SEQanswers

Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation



Similar Threads
Thread Thread Starter Forum Replies Last Post
Failed chip-seq experiments Anomilie Bioinformatics 6 01-08-2015 11:35 AM
Chip and Input different sizes libraries (NEBNext ChIP-Seq Library) HelenaSC Sample Prep / Library Generation 2 08-21-2014 02:57 AM
Chip-Seq libraries suludana Illumina/Solexa 3 05-07-2010 09:22 AM

Reply
 
Thread Tools
Old 04-03-2019, 06:46 AM   #1
KB*
Member
 
Location: UK

Join Date: May 2018
Posts: 14
Default Why X-ChIP libraries QC failed?

Hi,

Please advise on the quality of the libraries. There are 10 in total (library ID, cell type, IP type)
15 - cell type 1, input;
16 - cell type 1, IP #1;
18 - cell type 1, IP #2;
19 - cell type 1, IP #3;
20 - cell type 1, IP with IgG;
21 - cell type 2, input;
22 - cell type 2, IP #1;
23 - cell type 2, IP #2;
25 - cell type 2, IP #3;
27 - cell type 2, IP with IgG.

These libraries were assessed in the sequencing facility and failed according to their report. While it is understandable for some of the libraries, I do not understand why other libraries failed. I would like somebody to comment on the report files and perhaps to suggest what could be done.

For example, I can:
- prepare a library again;
- repeat size-selection;
- increase the library concentration (from the library stocks I have).

I have prepared files with images copied from the report files. The reports which were done on my site (tapestation) look a bit different from the sequencing facility reports. I am not sure why.

At the top of the image #1 I have copied a part of the report table with library DNA concentration measured in the sequencing facility.

Thank you!!!
Attached Images
File Type: jpg summary-seqanswers-small-1.jpg (73.4 KB, 3 views)
File Type: jpg summary-seqanswers-small-2.jpg (40.1 KB, 2 views)
KB* is offline   Reply With Quote
Old 04-09-2019, 03:35 AM   #2
KB*
Member
 
Location: UK

Join Date: May 2018
Posts: 14
Default

It happens, the discussion continue here
http://seqanswers.com/forums/showthread.php?t=88202
KB* is offline   Reply With Quote
Reply

Tags
cleanup, complexity, generation, library amplification

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 06:07 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO