Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation
Similar Threads
Thread Thread Starter Forum Replies Last Post
single cell ATAC-seq! Fasteno Sample Prep / Library Generation 1 03-27-2017 12:23 AM
ATAC-Seq cell preparation from Tissue paramita7 Sample Prep / Library Generation 4 10-24-2016 07:37 AM

Thread Tools
Old 11-21-2016, 09:02 AM   #1
Junior Member
Location: UK

Join Date: Jun 2016
Posts: 1
Default ATAC-seq in mouse cell lines

This is my first post. I have done multiple ATAC-seq libraries on human cell lines with no problems. Now I'm doing some ATAC on mouse lines.

After 5+6 cycles, I get good nucleosome patterns on the bioanalyser and good concentration of DNA (using 100k cells) as determined by Qubit/bioanalyser.

My major problem is - when running the qPCR side reaction after the 5 cycles of amplification, (done to determine how many more cycles to amplify) I get nothing. Zero amplification on qPCR.

Does anyone have any suggestions?
There are several papers which have used the same Nextera primers (the ones listed in the Buenrostro paper), on mouse cell lines.

- I have tested two different SYBRs
- My beads work fine (see attached imagine of bioanalyser)
- Has always worked well on human cell lines.

Any help greatly appreciated,
Attached Images
File Type: gif 186889b7-b7c0-4f54-9a00-19a610451e3e.gif (116.6 KB, 50 views)
IMGarner is offline   Reply With Quote

atac, atac-seq, cycles, primers, qpcr

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:55 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO