Is partial reverse transcription of RNA possible?

Assume we are given an RNA sequence of, say, 300 bps. AACAGCUAGCUGAUCGAUGCUAGCUG....ACACUGUACG and now we want to reverse transcribe either the 5' or 3' end in vivo, but not the entire transcript,...

07 August 2017 2,631 3 View

Is it possible to co-express a sgRNA (CRISPR/Cas9) and a protein-coding gene?

I want to express a sgRNA for CRISPR/Cas9-based genome editing, which should be expressed at similar levels than a protein-coding gene? Are there any known systems or do you have anything in mind,...

01 February 2017 2,423 2 View

What is the best way to reduce error rates in array synthesized DNA oligonucleotide libraries?

I am looking for ways to reduce the error rates of array synthesised DNA oligonucleotide libraries of, say, approx. 100 000 unique sequences with 170 bps. These have error rates of approx. 0.5%...

10 November 2016 6,751 1 View

Are there good SNP-phenotype association databases?

Currently, I am looking for databases, which associate SNPs and phenotypes (like eye colour or breast cancer risk). These should get updated regularly with regards to recent GWAS etc. Ideally,...

10 November 2016 7,585 10 View

Is there a public patient database for Alzheimer's disease patients?

For a study I would like to monitor the history of Alzheimer's disease patients. Specifically, I would like to address whether which vaccines the patients have received prior diagnoses. If...

05 June 2016 2,272 1 View

Is it possible to remove one strand of double stranded DNA in vivo?

Assume we do have a double stranded DNA sequence in human cells, say ...ATCGATATCGATATTGCAGAGCATAGCTATAA... ...TAGCTATAGCTATAAGCTCTCGTATCGATATT... Now I want to cleave one strand, such that I do...

04 May 2016 4,698 3 View

Separation of smaller DNA fragments and larger fragments without using gel electrophoresis?

For an upcoming experiment I would have two kinds of DNA fragments in a sample after a particular reaction step: First there would be fragments of a length of approx. 170 bps and then there would...

04 May 2016 4,280 5 View

How do I insert DNA barcodes into animal cells and how do I transmit them to the neighbouring cells?

I am currently interested in equipping animal cells in a tissue with individual barcodes. These barcodes should get amplified in the cells (not to a cell degrading extent, of course), and also...

03 April 2016 6,164 0 View

Is it possible the cut the ends of DNA fragments to obtain sticky ends?

Assume we are given a DNA fragment like ACTTAGC....GCTCGGCA TGAATCG...CGAGCCGT so we have blunt ends. I am looking for a nuclease, that cleaves the end, such that we obtain sticky ends. Hence, the...

03 April 2016 8,033 3 View

What is the best way to automatically handle approx. 10 000 frozen DNA/RNA samples and to extract tiny amounts of the samples?

For an upcomig experiment I would have to make use of approx. 10 000 frozen DNA/RNA samples in microtubes, or, if necessary, in well plates. I would have to thaw them gently, to extract approx. 1...

03 April 2016 2,264 11 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

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

Is there a way to extract total RNA and protein from cell culture at the same time, without denaturing protein?

Hi all, Is there a way to extract RNA and protein from the same cell culture sample? Because we need to use the protein for gelatin zymography at later time, we are looking for a method that can...

22 February 2021 5,341 5 View