

Is it possible to compare gene expression levels between two bacterial culture (with uneven population)?

I exposed my bacteria to different factors which may affect the expression of a gene. However it has affected the growth of one of my bacteria exposed in a certain stimuli. I can't compare CT...

10 November 2012 10,003 7 View

Is there any protocol for the estimation of carbon content of the different parts of bamboo tree?

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10 November 2012 7,239 1 View

Can we use the same primer for 16s among different strains of bacteria?

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10 November 2012 1,204 12 View

How can you account for the relative instability of mRNA compared to DNA?

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10 November 2012 5,269 2 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

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

Could you please suggests a tutorial or paper or any other materials to learn multiple gene expression in TCGA and GTEx databases?

I would like to analyze multiple gene expressions in normal and cancer tissue by using the data in the TCGA and GTEx databases. Please suggest a tutorial or paper showing step by step analysis of...

23 February 2021 9,007 3 View

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

Which CpGs have a significant effect on gene expression?

It is known that methylated CpG around TSS decreases gene expression. However, It is difficult to know exactly which CpG has a greater impact on gene expression. Are there any databases known...

20 February 2021 5,634 3 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

Purification of proteins from baculovirus-infected insect cells?

18 February 2021 6,665 6 View

Found that there was a multiple band when amplifiying targeted gene ?

i few days ago amplified specific gene using PCR with specific primers, but there was a multiple band in electrophoregram i found. out of 10 sample amplified, there was multiple band and there was...

18 February 2021 5,131 5 View