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Old 04-03-2019, 06:46 AM   #1
Location: UK

Join Date: May 2018
Posts: 15
Default Why X-ChIP libraries QC failed?


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!!!
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Old 04-09-2019, 03:35 AM   #2
Location: UK

Join Date: May 2018
Posts: 15

It happens, the discussion continue here
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cleanup, complexity, generation, library amplification

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