Which program is good for finding the core genome and singleton genes of mulitple chloroplast genomes?

Dear all, I am interested in finding the core genome and singleton genes from a dataset of multiple chloroplast genomes (n=12). I don't have much experience in bidirectional BLAST. Can anyone...

06 July 2016 2,163 2 View

How to do PCR using highly degraded DNA as templates?

Dear all, One of my friends has to amplify some species-specific genes from cooking oil, which contained little and mostly degraded DNA. I think paleontologists often work on degraded ancient DNA....

06 July 2016 2,899 5 View

Which literature first proposed "you are what you eat" in (microbial)ecology?

Can anyone send me the PDF? Thanks

04 May 2016 2,376 2 View

Can transcriptional elongation factor 1 alpha (tef) be used as a phylogenetic marker for protists and metazoa?

Hello, I know tef can be used as a phylogenetic marker for fungi. But what about other organisms? For eukaryotes, 18S rRNA is definitely too conservative in many cases. By the way, COI is used in...

01 February 2016 3,816 2 View

Is univariate or multivariate analysis most suitable for my data?

11 December 2015 5,403 4 View

Where to find the output of kmernorm?

04 May 2015 9,150 0 View

Is RNA-seq reads number related to the quality of RNA preparation?

Dear all, I don't have much experience of RNA-seq. I noticed that the reads number of one treatment (3 individuals) was lower than the other treatment. Similarly, the signal intensity of samples...

04 May 2015 3,222 9 View

Why 16S rRNA gene can't be found in my single-cell genome assembly ?

01 February 2015 2,428 11 View

Which genes are responsible for fungal hyphae development?

01 February 2015 6,048 5 View

Would horizontal gene transfer happen on house-keeping/ultraconservative genes?

Hi guys, just a random question. As HGT frequently happen in microbial world, could house-keeping genes, e.g. gyrB, COI, rRNA be horizontally transferred between microbes? Any input is...

31 December 2014 3,553 7 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 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

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

What is the best concentration of cDNA to be used for qPCR?

I have synthesised cDNA from 500ng/ul of RNA. The concentration of the cDNA Is about 5000ng/ul. Should I dilute my cDNA or just use it as it is for my qPCR? I usually use 2ul of cDNA for a 20ul...

24 February 2021 8,618 3 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 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

Is it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View

RNA degraded after good nanodrop readings?

23 February 2021 8,850 2 View