What are the best ways to reduce generation of chimeric molecules during PCR?

The chimeric molecules generated during PCR are really bad for our study on recombination, since the chimeras look exactly like recombination. I wonder what and how (would be better if protocol is...

06 July 2016 9,547 5 View

What is the average disance from a mismatched base for a base substitution occurring during mismatch repair?

Especially in mammalian cells.

05 June 2016 1,312 1 View

Would you like to share with me about isolation of single cells?

I am interested in all the methods or instruments used to isolate single cells especially from mammalian tissues. Any experience of you is appreciated.

09 October 2015 412 1 View

What percent of template can be synthesized during PCR?

For example, the parameters for PCR are denaturing at 95, annealing at 58 and elongation at 72, while the melting temperatures of primers are around 60.

04 May 2015 4,344 13 View

Does anyone have experience about the efficiency for linear DNA synthesis?

We are trying to synthesize mouse DNA using "linear" synthesis in very limited number of cycles without "denaturing". Do you have any experience for linear DNA synthesis, especially about the the...

11 December 2014 5,867 0 View

Which PCR product clean-up kit you would like to recommend?

I am trying to clean the PCR products for deep sequencing, and I would like to know which kit of which company you think is the best (based on your experience if you have done). Thanks.

11 December 2014 2,965 7 View

How likely DNA double strands are seperated (melted) at lower than melting temperature?

For example, how many percent (if any) of DNA is melted at 5 degree lower than the melting temperature? Thanks.

11 December 2014 578 8 View

Do you know of any high-yield genomic DNA extraction kit/protocol?

11 December 2014 945 3 View

Is there a way to reduce the interference from genomic DNA on your template-primer pairing?

For example, whether long DNA fragments or shorter ones (such as with restriction enzymes) interfere with the pairing of the primers to the templates of interest with different efficiency or not.

11 December 2014 2,314 2 View

Is digestion of genomic DNA helpful to increase the pairing of primer to a specific genomic region of interest?

We are trying to test the efficiency of pairing of a primer to a region of mouse genome. We are thinking of digesting genomic DNA before pairing and wonder whether the longer or the shorter...

11 December 2014 6,149 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

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

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

No mRNA increase in PCR after successful transfection in ARPE-19 cells ?

Hello, i am a bit curious about my results. I transfected the human cell Line ARPE-19 with a Plasmid containing a GFP tagged p53 (p53-GFP, Plasmid #11770). After 24h i checked under the...

18 February 2021 3,811 7 View