institute of biotechnology >> brc >> genomic diversity facility >> LIMS >> user guide
 

Genomic Diversity Facility LIMS(Retired)User Guide

Extraction plate submission, prep, and shipment

Special Instructions for Submitting  Extraction of grass species for genotyping.

 

1. Creating and submitting extraction plates in your project

Follow the same steps for creating a plate in your project as found in the user guide. The LIMS will assign the blank(s) for your extraction plate.  When editing the plate's template please use the following values for required fields and uploads:
    DNA concentration:  50
    Volume:  30
    DNA Mass: 1500
    Gel upload: attach a picture of your species 

Extraction plate preparation 

We require that fresh or lyophilized tissue be collected in 1.1 ml tubes in strips of 8, racked. (http://www.usascientific.com/1.1ml-8-strip-tube-rack.aspx)

If you are unsure if your rack and strip tubes meet our requirements please message an admin.  We do not accept single tubes or 12 tube strips, racked.

1.    Label a Costar Rack (96-well format with tubes in strips of 8) with the plate name exactly as it appear in the LIMS. 
2.    Label the H well of each strip of 8-tube strips “H1, H2, …, H12”
3.    When preparing samples, do not separate tubes. Do not order samples with connected tubes across rows.
4.    Put one Steel ball (3.97mm) into each of labeled 8-strip tube 
5.    While harvesting keep rack on ice and add fresh leaf tissue to each tube:
        a.    Do not load more than 0.13 g of fresh tissue per tube. 
        b.    10 hole punches per tube or
        c.     one 4cm x 0.5cm strip,  removing the midrib and folding 3 times into a  loose ball. 
6.    While harvesting keep rack on ice and store at -80C until ready for shipment. 
a.    If you will be sending us fresh leaf material, please proceed to step 10.
Lyophilizing Fresh tissue 
7.    Prior to lyophilizing, remove costar racks from -80C storage and cover tubes with breathable sealing tape.
8.    Lyophilize fresh tissue for 48 hours.
9.    After 48 hours, check that samples are dry and seal the tubes with compatible 8-strip caps.
10.    Store the lyophilized tissue in -80C until ready for shipment. 

Shipping Extraction Plates
11.    Once your plate has been approved for shipment in the LIMS. Ship samples to the address provided. 
        a.    Ship fresh tissue cold, on ice packs or wet ice. Dry ice is not required, but also accepted.
        b.    Ship Lyophilized tissue at room temperature. No ice or ice packs are needed.

Please do not ship samples until the plate(s) have been approved for shipment in our LIMS.
Do not ship pre-ground samples to our facility.

Version 1.2 Updated 2016-03-10