[DRYTCYV]

Hi,

Anyone tried KAPA HyperPlus Kits?
They say that this is the direct nextera competitor.

Cheers,

[nucacidhunter]

It could be considered a competitor to NEB dsDNA Fragmentase but not Nextera. Nextera does not require end repair and adapter ligation unlike Hyper.

[SNPsaurus]

Our local facility looked at the Hyper kit and it looked less biased than Nextera in terms of k-mer preference of the ends.

I think it is a competitor to Nextera since it approaches it in terms of workflow speed and amount of hands-on time needed. At least I am evaluating it as a replacement for our Nextera-based libraries.

[SCIL2019]

Larger fragemtns atac

Hi all,

I am having a bit of an issue with this library/sample. I am getting larger fragments peak and then 200 bp peak is gone. This is using 10x ATAC kit.

I usually don;t see such a nhigfh large peak yield, likely because I remove it with dual sided selection. here, I also did dual sided selection but for some reason it's still there...and what's more odd is that I can see the 75 bp dimer too.

Ideas?

Thank you!

[nucacidhunter]

Regardless of size distribution, library does not seem to have typical periodicity expected in ATAC-seq libraries indicating that there was ambient DNA in nuclei stock or nuclei disintegrated during transposition. Presence of 74bp fragment also raises question about accuracy of size selection.

[SCIL2019]

Thanks J for your comment.!

If you look carefully the size distribution you refer is there, just not well defined. 10x has indicated this is something they have observed also. This seems to happen when there is additional Mg in the tagmentation reaction.

Size selection could have been an issue but (re 74 bp fragment) but these never failed. Yet, I’ll definitely consider this.

On the other hand, the ambient DNA or nuclei desintegration during transition (not sure how that can happen, though) you mentioned would have generated a large peak at about 200 bp, re naked DNA. This is not the case, it shows basically no 200 bp peak and a large high molecular weight fragments. Nuclei prep is not the issue.

Thanks again for your helpful note!