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  • 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 Files

  • #2
    It happens, the discussion continue here
    Techniques and protocol discussions on sample preparation, library generation, methods and ideas

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