CRUK-CI Genomics Help

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submission:lps_submissions [2024/11/25 16:17] – Johanna Barbierisubmission:lps_submissions [2026/02/18 11:23] (current) – [Genomics Core Library Preparation Submission] Johanna Barbieri
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 |NEBNext Single cell / low input RNA Library Prep Kit for Illumina|Total RNA/cells|NEB low input RNA|2pg - 200ng, or cell(s)|8|24|Please discuss your input requirements prior to submission.| |NEBNext Single cell / low input RNA Library Prep Kit for Illumina|Total RNA/cells|NEB low input RNA|2pg - 200ng, or cell(s)|8|24|Please discuss your input requirements prior to submission.|
 |Illumina DNA PCR-Free Library Prep, Tagmentation|Genomic DNA|Illumina DNA PCR Free, Tag|25-2000|30|24|This kit provides a "low-input" protocol for small input mass. It will also self-normalise samples above 300 ng.| |Illumina DNA PCR-Free Library Prep, Tagmentation|Genomic DNA|Illumina DNA PCR Free, Tag|25-2000|30|24|This kit provides a "low-input" protocol for small input mass. It will also self-normalise samples above 300 ng.|
-|Illumina DNA Prep with Enrichment|Genomic DNA|Illumina DNA Prep with Enrichment|100-500|30|16?|Also suitable for FFPE extracted material using a modified protocol.| +|Illumina DNA Prep with Enrichment|Genomic DNA|Illumina DNA Prep with Enrichment|10-1000|30|16|Also suitable for FFPE extracted material using a modified protocol.| 
-|ThruPLEX DNA-Seq?|ChIP'ed DNA|Thruplex DNA Seq?|5-200?|30|24| +|ThruPLEX DNA-Seq|ChIP'ed DNA|Thruplex DNA Seq|50pg - 50ng |10|24| 
-|Watchmaker RNA with Polaris depletion| Total RNA| Other| 1-1000| 11?| Any number|Also suitable for FFPE extracted material using a modified protocol.|+|Watchmaker RNA with Polaris depletion| Total RNA| Other| 1-1000| 18| Any number|Also suitable for FFPE extracted material using a modified protocol.|
  
-Please provide an additional 15% volume per well.\\+*Please provide an additional 15% volume per well.\\
 We run a positive and negative control with every library prep. We run a positive and negative control with every library prep.
  
 ==== Complete the Pool Information Fields ==== ==== Complete the Pool Information Fields ====
  
- * 96 well barcoded plates and seals are available from the Genomics Core (Room 026). Barcoded plates can also be obtained either from CRUK reception or via UMS for University users.+  * 96 well barcoded plates and seals are available from the Genomics Core (Room 026). Barcoded plates can also be obtained either from CRUK reception or via UMS for University users.
   * Prepare your samples in //columns// following the concentration and volumes in the table above.   * Prepare your samples in //columns// following the concentration and volumes in the table above.
   * If applicable, plate your samples according to the randomisation layout provided by your bioinformatic contact (discussed at your experimental design meeting).\\   * If applicable, plate your samples according to the randomisation layout provided by your bioinformatic contact (discussed at your experimental design meeting).\\
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   * Run your completed submission form through this submission application. Be sure to click the "Confirm Submission" button to finish the submission process.   * Run your completed submission form through this submission application. Be sure to click the "Confirm Submission" button to finish the submission process.
   * Hand your plate to a member of Genomics. RNA plates are stored at -80°C until processing.   * Hand your plate to a member of Genomics. RNA plates are stored at -80°C until processing.
 +
 +==== Library Prep Submission Recommendations ====
 +
 +  - When eluting or diluting your sample, avoid using buffers containing high concentrations of EDTA and use DNAse as recommended in the kit manufacturer's instructions for RNA extraction.
 +  - Quantify your nucleic acid using a fluorescent based method.
 +  - When submitting DNA, we recommend performing QC to include size information using the Agilent Tape Station or equivalent.
 +  - When submitting RNA, check the quality of each sample on the Bioanalyzer or Tapestation. If the RIN is <8, you can contact the Genomics Core for advice. A low quality score won't necessarily stop it being processed but can certainly lead to poor sequencing results, it is better to have this information if possible.
 +  - For any ChIP-seq experiment, you will have performed the chromatin immunoprecipitation and just submit the ChIP'ed DNA.
 +  - When submitting ChIP'ed DNA, check the fragmentation profile of your input(s) material. Please discuss with the Genomics Core if the fragments appear larger than 700bp.
 +  - We do not specify a minimum quantity for a ChIP-seq experiment; please submit what you have. Always include at least one input control.
 +  - Please upload QC data to the relevant project in our LIMS.
 +
 +
 +==== Library Prep Submission Recommendations ====
 +
 +  - This is the[[https://genomicshelp.cruk.cam.ac.uk/forms/CRUKCI_LPS_Submission.xlsx|submission form for library prep]] specifically. Do not use this form to submit sequencing ready samples.
 +  - There are different batch sizes depending on library prep, please see our price card or the table above for details.
 +  - Researchers from within the CRUK-CI are strongly encouraged to attend an experimental design meeting prior to collecting samples for library prep submission.
 +  - Contact[[:CRIExperimentalDesign@cruk.cam.ac.uk|CRIExperimentalDesign@cruk.cam.ac.uk]] to book a free experimental design session.
 +  - If you have any questions, contact the[[:genomics-helpdesk@cruk.cam.ac.uk|Genomics Helpdesk]].