Number of genomes sequenced?

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How long can agarose embedded tissues be kept?

I am embedding PFA fixed tissues in low melting point agarose prior to sectioning and I am wondering how long can these can be kept whilst maintaining tissue integrity and fluorescent signal?...

14 February 2021 6,688 3 View

Can anyone direct me to a paper or chapter that discusses calculating sample size in a self-selecting survey study?

Our study is investigating clinical knowledge in a specific area in healthcare workers at a large metropolitan hospital. Participants will self-select to complete the survey via email invitation...

11 January 2021 7,934 2 View

Align list of short sequences to miRBase?

I have a list of short sequences from miRNA sequencing in an Excel format and want to align these to miRBase. How can I do this? Is there a function in R? I converted the Excel list into a fasta...

08 September 2020 9,908 3 View

How to get return loss below -10dB for monopole antenna which has very less or no ground plane (or directly interfaced with sma connector) ?

I am designing a monopole antenna For 59MHz frequency . The lamda length is 5m. I tried for lamda/2 which is directly interfaced to sma connector. Couldn't get proper return loss.( According to...

11 March 2020 4,885 2 View

Can anyone recommend a stain to identify mast cells/eosinophilic granular cells (EGC) in fish?

Hi, I was wondering if someone can recommend a stain where fish EGCs or mast cells show significant metachromasia. Toluidine blue did not work in my fish species. I did find recommendations on...

04 March 2020 7,817 1 View

Alpha/betha TCR detection in naive TCs without activation?

Hello together, I want to see differences in TCR expression in naive CD4/CD8 TCs. The problem is, if I would stain the TCR with soluble antibodies to check via FACS, this would lead to a weak...

23 November 2019 1,430 1 View

Questions about RNA extraction?

Hello, I have a problem with my gene expression results. The results of my endogenous gene are oscillating between samples, generating false negative results. It takes about 12 hours after sample...

08 October 2019 569 3 View

Why did I get RMSD plot with 10ns if the MD was 100ns trajectory?

I am new in gromacs and I'm experiencing some difficulties in the analysis of my results. I calculated the RMSD of backbone and ligand from the MD with a trajectory of 100ns (nsteps = 50000000),...

04 September 2019 3,669 6 View

Doubt about secondary antibody to immunohistochemistry?

I bought a secondary antibody to use for immunohistochemistry, but the manufacturer says the antibody is only validated for Western Blotting, not Immuno. Because of this, I don't think which...

26 August 2019 5,356 7 View

High background on stain free blot after transfer and its complications for protein normalization(TGX Stainfree Biorad Gel)?

Hey, I have a question regarding the stain free blot technology of Biorad. After electroforesis I take a picture ("Stain-free gel") for activation of the trihalo-compound. Next I transfer the gel...

12 August 2019 7,734 8 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

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

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

I want to performe MALDI-TOF MS for bacterial identification, I would appreciate it if anyone can tell me the matrix solution preparation protocol ?

based on what I've studied on multiple papers, for peptide and protein identification Alpha-cyano-4-hydroxycinnamic acid (CHCA) is an appropriate matrix to use, I also know that the CHCA powder...

26 February 2021 6,799 3 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

Universal bacterial primers targeting a mRNA?

Hi, I'm looking for universal primers targeting a bacterial mRNA to quatify bacterial load by qPCR in a complexe mixture (eukaryote and prokaryote RNA). Ribosomal RNA being depleted, I absolutly...

22 February 2021 9,969 3 View

Does anyone have any ideas why drug-resistant malaria is increasing in Southeast Asia even when those drugs are no longer used?

When dealing with bacterial toxins, there are three varieties of microbes that develop in your petri dish: toxic, resistant, and susceptible. Initially, there are only toxic and vulnerable...

21 February 2021 6,084 5 View

How can I retrieve FASTA sequence from gene ID or UID of a Gene ? I have GeneBank IDs ?

I treid to use Entrez Batch, but it redirects me to NCBI site. Is there any script of Linux or Python through which I can download Fasta sequence of list of gene ID ?

21 February 2021 7,783 12 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

Piyush Kumar Tiwari

Dear Caroline,

Open NCBI, select SRA and put WGS into search box and see there are 847724 results.. Also you can filter the results by selecting genome, RNA, DNA as per your need.

Regards

Piyush

Caroline Marden

Can you tell me what SRA and WGS mean please. I can't find a way to then filter so it only shows bacteria or fungi. But I did find if I select genome, the next click on browse by organism, then click on eukaryotes, and in group click on fungi, then at levels deselect all but complete, there are only 19 complete fungal genomes, that doesn't seem many. So not sure if I am looking at the right thing?

Marius K. Somda

Dear Caroline

In definition WGS is Whole Genome Shotgun and SRA is sequenced Sequence Read Archive. Actual Number of genomes can be found by checking Genbank or NCBI databases. Please go to link https://www.ncbi.nlm.nih.gov/Traces/wgs/ and browse item by item to find information according genome sequenced.

Marius